METHOD OF INHIBITING CATHEPSIN K

Field of the Invention

This invention relates to a method of inhibiting cathepsin K by administering compounds with certain structural, physical and spatial characteristics that allow for the interaction of said compounds with specific residues of the active site of the enzyme. This interaction between the compounds of this invention and the active site inhibits the activity of cathepsin K and these compounds are useful for treating diseases in which said inhibition is indicated, such as osteoporosis and periodontal disease. This invention also relates to a novel crystalline structure of cathepsin K, the identification of a novel protease catalytic active site for this enzyme and methods enabling the design and selection of inhibitors of said active site.

Background of the Invention Cathepsin K is a member of the family of enzymes which are part of the papain superfamily of cysteine proteases. Cathepsins B, H, L, N and S have been described in the literature. Recently, cathepsin K polypeptide and the cDNA encoding such polypeptide were disclosed in U.S. Patent No. 5,501,969 (called cathepsin O therein). Cathepsin K has been recently expressed, purified, and characterized. Bossard, M. J., et al., (1996) J. Biol. Chem. 271, 12517-12524; Drake, F.H., et al., (1996) J. Biol. Chem. 271, 12511-12516; Bromme, D., et al., (1996) J. Biol. Chem. 271, 2126-2132. Cathepsin K has been variously denoted as cathepsin O, cathepsin X or cathepsin 02 in the literature. The designation cathepsin K is considered to be the more appropriate one (name assigned by Nomenclature Committee of the International Union of Biochemistry and Molecular Biology).

Cathepsins of the papain superfamily of cysteine proteases function in the normal physiological process of protein degradation in animals, including humans, e.g., in the degradation of connective tissue. However, elevated levels of these enzymes in the body can result in pathological conditions leading to disease. Thus, cathepsins have been implicated in various disease states, including but not limited to, infections by pneumocystis carinii, trypsanoma cruzi, trypsanoma brucei brucei, and Cnthidia fusiculata; as well as in schistosomiasis malaria, tumor metastasis, metachromatic leukodystrophy, muscular dystrophy, amytrophy, and the like. See International Publication Number WO 94/04172, published on March 3, 1994, and

references cited therein. See also European Patent Application EP 0 603 873 Al, and references cited therein. Two bacterial cysteine proteases from P. gingivallis, called gingipains, have been implicated in the pathogenesis of gingivitis. Potempa, J., et al. (1994) Perspectives in Drug Discovery and Design, 2, 445-458. Cathepsin K is believed to play a causative role in diseases of excessive bone or cartilage loss. Bone is composed of a protein matrix in which spindle- or plate- shaped crystals of hydroxyapatite are incorporated. Type I Collagen represents the major structural protein of bone comprising approximately 90% of the structural protein. The remaining 10% of matrix is composed of a number of non-collagenous proteins, including osteocalcin, proteoglycans, osteopontin, osteonectin, thrombospondin, fibronectin, and bone sialoprotein. Skeletal bone undergoes remodeling at discrete foci throughout life. These foci, or remodeling units, undergo a cycle consisting of a bone resoφtion phase followed by a phase of bone replacement. Bone resorption is carried out by osteoclasts, which are multinuclear cells of hematopoietic lineage. The osteoclasts adhere to the bone surface and form a tight sealing zone, followed by extensive membrane ruffling on their apical (i.e., resorbing) surface. This creates an enclosed extracellular compartment on the bone surface that is acidified by proton pumps in the ruffled membrane, and into which the osteoclast secretes proteolytic enzymes. The low pH of the compartment dissolves hydroxyapatite crystals at the bone surface, while the proteolytic enzymes digest the protein matrix. In this way, a resoφtion lacuna, or pit, is formed. At the end of this phase of the cycle, osteoblasts lay down a new protein matrix that is subsequently mineralized. In several disease states, such as osteoporosis and Paget's disease, the normal balance between bone resoφtion and formation is disrupted, and there is a net loss of bone at each cycle. Ultimately, this leads to weakening of the bone and may result in increased fracture risk with minimal trauma.

The abundant selective expression of cathepsin K in osteoclasts strongly suggests that this enzyme is essential for bone resoφtion. Thus, selective inhibition of cathepsin K may provide an effective treatment for diseases of excessive bone loss, including, but not limited to, osteoporosis, gingival diseases such as gingivitis and periodontitis, Paget's disease, hypercalcemia of malignancy, and metabolic bone disease. Cathepsin K. levels have also been demonstrated to be elevated in chondroclasts of osteoarthritic synovium. Thus, selective inhibition of cathepsin K may also be useful for treating diseases of excessive cartilage or matrix degradation, including, but not limited to, osteoarthritis and rheumatoid arthritis. Metastatic neoplastic cells also typically express high levels of proteolytic enzymes that

degrade the surrounding matrix. Thus, selective inhibition of cathepsin K may also be useful for treating certain neoplastic diseases.

Suφrisingly, it has been found that a broad, structurally diverse series of compounds have common structural, physical and spatial characteristics that allow for the interaction of said compounds with specific residues of the active site of cathepsin K and are useful for treating diseases in which inhibition of bone resoφtion is indicated, such as osteoporosis and periodontal disease. Thus, this invention relates to the method of inhibiting cathepsin K using compounds having the characteristics hereinbelow defined.

Summary of the Invention In one aspect, the present invention provides a method for inhibiting cathepsin K by administering compounds with certain structural, physical and spatial characteristics that allow for the interaction of said compounds with specific residues of the active site of the enzyme. This interaction inhibits the activity of cathepsin K and, thus, treats diseases in which bone resoφtion is a factor.

In another aspect, the present invention provides a novel cysteine protease in crystalline form.

In yet another aspect, the invention provides a novel protease composition characterized by a three dimensional catalytic site formed by the atoms of the amino acid residues listed in Table XXLX.

In still another aspect, the invention provides a method for identifying inhibitors of the compositions described above which methods involve the steps of: providing the coordinates of the protease structure of the invention to a computerized modeling system; identifying compounds which will bind to the structure; and screening the compounds or analogs derived therefrom identified for cathepsin K inhibitory bioactivity.

Other aspects and advantages of the present invention are described further in the following detailed description of the preferred embodiments thereof.

Brief Description of the Drawings Figure 1 is the amino acid sequence of cathepsin K aligned with the amino acid sequences of other cysteine proteases.

Figure 2 is a ribbon diagram of cathepsin K. The amino and carboxyl- termini are indicated by N and C. The drawing was produced using the program MOLSCRIPT [Kraulis, P., J. Appl. Crystallogr., 24, 946-950 (1991)].

Figure 3 is a ribbon diagram of cathepsin K in complex with E-64, a known inhibitor of cysteine proteases. The drawing was produced using the program MOLSCRIPT.

Figure 4 is an illustration of the active site of cathepsin K. Figure 5 is a stereoview of the active site of cathepsin K. For clarity, no hydrogen atoms or water molecules are shown.

Figures 6, 8, 10, 12, 14, 16, 18, 20, and 22 are illustrations of the active site of cathepsin K in complex with novel inhibitors of cathepsin K. (Figure 6: Inhibitor = 3(S)-3-[(N-benzyloxycarbonyl)-L-leucinyl]amino-5-methyl-l-(l -propoxy)-2- hexane; Figure 8: Inhibitor = bis-(cbz-leucinyl)-l,3-diamino-propan-2-one; Figure 10: Inhibitor = 2,2'-N,N'-bis-benzyloxycarbonyl-L-leucinylcarbohydrazide; Figure 12: Inhibitor = (lS)-N-[2-[(l-benzyloxycarbonylamino)-3-methylbutyl]thiazol- 4- ylcarbonyl]-N'-(N-benzyloxycarbonyl-L-leucinyl)hydrazide; Figure 14: Inhibitor = 2-[N-(3-benzyloxybenzoyl)]-2'-[N'-(N-benzyloxycarbonyl-L- leucinyl)]carbohydrazide; Figure 16: Inhibitor = 4-[N-[(phenylmethoxy)carbonyl]- L-leucyl]-l-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrroli dinone; Figure 18: Inhibitor = 4-[N-[(4-pyridylmethoxy)carbonyl]-L-leucyl]- 1 -[N-[(phenylmethoxy) carbonyl]-L-leucyl]-3-pyrrolidinone; Figure 20: Inhibitor = 4-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-l-N[N-(methyI)-L-leucyl) ]-3-pyrrolidinone; Figure 22: Inhibitor = l-N-(N-imidazole acetyl-Ieucinyl)-amino-3-N-(4-phenoxy- phenyl-sulfonyl)-amino-propan-2-one. Figures 7, 9, 11, 13, 15, 17, 19, 21 and 23 are stereoviews of the active site of cathepsin K in complex with novel inhibitors of cathepsin K. (Figure 7: Inhibitor = 3(S)-3-[(N-benzyloxycarbonyl)-L- leucinyl]amino-5-methyl-l-(l-propoxy)-2-hexane; Figure 9: Inhibitor = bis-(cbz- leucinyl)- 1 ,3-diamino-propan-2-one; Figure 11 : Inhibitor = 2,2'-N,N'-bis- benzyloxycarbonyl-L-leucinylcarbohydrazide; Figure 13: Inhibitor = (lS)-N-[2-[(l- benzyloxycarbonylamino)-3-methyIbutyl]thiazol-4-ylcarbonyl]- N'-(N- benzyloxycarbonyl-L-leucinyl)hydrazide; Figure 15: Inhibitor = 2-[N-(3- benzyloxybenzoyl)]-2'-[N'-(N-benzyloxycarbonyl-L-leucinyl)]c arbohydrazide; Figure 17: Inhibitor = 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-l-[N-

[(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone; Figure 19: Inhibitor = 4- [N- [(4-pyridylmethoxy)carbonyl]-L-leucyl]- 1 -[N-[(phenylmethoxy) carbonyl]-L-leucyl]-3-pyrrolidinone; Figure 21: Inhibitor = 4-[N-[(4- pyridylmethoxy)carbonyl]-L-leucyl]-l-[N-[(phenylmethoxy) carbonyl]-L-leucyl]-3-pyrrolidinone; Figure 23: Inhibitor = l-N-(N-imidazole acetyl-leucinyl)-amino-3-N-(4-phenoxy-phenyl-sulfonyl)-amino -propan-2-one.

These views depict the interaction of each inhibitor with all atoms of residues of the active site of cathepsin K within 5A of the inhibitors. For clarity, no hydrogen atoms or water molecules are shown.

Table I provides the three dimensional protein coordinates of the cathepsin K crystalline structure of the invention.

Tables II-X provide the three dimensional coordinates for the cathepsin K complex with specific inhibitors of the present invention.

Tables XI-XHX provide listings of the three atom angles between atoms of the inhibitors and the protein for all inhibitor atoms within 5 Angstroms of the protein.

Tables XX-XX VTII provide listings of the distances between atoms of the inhibitors and the protein for all inhibitor atoms within 5 Angstroms of the protein. Table XXIX provides the atoms of the amino acid residues of the catalytic site.

Detailed Description of the Invention The present invention provides a novel cysteine protease crystalline structure, a novel cysteine protease active site, and methods of use of the crystalline form and active site to identify protease inhibitor compounds. In particular, the present invention provides a method for inhibiting cathepsin K by administering compounds with certain structural, physical and spatial characteristics that allow for the interaction of said compounds with specific residues of the active site of the enzyme. This interaction inhibits the activity of cathepsin K and, thus, treats diseases in which bone resoφtion is a factor. Specifically, the inhibitors of cathepsin K used in the present invention interact with any two or more of the following:

1. Tyrosine 67 sidechain;

2. Hydrophobic pocket lined with atoms from methinoine 68, leucine 209, alanine 163, alanine 134 and portions of tyrosine 67; 3. Hydrogen bonds donated by glycine 66 amide nitrogen;

4. Cysteine 25 the active site nucleophile;

5. Mainchain interactions from residues glutamine 21, cysteine 22, and glycine 23;

6. Tryptophan 184 sidechain; and 7. Hydrophobic contacts with the sidechain atoms of glutamine 143 and asparagine 161 and the mainchain of alanine 137 and serine 138.

Preferably, the inhibitors of cathepsin K used in the present invention interact with any three or more of the above-identified regions of the active site. The compounds used in the methods of the present invention possess an electrophilic carbon and either a hydrophobic group whose centroid is 5.44-6.94A from the carbon or an aromatic group whose centroid is 9.24- 11.24A from the carbon, or both the hydrophobic and the aromatic groups in which case the centroids of these two groups should be 15.67-16.67A apart. These features must be able to make the appropriate interactions with the cathepsin K active site. The electrophilic carbon atom should be 1.7-4.0A from the side chain sulfur atom (SG) on the amino acid cysteine 25. The hydrophobic group should be near the following amino acids with appropriate distance ranges between the centroid of the side chain atoms and the centroid of the hydrophobic group given in parentheses: tyrosine 67 (4.91- 5.91A), methionine 68 (5.74-6.74A), alanine 134 (4.15-5.15A), leucine 160 (6.18- 7.18A), and leucine 209 (5.71-6.71A). The aromatic group should be near the either tryptophan 184 (4.10-7. lOA) or tryptophan 188 (4.10-7. lOA) or both.

The key structural features of the inhibitors of the present invention include an electrophilic carbon, preferably the carbon of a carbonyl group, a hydrophobic group, preferably an isobutyl group, and an aromatic group, preferably a phenyl group. The electrophilic carbon of the inhibitor may be in the same compound with two hydrophobic groups, such as two isobutyl groups, or two aromatic groups, such as two phenyl groups, or one hydrophobic group and one aromatic group.

Suitably, the method of inhibiting cathepsin K of the present invention comprises administering to a mammal, preferably a human, in need thereof a compound that fits spatially into the active site of cathepsin K, said compound comprising any two or more of the following:

(i) an electrophilic carbon atom that binds to the side chain sulfur atom of cysteine 25 wherein said electrophilic carbon atom is 1.7-4.0A from said sulfur atom;

(ii) a hydrophobic group that interacts with tryptophan 184 wherein the distance between the centroid of said hydrophobic group and the centroid of the side chain atoms of tryptophan 184 is 4.10-7.10A;

(iii) a hydrophobic group that interacts with tyrosine 67, methionine 68, alanine 134, leucine 160, and leucine 209, creating a hydrophobic pocket, and has distance ranges between the centroid of said hydrophobic group and the centroids of the side chain atoms of the amino acid residues of said hydrophobic pocket which are tyrosine 67: 4.91- 5.9lA, methionine 68: 5.74-6.74 A, alanine 134: 4.15-5.15A, leucine 160: 6.18-7.18A, and leucine 209: 5.71-6.7lA;

(iv) a hydrophobic group that interacts with tyrosine 67 wherein the distance between the centroid of said hydrophobic group and the centroid of the side chain atoms of tyrosine 67 is 4.10-7.10A;

(v) an amino group with a pKa of less than 7 or an oxygen atom, each of which interacts with a hydrogen atom donated by the amide nitrogen of glycine 66 wherein the distance between these two atoms is 2.7-3.5 A;

(vi) a hydrophobic group that interacts with the main chain atoms of glutamine 21, cysteine 22 and glycine 23 wherein the distance between the centroid of said hydrophobic group and the centroids of glutamine 21 , cysteine 22 and glycine 23 are 3.7-5.4, 4.9-5.7 and 5.4-6.7A, respectively; or

(vii) a hydrophobic group that interacts with the side chain atoms of glutamine 143 and asparagine 161 and the main chain of alanine 137 and serine 138 wherein the distance between the centroid of the hydrophobic group and the centroids of glutamine 143, asparagine 161, alanine 137, and serine 138 are 7.9- 9.6A, 4.7-5.4A, 4.2-5.5A, and 4.6-6.4A, respectively. Preferably, the inhibitors of cathepsin K used in the present invention comprise three or more of the above. Suitably, the method of inhibiting cathepsin K of the present invention comprises administering to a mammal, preferably a human, in need thereof, a compound that fits spatially into the active site of cathepsin K, said compound comprising:

(i) an electrophilic carbon atom that binds to the side chain sulfur atom of cysteine 25 wherein said electrophilic carbon atom is 1.7-4.θA from said sulfur atom; and

(ii) a hydrophobic group that interacts with tryptophan 184 wherein the distance between the centroid of said hydrophobic group and the centroid of the side chain atoms of tryptophan 184 is 4.10-7.10A. Preferably, the hydrophobic group that interacts with tryptophan 184 is an aromatic group and the centroid of this aromatic group is 9.24-11.24 A from the centroid of the electrophilic carbon that binds to the side chain sulfur atom of cysteine 25. Preferably, the electrophilic carbon that binds to the side chain sulfur atom of cysteine 25 is a carbonyl carbon.

Suitably, the method of the present invention further comprises a compound with a hydrophobic group that: has a centroid which is 5.44-6.94 A from said electrophilic carbon; interacts with tyrosine 67, methionine 68, alanine 134, leucine 160, and leucine 209, creating a hydrophobic pocket; and

has distance ranges between the centroid of said hydrophobic group and the centroids of the side chain atoms of the amino acid residues of said hydrophobic pocket which are tyrosine 67: 4.91- 5.9lA, methionine 68: 5.74-6.74A, alanine 134: 4.15-5.15A, leucine 160: 6.18-7. lδA, and leucine 209: 5.71-6.7lA. Preferably, this hydrophobic group is an isobutyl group.

Alternately, the method of the present invention further comprises a compound with a hydrophobic group that interacts with tyrosine 67 wherein the distance between the centroid of said hydrophobic group and the centroid of the side chain atoms of tyrosine 67 is 4.10-7.10A. Preferably, this hydrophobic group is an aromatic group.

Alternately, the method of the present invention further comprises a compound with an amino group with a pKa of less than 7 or an oxygen atom, each of which interacts with a hydrogen atom donated by the amide nitrogen of glycine 66 wherein the distance between these two atoms is 2.7-3.5 A. Preferably, the compound comprises an oxygen atom, such as an oxygen atom of a carbonyl group or an oxygen atom of a hydroxyl group.

Alternately, the method of the present invention further comprises a compound with a hydrophobic group that interacts with the main chain atoms of glutamine 21, cysteine 22 and glycine 23 wherein the distance between the centroid of the hydrophobic group and the centroids of glutamine 21 , cysteine 22 and glycine 23 are 3.7-5.4, 4.9-5.7 and 5.4-6.7A, respectively. Preferably, this hydrophobic group is an isobutyl group.

Alternately, the method of the present invention further comprises a compound with a hydrophobic group that interacts with the side chain atoms of glutamine 143 and asparagine 161 and the mainchain of alanine 137 and serine 138 wherein the distance between the centroid of the hydrophobic group and the centroids of glutamine 143, asparagine 161, alanine 137, and serine 138 are 7.9- 9.6A, 4.7-5.4A, 4.2-5.5A, and 4.6-6.4A, respectively.

Compounds used in the method of the present invention include, but are not limited to, the following:

3(S)-3-[(N-benzyloxycarbonyl)-L-leucinyl]amino-5-methyl- 1 -( 1 -propoxy)- 2-hexanone;

4-[N-[(4-pyridylmethoxy)carbonyl]-L-leucyl]-l-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone; 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-l-N-[N-(methyl)-L-l eucyl)]-3- pyrrolidinone;

4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]- 1 -[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone; bis-(Cbz-leucinyl)- 1 ,3-diamino-propan-2-one; 2-[N-(3-benzyloxybenzoyl)]-2'-[N'-(N-benzyloxycarbonyl-L- leucinyl)]carbohydrazide;

( 1 S)-N-[2-[( 1 -benzyloxycarbonylamino)-3-methylbutyl]thiazol-4- ylcarbonyl]-N'-(N-benzyloxycarbonyl-L-leucinyl)hydrazide; l-N-(N-imidazole acetyl-leucinyl)-amino-3-N-(4-phenoxy-phenyl-sulfonyl)- amino-propan-2-one; and 2,2'-N,N'-bis-benzyloxycarbonyl-L-leucinylcarbohydrazide; or a pharmaceutically acceptable salt thereof.

As stated herein, the interaction of the inhibitor at the side chain sulfur atom of cysteine 25 has as one of its requirements that the inhibitor contain an "electrophilic carbon" atom. By this term is meant an electron deficient carbon. This term includes, but is not limited to, a carbonyl carbon atom. This term also includes an epoxide, a thiocarbonyl, an imine, and a nitrile. Suitably, this term may also be represented by the formula -C=N-X, wherein X may be optionally tied back to C in a ring or wherein X is CH2, H, O, S or NR ^a in which R ^a is H of Chalky 1. The hydrophobic groups that interact with tryptophan 184 or tyrosine 67 include, but are not limited to, aromatic groups. These hydrophobic groups include phenyl, C _j .galkyl and heteroaryl, which is defined hereinbelow. The hydrophobic groups that interact with the hydrophobic pocket lined with atoms from tyrosine 67, methionine 68, alanine 134, leucine 160, and leucine 209 not only includes isobutyl, but also includes C ^alkyl, C3_6cycloalkyl and adamantyl. The hydrophobic groups that interact with the main chain atoms of glutamine 21, cysteine 22 and glycine 23 or the side chain atoms of glutamine 143 and asparagine 161 and the mainchain of alanine 137 and serine 138 include Ci.jøalkyl, ^b+i, in which b is 1-3, and aryl and heteroaryl, each of which are defined hereinbelow.

As used herein, the term "centroid" means the position for the stated atoms calculated by averaging the x coordinates of the atoms to obtain the x coordinate of the centroid, averaging the y coordinates of the atoms to obtain the y coordinate of the centroid, and averaging the z coordinates of the atoms to obtain the z coordinate of the centroid.

The compounds used in the method of the present invention include, but are not limited to, the compounds of formula (I):

D- C ^• Q I wherein:

D =

Q =

where:

A = absent,

L = C ₂ .6alkyl, Ar-C ₀ -6alkyl, Het-C ₀ -6alkyl, CH(R ⁶⁶ )NR6 R68 _>

CH(R ⁶⁶ )Ar, CH(R ⁶⁶ )OAr", NR ⁶⁶ R ⁶⁷ ; M = C(O), SO2;

G =

J = C(O), SO ₂ ; T = Ar, Het;

V = C3-7cycloalkyl;

W = H, -CN, -CF ₃ , -NO2, -COR ⁷ , -CO ₂ R ⁶ , -CONHR ⁶ ,

-SO ₂ NHR ⁶ , -NHSO ₂ R ⁶ , -NHCOR ⁷ , -O-COR ⁶ , -SR ⁶ , NR'R ⁶ , NR'(C=NH)NHR ⁵ , Cl, Br, I, F; X = Y = Z = N, O, S or CR ⁴ ,

provided that at least two of X, Y and Z are heteroatoms and at least one of X, Y and Z is N, or one of X, Y and Z is

C=N, C=C or N=N and the other two are CR ⁴ or N, provided that X, Y and Z together comprise at least two N;

~ indicates a single or double bond in the five-membered heterocycle; m = 0, 1, 2; n = 1 to 6; f = 0, 1, 2;

Ar = phenyl, naphthyl, optionally substituted by one or more of

Ph-Co-6alkyl, Het-C ₀ -6alkyl, Ci^alkoxy, Ph-C()-6alkoxy,

Het-C ₀ -6alkoxy, OH, (CH ₂ )i-6NR ⁵⁸ R ⁵⁹ ,

O(CH ₂ )i-6NR ⁵⁸ R ⁵⁹ ; Ar' = phenyl or naphthyl, optionally substituted by one or more of

Ph-Co_6alkyl, Het-Co- >alkyl, Cj^alkoxy, Ph-Cø-όalkoxy,

Het-C ₀ _6alkoxy, OH, (CH )ι_6NR ⁵⁸ R ⁵⁹ ,

O(CH ₂ )i-6NR ⁵⁸ R ⁵⁹ , or halogen; R' = H, Ci-6alkyl, Ar-C ₀ -6alkyl, Het-C ₀ _6alkyl; R^ H, Ci-6alkyl;

R ² = C4-6alkyl, C4-6alkenyl, benzyl;

R ³ = Ci-6alkyl, Ar-Cθ-6alkyl, Het-C()-6alkyl, R ⁵ CO-, R5SO ₂ -, R ⁵ OC(O)-, R^NHCO-;

R ⁴ = H, Ci-6alkyl, Ar-Q)-6alkyl, Het-C()-6alkyl; R5 = Ar-0-6alkyl, Het-Co_6alkyl;

R ⁶ = H, Ci-6alkyl, CH ₂ CF ₃ , Ar-Cθ-6alkyl, Het-C ₀ -6alkyl;

R ⁷ = Cj.-6alkyl, Ar-CQ-6alkyl, Het-C()-6alkyl;

R ⁸ = H; C2-6 alkenyl; C2-6alkynyl; Het; Ar; Ci-6alkyl, optionally substituted by OR', SR', NR'2, CO2R', CO ₂ NR'2, N(C=NH)NH ₂ , Het or Ar;

R ⁹ = H, Ci-6alkyl, Ar-Co_6alkyl, Het-Crj-6alkyl; R ¹⁰ = C 1 -6alkyl, Ar-C ₀ -6alkyl, Het-Co-6alkyl;

R ^{1 1} = H, Ci-6alkyl, Ar-Cj^alkyl, Het-Co-6alkyl, or

R ¹² = H, C-..6alkyl, Ar-Crj-βalkyl, Het-Co-6alkyl;

R ¹³ = H, Ci.galkyl, Ar-Co_6alkyl, Het-C()-6alkyl;

R ¹⁵ = H, Cj.galkyl, C2-6alkenyl, C2_6alkynyl, Ar, Het, or Ci.galkyl optionally substituted by OR ⁹ , NR ⁹ 2, CONR ⁹ ₂ , N(C=NH)NH-, Het or Ar; Rl6 - C2-6 lkyl, C2-6alkenyl, C2_6alkynyl, Ar, Het, or C2_6alkyl optionally substituted by OR ⁹ , SR ⁹ , NR ⁹ 2, CO2R ⁹ ,

CONR ⁹ ₂ , N(C=NH)NH-, Het or Ar; R ¹⁹ = H, Cj^alkyl, C2_6alkenyl, C2_6alkynyl, Ar, Het, or Cμ 6alkyl optionally substituted by OR ⁹ , SR ⁹ , NR ⁹ 2, CO2R ⁹ , CONR ⁹ ₂ , N(C=NH)NH-, Het or Ar; RI ⁷ = R ⁷² = H, Ci-βal yl, R ¹⁰ , R ¹⁰ C(O)-, RIOC(S)-, R ¹⁰ OC(O)-;

R21 _ _R 26 _ C5_6alkyl; C2-6alkenyl; C3-I icycloalkyl; T-C3- 6alkyl; V-Ci-6alkyl; T-C2-6alkenyl; T- (CH2)nCH(T)(CH2)n; optionally substituted by one or two halogens, SR ²⁰ , OR ²⁰ ,NR ²⁰ R ²⁷ or Cι_4alkyl;

R27 = _R 28co, R ⁸ OCO;

R ²⁸ = Ci-6alkyl; C3. 1 icycloalkyl; Ar; Het; T-Ci-6alkyl;

T-(CH2)nCH(T)(CH2)n; optionally substituted by one or two halogens, SR ²⁰ , OR ²⁰ , NR ² θR ⁷³ , Ci-βalkyl;

_R 20 - _R 22 - _R 23 _{= R} 24 _ _R 25 _ _R 73 _ _H> C^alkyl, Ar-C ₀ . galkyl, Het-C ₀ -6alkyl;

R ² =

Cbz-leucinyl-; 2-, 3-, or 4-pyridyl methyloxycarbonyl-leucinyl-; 4-imidazole acetyl-leucinyl-, phenyl acetyl-leucinyl, N,N-dimethyl-glycinyl leucinyl, 4- pyridyl acetyl-leucinyl, 2-pyridyl sulfonyl-leucinyl, 4-pyridyl carbonyl- leucinyl, acetyl-leucinyl, benzoyl-leucinyl, 4-phenoxy-benzoyl-, 2- or 3- benzyloxybenzoyl-, biphenyl acetyl, lpha- isobutyl-biphenyl acetyl, Cbz- phenylalaninyl, Cbz-norleucinyl-, Cbz-norvalinyl-, Cbz-glutamyl-, Cbz- epsilon- (t-butyl ester)-glutamyl; acetyl-leucinyl-, 6- or 8- quinoline carbonyl, biphenyl acetyl, alpha- isobutyl-biphenyl acetyl, acetyl, benzoyl, 2- or 3- benzyloxy benzoyl, 4-phenoxy benzoyl-, Cbz-amino acid-; 2-,3-, or 4- pyridylmethyloxycarbonyl-aminoacid-; aryl C-j-Cgalkyloxy carbonyl- amino acid-, heteroaryl Crj-C6alkyloxy carbonyl-amino acid-,aryl C _Q - C6alkyloxy carbonyl-amino acid-, heteroaryl Crj-C _fj alkyloxy carbonyl- amino acid-, Cj-Cgalkyloxy carbonyl-amino acid-; Cι-C6alkyl carbonyl, aryl Cø-Cgalkyl carbonyl, heteroaryl Cø-Cgalkyl carbonyl, aryl Cø-Cgalkyl carbonyl, heteroaryl C _Q -Cgalkyl carbonyl, Cj-Cgalkyl sulfonyl, aryl C _Q -

Cgalkyl sulfonyl, heteroarylCo-C alkyl sulfonyl, aryl Cø-C^alkyl sulfonyl, heteroaryl Crj-Cgalkyl sulfonyl;

R30 = -H, C ₁ - ₆ alkyl;

R31 =

Cbz-leucinyl-; 2-, 3-, or 4-pyridyl methyloxycarbonyl-leucinyl-; 4-imidazole acetyl-leucinyl-, phenyl acetyl-leucinyl, N,N-dimethyl-glycinyl leucinyl, 4- pyridyl acetyl-leucinyl, 2-pyridyl sulfonyl-leucinyl, 4-pyridyl carbonyl- leucinyl, acetyl-leucinyl, benzoyl-leucinyl, 4-phenoxy-benzoyl-, 2- or 3- benzyloxybenzoyl-, biphenyl acetyl, alpha- isobutyl-biphenyl acetyl, Cbz- phenylalaninyl, Cbz-norleucinyl-, Cbz-norvalinyl-, Cbz-glutamyl-, Cbz- epsilon- (t-butyl ester)-glutamyl; acetyl-leucinyl-, 6- or 8- quinoline

carbonyl, biphenyl acetyl, alpha- isobutyl-biphenyl acetyl, acetyl, benzoyl, 2- or 3- benzyloxy benzoyl, 4-phenoxy benzoyl-, Cbz-amino acid-; 2-,3-, or 4- pyridylmethyloxycarbonyl-aminoacid-; aryl Cg-Cgalkyloxy carbonyl- amino acid-, heteroaryl Cø-Cgalkyloxy carbonyl-amino acid-,aryl CQ- Cgalkyloxy carbonyl-amino acid-, heteroaryl Cø-Cgalkyloxy carbonyl- amino acid-, Ci-Cgalkyloxy carbonyl-amino acid-; Cι-C6alkyl carbonyl, aryl CQ-Cβalkyl carbonyl, heteroaryl CQ-C6alkyl carbonyl, aryl Co-Cgalkyl carbonyl, heteroaryl Cg-Cgalkyl carbonyl, C \ -Cgalkyl sulfonyl, aryl CQ- Cgalkyl sulfonyl, heteroaryl C -Cgalkyl sulfonyl, aryl Cg-Cgalkyl sulfonyl, heteroaryl CQ-Cgalkyl sulfonyl;

R ³² = OCH2Ar, OCH2Cι _6alkyl, aryl substituted C _Q - _β alkyl, heteroaryl substituted C()-6alkyl,4-imidazole methylene; 2-, 3-, or 4-pyridylmethylneneoxy; 4-pyridyl methylene, 2- pyridyl sulfonyl, 4-pyridyl, aryl substituted CQ-(,al y\oxy , heteroaryl substituted Cø-galkyloxy;

R ³³ = C!- ₆ alkyl, -CH ₂ Ph, -CH ₂ CH ₂ CO2R ³⁴ ; R ³⁴ = -H, C!- ₆ alkyl;

R ³⁵ = Ar, HetAr;

R36 ₌ Aryl, heteroaryl, pyridyl, isoquinolinyl; R ³⁷ = C ! - ₆ alky 1, -CH ₂ Ph, -CH ₂ CH ₂ CO ₂ R ³⁴ ;

R ³⁸ = Cbz; Chalky 1 or aryl substituted Cbz; Ci-galkyl -CO; benzoyl; Cj-galkyl or aryl substituted benzoyl;

R ³ =

Cbz-leucinyl-; 2-, 3-, or 4-pyridyl methyloxycarbonyl-leucinyl-; 4-imidazole acetyl-leucinyl-, phenyl acetyl-leucinyl, N,N-dimethyl-glycinyl leucinyl, 4- pyridyl acetyl-leucinyl, 2-pyridyl sulfonyl-leucinyl, 4-pyridyl carbonyl- leucinyl, acetyl-leucinyl, benzoyl-leucinyl, 4-phenoxy-benzoyl-, 2- or 3- benzyloxybenzoyl-, biphenyl acetyl, alpha- isobutyl-biphenyl acetyl, Cbz- phenylalaninyl, Cbz-norleucinyl-, Cbz-norvalinyl-, Cbz-glutamyl-, Cbz- epsilon- (t-butyl ester)-glutamyl; acetyl-leucinyl-, 6- or 8- quinoline

carbonyl, biphenyl acetyl, alpha- isobutyl-biphenyl acetyl, acetyl, benzoyl, 2- or 3- benzyloxy benzoyl, 4-phenoxy benzoyl-, Cbz-amino acid-; 2-,3-, or 4- pyridylmethyloxycarbonyl-aminoacid-; aryl CQ-Cgalkyloxy carbonyl- amino acid-, heteroaryl CQ-Cgalkyloxy carbonyl-amino acid-,aryl CQ- C _fj alkyloxy carbonyl-amino acid-,heteroaryl Cø-Cβalkyloxy carbonyl-amino acid-, Cj-Cgalkyloxy carbonyl-amino acid-; Cj-Cgalkyl carbonyl, aryl CQ- Cgalkyl carbonyl, heteroaryl Cø-Cgalkyl carbonyl, aryl Cø-Cόalkyl carbonyl, heteroaryl Cr _j -Cgalkyl carbonyl, Cj-Cgalkyl sulfonyl, aryl CQ- Cgalkyl sulfonyl, heteroaryl C _Q -Cgalkyl sulfonyl, aryl Cø-Cgalkyl sulfonyl, heteroaryl Cø-CGal yl sulfonyl;

R^ H and C^alkyl; R ⁴¹ = H and C ₁ - ₆ alkyl;

R ⁴² = C _j -galkyl, aryl substituted Cj-όalkyl and hetero aryl substituted C _j -galkyl,; H when R ⁴³ is Cj-galkyl, aryl substituted Ci-galkyl; and heteroaryl substituted Cj-galkyl;

R43 ₌ C _j -galkyl, aryl substituted Ci-βalkyl and hetero aryl substituted Cj-galkyl,; H when R ⁴² is Chalky., aryl substituted Cτ,-6alkyl; and heteroaryl substituted Cj-galkyl;

R ⁴⁴ = CH(R ⁵³ )NR ⁴⁵ R ⁵⁴ , CH(R ⁵⁵ )Ar, C5. ₆ alkyl; R ⁴ 5 = R46 _{= R} 47 = _R 48 _{= R} 49 _{= R} 50 _ _R 51 _{= H> c j} _ ₆ alkyl,

Ar-Co-6alkyl, Het-Co-6alkyl; R- ⁵² = Ar, Het, CH(R ⁵⁶ )Ar, CH(R ⁵⁶ )OAr, N(R56)Ar, C galkyl,

CH(R ⁵⁶ )NR ⁴ 6R5 ⁷ ; R ⁵³ = C ₂ -6alkyl, Ar-Co.6 lkyl, Het-C ₀ _6alkyl, R^ and R ⁴ ^ may be connected to form a pyrrolidine or piperidine ring; _R 54 _{= R} 57 _{= R} 47, R47 _C(0 ), R ⁴⁷ C(S), R ⁷ OC(O);

R55 _{= R} 56 _{= R} 58 _{= R} 59 _ _H , C^alkyl, Ar-C ₀ -6alkyl, Het-Co-6alkyl;

Ar-Co-6alkyl, or Het-Cø-όalkyl; R ⁶⁵ = C i _ ₆ alkyl, Ar, Het, CH(R ⁶⁹ ) Ar, CH(R ⁶⁹ )O Ar, N(R ⁶⁹ ) Ar,

CH(R6 ⁹ )NR ⁶¹ R ⁷⁰ ; R66 _ _R 69 _{= R} 71 _ H, C^galkyl, (CH )θ-6-C3-6cycloalkyl,

Ar-CQ-6alkyl, Het-C()-6alkyl; R ⁶⁷ = Cι_ ₆ alkyl, (CH ₂ )θ-6-C3-6cyclo ^alk y ¹ . Ar-C ₀ .6alkyl, Het-C()-6alkyl; R^ ^an d ^* ^ ⁷ may be combined to form a 3-7 membered monocyclic or 7-10-membered bicyclic carbocyclic or heterocyclic ring, optionally substituted with 1-4 of Cι_6alkyl, Ph-Cø-όalkyl, Het-Co_6alkyl, Cj^alkoxy,

Ph-C ₀ -6alkoxy, Het-C ₀ -6alkoxy, OH, (CH ₂ )ι_6NR ⁵⁸ R ⁵⁹ ,

O(CH ₂ )i-6NR ⁵⁸ R ⁵⁹ ;

_R 68 _ _R 70 _ R62 _> R62 _C(0 ), R62 _C (S), R62ØC(O),

R ⁶² OC(O)NR ⁵⁹ CH(R ⁷ l)(CO); and pharmaceutically acceptable salts thereof.

The compounds of Formula I are hydrazidyl, bis-hydrazidyl and bis- aminomethyl carbonyl compounds having in common key structural features required of protease substrates, most particularly cathepsin K substrates. These structural features endow the present compounds with the appropriate molecular shape necessary to fit into the enzymatic active site, to bind to such active site, thereby blocking the site and inhibiting enzymatic biological activity. Referring to Formula I, such structural features include the central electrophilic carbonyl, a peptidyl or peptidomimetic molecular backbone on either side of the central carbonyl, a terminal carbobenzyloxy moiety (e.g., Cbz-leucinyl), or a mimic thereof, on the backbone on one or both sides of the carbonyl, and optionally, an isobutyl side chain extending from the backbone on one or both sides of the carbonyl.

Abbreviations and symbols commonly used in the peptide and chemical arts are used herein to describe the compounds of the present invention. In general, the amino acid abbreviations follow the IUPAC-IUB Joint Commission on Biochemical Nomenclature as described in Eur. J. Biochem., 158, 9 ( 1984). The term "amino acid" as used herein refers to the D- or L- isomers of alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine.

"Ci-6alkyl" as applied herein is meant to include substituted and unsubstituted methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl and t-butyl, pentyl, n-pentyl, isopentyl, neopentyl and hexyl and the simple aliphatic isomers thereof. Any Ci-6alkyl group may be optionally substituted independently by one or two halogens, SR', OR", N(R')2» C(0)N(R')2. carbamyl or Cι_4alkyl, where R' is Ci-6alkyl. Cøalkyl means that no alkyl group is present in the moiety. Thus, Ar- Cøalkyl is equivalent to Ar.

"C3-1 icycloalkyl" as applied herein is meant to include substituted and unsubstituted cyclopropane, cyclobutane, cyclopentane, cyclohexane, cycloheptane, cyclooctane, cyclononane, cyclodecane, cycloundecane.

"C2-6 alkenyl" as applied herein means an alkyl group of 2 to 6 carbons wherein a carbon-carbon single bond is replaced by a carbon-carbon double bond. C2-6alkenyl includes ethylene, 1-propene, 2-propene, 1-butene, 2-butene, isobutene and the several isomeric pentenes and hexenes. Both cis and trans isomers are included.

"C2-6alkynyl" means an alkyl group of 2 to 6 carbons wherein one carbon- carbon single bond is replaced by a carbon-carbon triple bond. C2-6 alkynyl includes acetylene, 1-propyne, 2-propyne, 1-butyne, 2-butyne, 3-butyne and the simple isomers of pentyne and hexyne. "Halogen" means F, Cl, Br, and I.

"Ar" or "aryl" means phenyl or naphthyl, optionally substituted by one or more of Ph-Cø_6alkyl, Het-Cø_6alkyl, C^galkoxy, Ph-Cø.galkoxy,

Het-C ₀ . ₆ alkoxy, OH, (CH ₂ )ι_6NR ⁵⁸ R ⁵⁹ , O(CH ₂ )i-6NR ⁵⁸ R ⁵⁹ ; where R ⁵⁸ , R ⁵⁹ is H, Cι_ ₆ alkyl, Ar-C ₀ . ₆ alkyl; Het-Cø_6alkyl, from Ci-4alkyl, OR', N(R') ₂ , SR', CF3, NO ₂ , CN, CO ₂ R', CON(R'), F, Cl, Br and I.

As used herein "Het" or "heterocyclic" represents a stable 5- to 7-membered monocyclic or a stable 7- to 10-membered bicyclic heterocyclic ring, which is either saturated or unsaturated, and which consists of carbon atoms and from one to three heteroatoms selected from the group consisting of N, O and S, and wherein the

nitrogen and sulfur heteroatoms may optionally be oxidized, and the nitrogen heteroatom may optionally be quaternized, and including any bicyclic group in which any of the above-defined heterocyclic rings is fused to a benzene ring. The heterocyclic ring may be attached at any heteroatom or carbon atom which results in the creation of a stable structure, and may optionally be substituted with one or two moieties selected from Cøalkyl, OR', N(R')2, SR', CF3, NO ₂ , CN, CO2R', CON(R'), F, Cl, Br and I, where R' is Ci-6alkyl. Examples of such heterocycles include piperidinyl, piperazinyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2- oxopyrrolodinyl, 2-oxoazepinyl, azepinyl, pyrrolyl, 4-piperidonyl, pyrrolidinyl, pyrazolyl, pyrazolidinyl, imidazolyl, pyridyl, pyrazinyl, oxazolidinyl, oxazolinyl, oxazolyl, isoxazolyl, morpholinyl, thiazolidinyl, thiazolinyl, thiazolyl, quinuclidinyl, indolyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzopyranyl, benzoxazolyl, furyl, pyranyl, tetrahydrofuryl, tetrahydropyranyl, thienyl, benzoxazolyl, thiamo holinyl sulfoxide, thiamorpholinyl sulfone, and oxadiazolyl. "HetAr" or "heteroaryl" means any heterocyclic moiety encompassed by the above definition of Het which is aromatic in character, e.g., pyridine.

It will be appreciated that the heterocyclic ring, , includes thiazoles, oxazoles, triazoles, thiadiazoles, oxadiazoles, isoxazoles, isothiazols, imidazoles, pyrazines, pyridazines, pyrimidines, triazines and tetrazines which are available by routine chemical synthesis and are stable. The single and double bonds (i.e., ^-) in such heterocycles are arranged based upon the heteroatoms present so that the heterocycle is aromatic (e.g., it is a heteroaryl group). The term heteroatom as applied herein refers to oxygen, nitrogen and sulfur. When the heteroaryl group comprises a five membered ring, W is preferably an electron withdrawing group, such as halogen, -CN, -CF ₃ „ -NO ₂ , -COR ⁷ , -CO ₂ R ⁶ , -CONHR ⁶ , -SO ₂ NHR ⁶ , -

NHSO R ⁶ , -NHCOR ⁷ , -O-COR ⁶ , -SR ⁶ or NR'R ⁶ , or a similar electron withdrawing substituent as known in the art.

Certain radical groups are abbreviated herein. t-Bu refers to the tertiary butyl radical, Boc refers to the t-butyloxycarbonyl radical, Fmoc refers to the fluorenylmethoxycarbonyl radical, Ph refers to the phenyl radical, Cbz refers to the benzyloxycarbonyl radical.

Certain reagents are abbreviated herein. DCC refers to dicyclohexylcarbodiimide, DMAP is 2,6-dimethylaminopyridine, EDC refers to N- ethyl-N'(dimethylaminopropyl)-carbodiimide. HOBT refers to 1- hydroxybenzotriazole, DMF refers to dimethyl formamide, BOP refers to

benzotriazol- 1 -yloxy-tris(dimethylamino)phosphonium hexafluorophosphate, DMAP is dimethylaminopyridine, Lawesson's reagent is 2,4-bis(4-methoxyphenyl)- 1 ,3-dithia-2,4-diphosphetane-2,4-disulfιde, NMM is N-methylmorpholine, TFA refers to trifluoroacetic acid, TFAA refers to trifluoroacetic anhydride and THF refers to tetrahydrofuran. Jones reagent is a solution of chromium trioxide, water, and sulfuric acid well-known in the art.

Compounds of formula (I) are prepared according to the methods detailed in Schemes 1-25.

Scheme 1

a a) i-BuOCOCI, NMM, CH ₂ N ₂ , EtOAc, Et2θ; b) HBr, AcOH, EtOAc, Et2θ; c) H2NCSCθ2Et, EtOH; d) NaOH, H ₂ 0, THF; e) hBuOCOCI, NMM, NH ₂ , THF or BOP, EtsN, RNH2, CH ₂ CI ₂ ; f) TFAA, pyridine, CH2CI2; g) R ⁴ OH, Boc ₂ 0, Pyridinθ or R ⁴ OH, EDCI, CH2CI2; h) piperidinβ, DMF; i) BOP, EtaN, D-CO2H, CH2CI2

a) Mel, THF; b) R'M-^, t-PrOH; c) Bromomethyl ketone, EtOH

Scheme 2

4

fi 2

a) i-BuOCOCI, NMM, NH ₃ , THF; b) Lawesson's reagent, THF; c) BrCH ₂ COCO ₂ Et, TFAA, Pyridine, CH ₂ C1 ₂ ; d) TFA; e) DCO ₂ H, EDC-HC1, HOBT, Et ₃ N, DMF; f) NaOH, H ₂ O, THF

Scheme 2A

a) Boc-amino acid, EDC ^* »HC1, 1-HOBT, DMF; b) TFA; c) R ⁵ OCOCl, -Pr ₂ NEt

Scheme 3

R' R'

NHNH ₂

BocHN BocHN N A C0 ₂ Et

\ H

C0 ₂ Et

S

a) Boc ₂ O, Et ₃ N, THF; b) hydrazine hydrate, MeOH; c) EtO ₂ CCOCl, Pyridine, CH ₂ C1 ₂ ; d) Lawesson's reagent, toluene; e) TFA, CH ₂ C1 ₂ ; f) DCO ₂ H, EDC ^» HCl/HOBT, Et ₃ N, DMF

Scheme 4

1 2

5 a) SOCl ₂₎ pyridine, Et ₂ O, toluene; b) TFA, CH ₂ C1 ₂ ; c) DCO ₂ H, ED HC1/HOBT, Et ₃ N, DMF; d) NH ₃ , EtOH

Scheme 5

a) EDC-HC1/HOBT, Et ₃ N, DMF; b) H ₂ NNH ₂ »H ₂ O, MeOH; c) CSC1 ₂ , Et ₃ N, CHC1 ₃

Scheme 6

3

a) H ₂ NCS ₂ NH ₄ ⁺ , EtOH; b) H ₂ NCSNH ₂ , EtOH

Scheme 7

a) Et ₂ NO; b) H ₂ NCH ₂ CH(NH ₂ )C0 ₂ H

Scheme 8

2 3.

a) i. /-BuOCOCl, NMM, THF; ii. CH ₂ N ₂ , Et ₂ O; b) HBr, AcOH, Et ₂ O; c) H ₂ NCSCO ₂ Et, EtOH; d) R ^* 53NHNH ₂ , EtOH; e) R ⁶⁵ CO ₂ H, EDC ^* »HC1, 1-HOBT, DMF.

a) /-BuOCOCl, NMM, NH3, THF; b) Lawesson's reagent, THF; c) i. EtO ₂ CCOCH ₂ Br, ii. TFAA, Py, CH C1 ₂ ; d) H2NNH ₂ *» ^H 2 ', EtOH; e) R ⁶ 5so ₂ Cl, Py, CH ₂ C1 ₂ ; f) R ⁶⁵ CO ₂ H, EDC ^* »HC1, 1-HOBT, DMF.

Scheme 10

aEt

_R 16 _R 16 o

O R ¹⁵ O R ¹⁵ O

4 5

a) EDC-HCl, HOBT, DMF; b) H ₂ NNH2*H ₂ O, EtOH; c) R ¹⁴ -B-CO ₂ H, EDC'HCL, HOBT, DMF

Scheme 11

O

H,NH A A. NHNH

Scheme 12A

R

N-

R ²¹ CONHNH ^π 2, > R ²¹ CONHNHCHoR »A o . 3

a) i. PhCHO, EtOH; ii. BH3 THF; b) CI ₂ CO, PhMe; c) H ₂ NNH ₂ ^* H ₂ 0, MeOH; d) R 5°2* ^* -,C0 ₂ H,

EDC HCI, 1-HOBT, DMF; e)

Scheme 13

H,N^ ^ ^NH.

a) HBTU, NMM, DMF; b) Jones, acetone

a) NMM, DMF; b) Jones, acetone

Scheme 15

a) EDCI, HOBT, DMF; b) NMM, DMF, 3) Jones, acetone

Scheme 17

a) NaN3, MeOH, H2O; b) Tosyl chloride, triethylamine, CH2CI2; c) Ellman dihydropyran resin (3), PPTS, C1(CH2)2C1; d) PhCH2NH2, toluene, 80 degrees C; e) HATU, N-methyl morpholine, NMP; f) HS(CH ₂ )3SH, MeOH, Et3N; g) Cbz-leucine (6), HBTU, N-methyl morpholine, NMP; h) TFA, CH2CI2, Mβ2S; i) Jones reagent, acetone

Sςhe e 18

a) 4-pyridyl methyl amine, isopropanol, reflux; b) Cbz-leucine, HBTU, N-methyl morpholine, DMF; c) hydrazine, MeOH, reflux; d) 2- dibenzofuransulfonyl chloride, N-methyl morpholine, DMF; e) Jones reagent, acetone

Scheme 19

a) KOH, MeOH/H2O; b) R ⁶⁶ NHNH ₂ , EtOH; c) EDC ^* »HC1, 1-HOBT, DMF

Scheme 20

E,0 ₂ CCOCH ₂ Br — * C0 ₂ E,

a) Thiourea, EtOH; b) i. NaNO2, 16% aqueous HBr; ii. CuBr, 16% aqueous HBr; iii. HBr (cat.), EtOH; c) ArB(OH)2, Pd(PPh ₃ ) ₄ , CsF, DME; d) ArSnMe ₃ , Pd(PPh ₃ ) ₄ , PhMe; e) H ₂ NNH2-»H ₂ O, EtOH; e) R ⁶⁵ CO ₂ H, EDC«HC1, 1-HOBT, DMF.

Scheme 21

RCOCI — → RCONHR ⁶⁴ — → RCH ₂ NHR ⁶⁷ — ^→ RCH ₂ NR ⁶⁷ CSNH ₂ ^~ ^→

1 2 3 4

a) R67NH ₂ , Py, CH ₂ C1 ₂ ; b) LiAlH4, THF; c) i. C1 ₂ CS, Py, CH ₂ C1 ₂ ; ii. NH ₃ , MeOH or I. PhCONCS, CHCI3; ii. K ₂ CO ₃ , MeOH, H ₂ O; d) EtO CCOCH Br, EtOH; e) H ₂ NNH ₂ *»H2θ, EtOH; e) R ⁶⁵ CO ₂ H, EDC ^* »HC1, 1-HOBT, DMF.

Scheme 22

1 2 3

a) H2NNH2*»H ₂ O, EtOH; b) LCO ₂ CO2i'-Bu, 200 °C; c) H ₂ NNH2 ^* »H ₂ O, EtOH; d) R ⁶⁵ CO ₂ H, EDC ^* »HC1, 1 -HOBT, DMF

Scheme 23

a (M = co, so ₂ )

a) TFA; b) R ⁶² CO ₂ H, EDC»HCl, 1-HOBT, DMF; c) R ⁶² SO ₂ Cl, ι-Pr ₂ NEt

Scheme 24

BocNH CO,H

a) EDCI, DMF; b) 2-PhCH ₂ OPhSO2Cl, NMM, DMF; c) TFA, DCM; d) 4-pyridyl acetic acid, HBTU, NMM, DMF; e) Jones

Scheme 25

a) HBTU, NMM, DMF, allyl amine; b) mCPBA, DCM; c) MeNH2, isopropanol, 70 C; d) Cbz-leucine, EDCI, DMF; e) Jones, acetone

In another aspect, the present invention provides a novel cysteine protease in crystalline form, as defined by the positions in Table I herein.

In still another aspect, the present invention provides a novel protease composition characterized by a three dimensional catalytic site formed by the atoms of the amino acid residues listed in Table XXIX herein.

The three dimensional (3D) structure of the instant protease reveals that human cathepsin K is highly homologous to other known cysteine proteinases of the papain family. Cathepsin-K folds into two subdomains separated by the active site cleft, a characteristic of the papain family of cysteine proteases. The overall fold of cathepsin K is very similar to that of papain and actinidin. There is an insertion of one additional residue in cathepsin K at residue alanine 79 compared to papain. This insertion is easily accommodated in the turn at the carboxy terminal end of the helix formed by residues methionine 68-lysine 77 of cathepsin K. There is a different conformation for the backbone atoms of residues asparagine 99 to lysine 103 at the surface of cathepsin K compared to that in papain. Other differences in the backbone conformations between cathepsin K and papain are: a two residue insertion in loop residues 126-127, a two residue insertion at residue aspartate 152, the insertion of 4 residues at glutamine 172 and a difference in the conformation of the loop around residue lysine 200. There are many more differences in the structure of human cathepsin K and human cathepsin B, however, the secondary structure is preserved well between these two enzymes.

Listed in Figure 1 are the known amino acid sequences for the papain superfamily of cysteine proteases cathepsin K, cathepsin S, cathepsin L, papain, actinidin, cathepsin H and cathepsin B, aligned to illustrate the homologies there between.

According to the present invention the crystal structure of human cathepsin K has been determined in the absence of inhibitor and in complex with nine separate inhibitors at resolutions from 3.0 to 2.2 Angstroms. The structures were determined using the method of molecular replacement and refined to R _c values ranging from 0.190-0.267 with the exception of the enzyme in the absence of inhibitor which was not refined.

Further refinement of the atomic coordinates will change the numbers in Table I. Refinement of the crystal structure from another crystal form will result in a new set of coordinates, determination of the crystal structure of another cysteine protease will also result in different set of numbers for coordinates in Table I which has an experimental error of approximately 0.4 Angstroms. Also for example, the

amino acid sequence of the cysteine proteases can be varied by mutation derivatization or by use of a different source of the protein.

Human cathepsin K contains 215 amino acids and the model of the enzyme provided herein is represented by all 215 residues. The cathepsin K crystal structure reveals an active site that is heretofor unknown and comprises a distinct three dimensional arrangement of atoms.

Table I discloses the protein coordinates of cathepsin K. These data are reported for the crystal structures described herein. The data are reported in Angstroms with reference to an orthogonal coordinate system in standard format, illustrating the atom, i.e., nitrogen, oxygen, carbon, sulfur (at α, β, γ, δ, or ε, positions in the amino acid residues); the amino acid residue in which the atom is located with amino acid number, and the coordinates X, Y and Z in Angstroms (A) from the crystal structure. Note that each atom in the active site and the entire structure has an unique position in the crystal. The data also report the B or Temperature Factor values, which indicate the degree of thermal motion of the atom in root mean square displacement measurements (A ² ). Figure 2 illustrates the cathepsin K structure of the invention, including the active site.

The active site of cathepsin K bound to E-64 is shown in Figure 3. The conformation of E-64 bound to cathepsin K resembles that seen in the published structures of the papain-E-64 complex (Varughese, K.I., Biochemistry 28, 1330- 1332 (1989)) and actinidin-E-64 Varughese, K.I. , Biochemistry 31, 5172-5176 (1992)). The covalent bond between the sulfur of cysteine 25 and the carbon C2 of the inhibitor is very clear in the electron density. Differences in the sidechain atoms lining the active site pockets on the enzyme of the various members of the papain family of cysteine proteases give rise to different interactions between the atoms of E-64 and the protein in these structures. In cathepsin K, the isobutyl atoms of the leucine lie well buried in the hydrophobic pocket formed by the side chain atoms of the cathepsin K residues leucine 160, alanine 134 and methionine 68 shielding these atoms of E-64 from solvent. In papain the leucyl side chain atoms of E-64 do not penetrate as deeply into this hydrophobic pocket. Another pocket of cathepsin K is occupied by the guanidinium atoms of E-64. A hydrogen bond forms between N4 of E-64 and the backbone carbonyl oxygen of glutamate 59 and the OD2 oxygen of aspartate 61. The carboxylate oxygen of aspartate 61 also makes a hydrogen bond with the N3 atom of E-64. The sidechain atoms of aspartate 61 lie at the entrance to this pocket in cathepsin K. These interactions are not possible in papain because the corresponding residue in papain is tyrosine 61 which blocks access. The carboxylate oxygens of E-64 make hydrogen bonding interactions with the ND1

atom of histidine 162 and the NE2 atom of glutamine 19. These interactions are also seen in papain and actinidin. The atoms of E-64 do not penetrate the complete region of the enzyme active site. As in papain, the backbone nitrogen atoms of residue glycine 66 in cathepsin K makes a hydrogen bond with the carbonyl oxygen atom 04 of the E-64. Also, the carbonyl oxygen of glycine 66 of cathepsin K forms a hydrogen bond with N2 of E-64. A portion of the regions of the active site are very similar in conformation in cathepsin K, papain and actinindin. A comparison of the active site of cathepsin K and cathepsin B reveals many more differences than observed in comparing papain or actinidin to cathepsin K. A portion of the active site of cathepsin B differs significantly from the corresponding portion of the active site in cathepsin K. The presence of the loop glutamate 107 - proline 116 in human cathepsin B is presumed responsible for the dipeptidyl carboxypeptidase activity of this enzyme and has no equivalent in cathepsin K, papain or actinidin. This loop makes this region of the active site of cathepsin B much smaller than in the other members of this papain family of cysteine proteases including cathepsin K. Despite the differences between the active sites of human cathepsin B and cathepsin K, the active site cysteine residues are almost exactly superimposed by an alignment of structurally homologous alpha carbon atoms in cathepsin B and cathepsin K. Differences in the hydrophobic pocket near leucine 160 in cathepsin K are also evident in cathepsin B. The residues forming this pocket are replaced by proline 78 in place of methionine 68 in cathepsin K and glutamate 243 in cathepsin B is structurally equivalent to leucine 160 in cathepsin K. Interestingly, the residues whose sidechain atoms form hydrogen bonds to the E-64 inhibitor in cathepsin K, namely histidine 162, glutamine 19 and aspartate 61, have structurally homologous residues in cathepsin B, namely histidine 197, glutamine 23 and aspartate 67 respectively.

Specific interactions of certain inhibitors of the present invention at the active site of cathepsin K are detailed hereinbelow.

3 (S)-3-[(N-benzyloxycarbonyl)-L-leucinyl]amino-5-methyl- 1 -( 1 -propoxy)- 2-hexanone makes hydrophobic contacts with the enzyme residues indole ring of tryptophan 184 and the sidechain atom CG of glutamine 19. Oxygen 026 forms a bifurcated hydrogen bond with the amide nitrogen of cysteine 25 and the NE2 atom of glutamine 19. The active site nucleophilic sulfur of residue cysteine 25 is covalently linked to carbon C25 of the inhibitor, which adopts a tetrahedral conformation.

Bis-(Cbz-leucinyl)-l,3-diamino-propan-2-one exhibits the same interaction as 3 (S)-3-[(N-benzyIoxycarbonyl)-L-leucinyl]amino-5-methyl-l-( l-propoxy)-2-

hexanone; carbon C21 of this inhibitor is covalently linked to SG of cysteine 25. The isopropyl atoms CC34,C35,C36 and C37 of the inhibitor form hydrophobic interactions with the sidechain atoms of residues on the enzyme surface, which form a hydrophobic pocket. This pocket is formed by atoms from methionine 68, leucine 209, alanine 163 and alanine 134 and portions of tyrosine 67.

2,2'-N,N'-bis-benzyloxycarbonyl-L-leucinylcarbohydrazide has interactions similar to bis-(Cbz-leucinyl)-l,3-diamino-propan-2-one and, in addition, the atoms C23-29 of the inhibitor CBZ group make an edge-face stacking interaction with the phenol ring of tyrosine 67. Inhibitor atom C21 is covalently bound the enzyme. The sulfur atom of (lS)-N-[2-[(l-benzyloxycarbonylamino)-3- methylbutyl]thiazol-4-ylcarbonyl]-N'-(N-benzyloxycarbonyl-L- leucinyl)hydrazide contacts the ND1 atom of histidine 163 and the indole ring of tryptophan 184. Carbon C22 is covalently attached to SG of cysteine 25.

The CBZ atoms C20-26 of 2-[N-(3-benzyloxybenzoyl)]-2'-[N'-(N- benzyloxycarbonyl-L-leucinyl)]carbohydrazide interact with the sidechain atoms of leucine 160. Carbon C19 is covalently attached to SG of cysteine 25.

Cathepsin K binds selectively one stereoisomer of 4-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-l-[N-[(phenylmethoxy)car bonyl]-L-leucyl]- 3-pyrrolidinone. Carbon C22 is covalently attached to SG of cysteine 25. Atoms C14 and C15 of the inhibitor 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-l-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone form hydrophobic contacts with the sidechain atoms of glutamine 143 and asparagine 161 and the mainchain of alanine 137 and serine 138.

4-[N-[(4-pyridylmethoxy)carbonyl]-L-leucyl]-l-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone interacts in a similar manner to 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-l-[N _r [(phenylmethoxy)carbonyl]-L- leucyl]-3-pyrrolidinone. Again one stereoisomer is bound. Carbon C 17 is covalently attached to SG of cysteine 25. The interaction of 4-[N- [(phenylmethoxy)carbonyl]-L-leucyl]- 1 -N[N-(methyl)-L-leucyl)]-3-pyrrolidinone is the same as for 4-[N-[(4-pyridylmethoxy)carbonyl]-L-leucyl]- 1 -[N-

[(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone, except carbon C22 is covalently attached to SG of cysteine 25.

Atom O24 of l-N-(N-imidazole acetyl-leucinyl)-amino-3-N-(4-phenoxy- phenyl-sulfonyl)-amino-propan-2-one forms a hydrogen bond interaction with the amide NH of glycine 66. Carbon C19 is covalently attached to SG of cysteine 25. In summary, all inhibitors exhibit an aromatic interaction with atoms of the indole of Tryptophan 184. Isopropyl atoms C12-15 of 2,2'-N,N'-bis-

benzyloxycarbonyl-L-leucinylcarbohydrazide and (lS)-N-[2-[(l- benzyloxycarbonylamino)-3-methylbutyl]thiazol-4-ylcarbonyl]- N'-(N- benzyloxycarbonyl-L-leucinyl)hydrazide make hydrophobic contacts with main chain atoms of residues glutamine 21, cysteine 22 and glycine 23. The NE2 atom of glutamine 19 is able to donate a hydrogen bond to oxygen atom 2,2'-N,N'-bis- benzyloxycarbonyl-L-leucinylcarbohydrazide:O22, 1 -N-(N-imidazole acetyl- leucinyl)-amino-3-N-(4-phenoxy-phenyl-sulfonyl)-amino-propan -2-one:O20, 2-[N- (3-benzyloxybenzoyl)]-2'-[N'-(N-benzyloxycarbonyl-L- leucinyl)]carbohydrazide:O20, 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-l-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone:O23, bis-(Cbz-leucinyl)- 1 ,3- diamino-propan-2-one:O22, 3(S)-3-[(N-benzyloxycarbonyl)-L-leucinyl]amino-5- methyl- 1 -( 1 -propoxy)-2-hexanone:O26, 4-[N-[(4-pyridylmethoxy)carbonyl]-L- leucyl]-l-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidi none:O42, (IS, 2'R)- N-2-[[(l-benzyloxycarbonyl)amino]-3-methylbutyl]thiazol-4-yl carbonyl-N ^, -2'- (benzyloxycarbonyl)amino-4'-methylpenanoylhydrazide:O23, 4-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-l-N[N-(methyl)-L-leucyl) ]-3- pyrrolidinone:O23. The backbone amide nitrogen of glycine 66 donates a hydrogen bond to 2,2'-N,N ^, -bis-benzyloxycarbonyl-L-leucinylcarbohydrazide:O39, 1-N-(N- imidazole acetyl-leucinyl)-amino-3-N-(4-phenoxy-phenyl-sulfonyl)-amino -propan- 2-one:O24, 2-[N-(3-benzyloxybenzoyl)]-2'-[N'-(N-benzyloxycarbonyl-L- leucinyl)]carbohydrazide:O37, 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]- 1 -[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone:O40, bis-(Cbz-leucinyl)- 1 ,3- diamino-propan-2-one:O39, (IS, 2'R)-N-2-[[( 1 -benzyloxycarbonyl)amino]-3- methylbutyl]thiazol-4-ylcarbonyl-N ^, -2'-(benzyloxycarbonyl)amino-4'- methylpenanoylhydrazide:O40, 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]- 1 -N[N- (methyl)-L-leucyl)]-3-pyrrolidinone:O31. The hydrophobic pocket lined with atoms from residues methionine 68, leucine 209, alanine 163 and alanine 134 and portions of tyrosine 67 interact with the isopropyl atoms; bis-(Cbz-leucinyl)-l,3- diamino-propan-2-one:C34-37, 2,2'-N,N'-bis-benzyloxycarbonyl-L- leucinylcarbohydrazide: C34-37, ( lS)-N-[2-[( l-benzyloxycarbonylamino)-3- methylbutyl]thiazol-4-yIcarbonyl]-N'-(N-benzyloxycarbonyl-L- leucinyl)hydrazide; :C35-38, 2-[N-(3-benzyloxybenzoyl)]-2 ^, -[N'-(N-benzyloxycarbonyl-L- leucinyl)]carbohydrazide:C32-35, 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]- 1 -[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone:C35-38, 4-[N-[(4- pyridylmethoxy)carbonyl]-L-leucyl]-l-[N-[(phenylmethoxy)carb onyl]-L-leucyl]-3- pyrrolidinone:C19-22, 1 -N-(N-imidazole acetyl-leucinyl)-amino-3-N-(4-phenoxy- phenyl-sulfonyl)-amino-propan-2-one:C26-29. All inhibitors except 3(S)-3-[(N-

benzyloxycarbonyl)-L-leucinyl]amino-5-methyl- 1 -( 1 -propoxy)-2-hexanone and 4- [N-[(phenylmethoxy)carbonyl]-L-leucyl]-l-N[N-(methyl)-L-leuc yI)]-3- pyrrolidinone have aromatic groups that interact with tyrosine 67 on the protein. All inhibitors are covalently linked to the cysteine 25 SG atom through an inhibitor carbon atom.

The crystal structure of the protease of the present invention reveals the three dimensional structure of novel active site formed by the atoms of the amino acid residues listed in Table XXIX.

This structure is clearly useful in the structure-based design of protease inhibitors, which may be used as therapeutic agents against diseases in which inhibition of bone resoφtion is indicated. The discovery of the novel cathepsin K catalytic site permits the design of potent, highly selective protease inhibitors.

Another aspect of this invention involves a method for identifying inhibitors of cathepsin K characterized by the crystal structure and novel active site described herein, and the inhibitors themselves. The novel protease crystal structure of the invention permits the identification of inhibitors of protease activity. Such inhibitors may bind to all or a portion of the active site of cathepsin K; or even be competitive or non-competitive inhibitors. Once identified and screened for biological activity, these inhibitors may be used therapeutically or prophylactically to block protease activity.

One design approach is to probe the cathepsin K of the invention with molecules composed of a variety of different chemical entities to determine optimal sites for interaction between candidate cathepsin K inhibitors and the enzyme. For example, high resolution X-ray diffraction data collected from crystals saturated with solvent allows the determination of where each type of solvent molecule sticks. Small molecules that bind tightly to those sites can then be designed and synthesized and tested for their cathepsin K inhibitor activity.

This invention also enables the development of compounds that can isomerize to short-lived reaction intermediates in the chemical reaction of a substrate or other compound that binds to or with cathepsin K. Thus, the time- dependent analysis of structural changes in cathepsin K during its interaction with other molecules is permitted. The reaction intermediates of cathepsin K can also be deduced from the reaction product in co-complex with cathepsin K. Such information is useful to design improved analogues of known cysteine protease inhibitors or to design novel classes of inhibitors based on the reaction intermediates of the cathepsin K enzyme and cathepsin K inhibitor co-complex. This provides a

novel route for designing cathepsin K inhibitors with both high specificity and stability.

Another approach made possible by this invention, is to screen computationally small molecule data bases for chemical entities or compounds that can bind in whole, or in part, to the cathepsin K enzyme. In this screening, the quality of fit of such entities or compounds to the binding site may be judged either by shape complementarity [R. L. DesJarlais et al., J. Med. Chem. 31:722-729 (1988)] or by estimated interaction energy [E. C. Meng et al, J. Comp. Chem.. 13:505-524 (1992)]. Because cathepsin K may crystallize in more than one crystal form, the structure coordinates of cathepsin K, or portions thereof, as provided by this invention are particularly useful to solve the structure of those other crystal forms of cathepsin K. They may also be used to solve the structure of cathepsin K mutants, cathepsin K co-complexes, or of the crystalline form of any other protein with significant amino acid sequence homology to any functional domain of cathepsin K. One method that may be employed for this purpose is molecular replacement. In this method, the unknown crystal structure, whether it is another crystal form of cathepsin K, a cathepsin K mutant, or a cathepsin K co-complex, or the crystal of some other protein with significant amino acid sequence homology to any functional domain of cathepsin K, may be determined using the cathepsin K structure coordinates of this invention as provided in Table I. This method will provide an accurate structural form for the unknown crystal more quickly and efficiently than attempting to determine such information ab initio.

Thus, the cathepsin K structure provided herein permits the screening of known molecules and/or the designing of new molecules which bind to the protease structure, particularly at the active site, via the use of computerized evaluation systems. For example, computer modeling systems are available in which the sequence of the protease, and the protease structure (i.e., atomic coordinates of cathepsin K and/or the atomic coordinate of the active site cavity, bond angles, dihedral angles, distances between atoms in the active site region, etc. as provided by Table I may be input. Thus, a machine readable medium may be encoded with data representing the coordinates of Table I in this process. The computer then generates structural details of the site into which a test compound should bind, thereby enabling the determination of the complementary structural details of said test compound.

More particularly, the design of compounds that bind to or inhibit cathepsin K according to this invention generally involves consideration of two factors. First,

the compound must be capable of physically and structurally associating with cathepsin K. Non-covalent molecular interactions important in the association of cathepsin K with its substrate include hydrogen bonding, van der Waals and hydrophobic interactions. Second, the compound must be able to assume a conformation that allows it to associate with cathepsin K. Although certain portions of the compound will not directly participate in this association with cathepsin K, those portions may still influence the overall conformation of the molecule. This, in turn, may have a significant impact on potency. Such conformational requirements include the overall three-dimensional structure and orientation of the chemical entity or compound in relation to all or a portion of the binding site, e.g., active site or accessory binding site of cathepsin K, or the spacing between functional groups of a compound comprising several chemical entities that directly interact with cathepsin K. The potential inhibitory or binding effect of a chemical compound with cathepsin K may be estimated prior to its actual synthesis and testing by the use of computer modeling techniques. If the theoretical structure of the given compound suggests insufficient interaction and association between it and cathepsin K, synthesis and testing of the compound is obviated. However, if computer modeling indicates a strong interaction, the molecule may then be synthesized and tested for its ability to bind to cathepsin K in a suitable assay. In this manner, synthesis of inoperative compounds may be avoided.

An inhibitory or other binding compound of cathepsin K may be computationally evaluated and designed by means of a series of steps in which chemical entities or fragments are screened and selected for their ability to associate with the individual binding pockets or other areas of cathepsin K.

One skilled in the art may use one of several methods to screen chemical entities or fragments for their ability to associate with cathepsin K and more particularly with the individual binding pockets of the cathepsin K active site or accessory binding site. This process may begin by visual inspection of, for example, the active site on the computer screen based on the cathepsin K coordinates in Table I. Selected fragments or chemical entities may then be position cathepsin K. Docking may be accomplished using software such as Quanta and Sybyl, followed by energy minimization and molecular dynamics with standard molecular mechanics forcefields, such as CHARMM and AMBER.

Specialized computer programs may also assist in the process of selecting fragments or chemical entities. These include:

• GRID [P. J. Goodford, "A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules", J. Med. Chem..21:849-857 (1985)]. GRID is available from Oxford University, Oxford, UK. • MCSS [A. Miranker and M. Karplus, "Functionality Maps of

Binding Sites: A Multiple Copy Simultaneous Search Method", Proteins: Structure. Function and Genetics. 11:29-34 (1991)]. MCSS is available from Molecular Simulations, Burlington, MA.

• AUTODOCK [D. S. Goodsell and A. J. Olsen, "Automated Docking of Substrates to Proteins by Simulated Annealing" , Proteins: Structure. Function. and Genetics. £: 195-202 (1990)]. AUTODOCK is available from Scripps Research Institute, La Jolla, CA.

• DOCK [I. D. Kuntz et al, "A Geometric Approach to Macromolecule-Ligand Interactions", J. Mol. Biol..16 .:269-288 (1982)]. DOCK is available from University of California, San Francisco, CA.

Additional commercially available computer databases for small molecular compounds includes Cambridge Structural Database and Fine Chemical Database, for a review see Rusinko, A., Chem. Des. Auto. News 8, 44-47 (1993).

Once suitable chemical entities or fragments have been selected, they can be assembled into a single compound or inhibitor. Assembly may be proceeded by visual inspection of the relationship of the fragments to each other on the three- dimensional image displayed on a computer screen in relation to the structure coordinates of cathepsin K. This would be followed by manual model building using software such as Quanta or Sybyl. Useful programs to aid one of skill in the art in connecting the individual chemical entities or fragments include:

• CAVEAT [P. A. Bartlett et al, "CAVEAT: A Program to Facilitate the Structure-Derived Design of Biologically Active Molecules", in Molecular Recognition in Chemical and Biological Problems". Special Pub., Royal Chem. Soc. 78, pp. 182-196 (1989)]. CAVEAT is available from the University of California, Berkeley, CA.

• 3D Database systems such as MACCS-3D (MDL Information Systems, San Leandro, CA). This area is reviewed in Y. C. Martin, "3D Database Searching in Drug Design", J. Med. Chem.. 25:2145-2154 (1992). • HOOK (available from Molecular Simulations, Burlington, MA).

Instead of proceeding to build a cathepsin K inhibitor in a step-wise fashion one fragment or chemical entity at a time as described above, inhibitory or other

type of binding compounds may be designed as a whole or "de novo" using either an empty active site or optionally including some portion(s) of a known inhibitor(s). These methods include:

• LUDI [H.-J. Bohm, "The Computer Program LUDI: A New Method for the De Novo Design of Enzyme Inhibitors", J. Comp. Aid. Molec. Design. 6:61-

78 (1992)]. LUDI is available from Biosym Technologies, San Diego, CA.

• LEGEND [Y. Nishibata and A. Itai, Tetrahedron. 4.7:8985 (1991)]. LEGEND is available from Molecular Simulations, Burlington, MA.

• LeapFrog (available from Tripos Associates, St. Louis, MO). Other molecular modeling techniques may also be employed in accordance with this invention. See, e.g., N. C. Cohen et al, "Molecular Modeling Software and Methods for Medicinal Chemistry", J. Med. Chem.. 22:883-894 (1990). See also, M. A. Navia and M. A. Murcko, "The Use of Structural Information in Drug Design", Current Opinions in Structural Biology. 2:202-210 (1992). For example, where the structures of test compounds are known, a model of the test compound may be superimposed over the model of the structure of the invention. Numerous methods and techniques are known in the art for performing this step, any of which may be used. See, e.g., P.S. Farmer, Drug Design, Ariens, E.J., ed., Vol. 10, pp 119-143 (Academic Press, New York, 1980); U.S. Patent No. 5,331,573; U.S. Patent No. 5,500,807; C. Veriinde, Structure.2:577-587 (1994); and I. D. Kuntz, Science. 257: 1078-1082 (1992). The model building techniques and computer evaluation systems described herein are not a limitation on the present invention.

Thus, using these computer evaluation systems, a large number of compounds may be quickly and easily examined and expensive and lengthy biochemical testing avoided. Moreover, the need for actual synthesis of many compounds is effectively eliminated.

Once identified by the modeling techniques, the protease inhibitor may be tested for bioactivity using standard techniques. For example, structure of the invention may be used in binding assays using conventional formats to screen inhibitors. Suitable assays for use herein include, but are not limited to, the enzyme-linked immunosorbent assay (ELISA), or a fluoresence quench assay. See, for example, the cathepsin K activity assay of Example 2 below. Other assay formats may be used; these assay formats are not a limitation on the present invention. In another aspect, the protease structure of the invention permit the design and identification of synthetic compounds and or other molecules which have a shape complimentary to the conformation of the protease active site of the

invention. Using known computer systems, the coordinates of the protease structure of the invention may be provided in machine readable form, the test compounds designed and/or screened and their conformations superimposed on the structure of the protease of the invention. Subsequently, suitable candidates identified as above may be screened for the desired protease inhibitory bioactivity, stability, and the like.

Once identified and screened for biological activity, these inhibitors may be used therapeutically or prophylactically to block cathepsin K activity.

The following examples illustrate various aspects of this invention. These examples do not limit the scope of this invention which is defined by the appended claims.

EXAMPLE 1: Analysis of the Structure of Cathepsin K

Λ. Expression, Purification and Crystallization Cathepsin K (see Fig. 1) was expressed and purified as described in

Bossard, M. J., et al., J. Biol. Chem. Ill, 12517-12524 (1996).

Crystals of cathepsin K were grown by vapor diffusion in hanging drops from a solution of 30% PEG 8000, 0.1 M Na ⁺ /K+ phosphate at pH 4.5 containing 0.2M Li2SO Crystals of the complex are tetragonal, space group ΫAτ -\^ ^w * ^m cell constants of a=57.7 Angstroms and c= 131.1 Angstroms. The crystals contain one molecule in the asymmetric unit and contain 36 % solvent with a V _m value of 2.3 AVDalton. The structure was determined by molecular replacement using X-PLOR [Brunger, A.T., et al., Science, 235, 458-460 (1987)]. The starting model consisted of the protein atoms from the cathepsin K E-64 complex structure described herein.

B. Model Building and Refinement

Using the three-dimensional electron density map obtained from above, the polypeptide chain of the cathepsin K can be traced without ambiguity. All 215 residues with side chains were built using the 3-D computer graphics program FRODO [Jones, T.A., J. Appl. Crystallogr., 11, 268-272 (1978)]. Each of these 215 amino acids residues was manually positioned in its electron density, allowing for a unique position for each atom in cathepsin K in which each position is defined by a unique set of atomic coordinates (X,Y,Z) as shown in Table I. Starting with these atomic coordinates, a diffraction pattern was calculated and compared to the experimental data. The difference between the calculated and experimentally determined diffraction patterns was monitored by the value of >. The refinement (using X-PLOR) of the structural model necessitates adjustments of

atomic positions to minimize the R-factor, where a value of below 20% is typical for a good quality protein structure and a value of higher than 25% usually indicates the need of further refinement.

EXAMPLE 2: Assays

Determination of cathepsin K proteolytic catalytic activity

All assays for cathepsin K were carried out with human recombinant enzyme. Standard assay conditions for the determination of kinetic constants used a fluorogenic peptide substrate, typically Cbz-Phe-Arg-AMC, and were determined in 100 mM Na acetate at pH 5.5 containing 20 mM cysteine and 5 mM EDTA. Stock substrate solutions were prepared at concentrations of 10 or 20 mM in DMSO with 20 uM final substrate concentration in the assays. All assays contained 10% DMSO. Independent experiments found that this level of DMSO had no effect on enzyme activity or kinetic constants. All assays were conducted at ambient temperature. Product fluorescence (excitation at 360 nM; emission at 460 nM) was monitored with a Perceptive Biosystems Cytofluor 13 fluorescent plate reader. Product progress curves were generated over 20 to 30 minutes following formation of AMC product.

Inhibition studies

Potential inhibitors were evaluated using the progress curve method. Assays were carried out in the presence of variable concentrations of test compound. Reactions were initiated by addition of enzyme to buffered solutions of inhibitor and substrate. Data analysis was conducted according to one of two procedures depending on the appearance of the progress curves in the presence of inhibitors. For those compounds whose progress curves were linear, apparent inhibition constants (Ki _t app) were calculated according to equation 1 (Brandt et al., Biochemistry, 1989, 28, 140):

v = VmA / [Kad + UKi, app) +A]

(1)

where v is the velocity of the reaction with maximal velocity V _m , A is the concentration of substrate with Michaelis constant of Ka, and / is the concentration of inhibitor.

For those compounds whose progress curves showed downward curvature characteristic of time-dependent inhibition, the data from individual sets was analyzed to give k ₀ bs according to equation 2:

[ AMC] = v _ss t + (vo - v _ss ) [1 - exp (-kobs-)J ^obs

(2)

where [AMC] is the concentration of product formed over time t, vø is the initial reaction velocity and v _S s is the final steady state rate. Values for kobs were then analyzed as a linear function of inhibitor concentration to generate an apparent second order rate constant (kobs / inhibitor concentration or k ₀ bs / [I]) describing the time-dependent inhibition. A complete discussion of this kinetic treatment has been fully described (Morrison et al., Adv. Enzymol. Relax. Areas Mol. Biol., 1988, 67, 201). This assay measures the affinity of inhibitors to cathepsin K. One skilled in the art would consider any compound exhibiting a Kj value of less than 50 micromolar to be a potential lead compound for further research. Preferably, the compounds used in the method of the present invention have a K _j value of less than 1 micromolar. Most preferably, said compounds have a K _j value of less than 100 nanomolar.

Human Osteoclast Resorption Assay

Aliquots of osteoclastoma-derived cell suspensions were removed from liquid nitrogen storage, warmed rapidly at 37°C and washed xl in RPMI-1640 medium by centrifugation (1000 rpm, 5 min at 4°C). The medium was aspirated and replaced with murine anti-HLA-DR antibody, diluted 1:3 in RPMI-1640 medium, and incubated for 30 min on ice The cell suspension was mixed frequently.

The cells were washed x2 with cold RPMI-1640 by centrifugation (1000 rpm, 5 min at 4°C) and then transferred to a sterile 15 rnL centrifuge tube. The number of mononuclear cells were enumerated in an improved Neubauer counting chamber.

Sufficient magnetic beads (5 / mononuclear cell), coated with goat anti-mouse IgG, were removed from their stock bottle and placed into 5 mL of fresh medium (this washes away the toxic azide preservative). The medium was removed by immobilizing the beads on a magnet and is replaced with fresh medium. The beads were mixed with the cells and the suspension was incubated for

30 min on ice. The suspension was mixed frequently. The bead-coated cells were immobilized on a magnet and the remaining cells (osteoclast-rich fraction) were

decanted into a sterile 50 mL centrifuge tube. Fresh medium was added to the bead- coated cells to dislodge any trapped osteoclasts. This wash process was repeated xlO. The bead-coated cells were discarded.

The osteoclasts were enumerated in a counting chamber, using a large-bore disposable plastic Pasteur pipette to charge the chamber with the sample. The cells were pelleted by centrifugation and the density of osteoclasts adjusted to 1.5xl0 ^** VmL in EMEM medium, supplemented with 10% fetal calf serum and 1.7g/liter of sodium bicarbonate. 3 mL aliquots of the cell suspension ( per treatment) were decanted into 15 mL centrifuge tubes. These cells were pelleted by centrifugation. To each tube 3 mL of the appropriate treatment was added (diluted to 50 uM in the EMEM medium). Also included were appropriate vehicle controls, a positive control (87MEM1 diluted to 100 ug mL) and an isotype control (IgG2a diluted to 100 ug/mL). The tubes were incubate at 37°C for 30 min.

0.5 mL aliquots of the cells were seeded onto sterile dentine slices in a 48- well plate and incubated at 37°C for 2 h. Each treatment was screened in quadruplicate. The slices were washed in six changes of warm PBS (10 mL / well in a 6-well plate) and then placed into fresh treatment or control and incubated at 37°C for 48 h. The slices were then washed in phosphate buffered saline and fixed in 2% glutaraldehyde (in 0.2M sodium cacodylate) for 5 min., following which they were washed in water and incubated in buffer for 5 min at 37°C. The slices were then washed in cold water and incubated in cold acetate buffer / fast red garnet for 5 min at 4°C. Excess buffer was aspirated, and the slices were air dried following a wash in water.

The TRAP positive osteoclasts were enumerated by bright-field microscopy and were then removed from the surface of the dentine by sonication. Pit volumes were determined using the Nikon/Lasertec ILM21W confocal microscope.

EXAMPLE 3: Method of Detecting Inhibitors

The three dimensional atomic structure can be readily used as a template for selecting potent inhibitors. Various computer programs and databases are available for the purpose. A good inhibitor should at least have excellent steric and electrostatic complementarity to the target, a fair amount of hydrophobic surface buried and sufficient conformational rigidity to minimize entropy loss upon binding. The approach usually comprises several steps: 1) Define a region to target, the active site cavity of cathepsin K can be selected, but any place that is essential to the protease activity could become a

potential target. Since the crystal structure has been determined, the spatial and chemical properties of the target region is known.

2) Docking a small molecule onto the target. Many methods can be used to archive this. Computer databases of three-dimensional structures are available for screening millions of small molecular compounds. A negative image of these compounds can be calculated and used to match the shape of the target cavity. The profiles of hydrogen bond donor-acceptor and lipophilic points of these compounds can also be used to complement those of the target. Anyone skilled in the art would be able to identify many small molecules or fragments as hits. 3) Linking and extending recognition fragments. Using the hits identified by above procedure, one can incorporate different functional groups or small molecules into a single, larger molecule. The resulting molecule is likely to be more potent and have higher specificity. It is also possible to try to improve the "seed" inhibitor by adding more atoms or fragments that will interact with the target protein. The originally defined target region can be readily expanded to allow further necessary extension.

A limited number of promising compounds can be selected through the process. They can then be synthesized and assayed for their inhibitory properties. The success rate can sometimes be as high as 20%, and it may still be higher with the rapid progresses in computing methods.

EXAMPLE 4: Crystallization of Enzvme with Inhibitors

A. Preparation of Inhibitors

Compound 1. Preparation of 4-rN-r henvlmethoxvtearbonvll-L-leucvll-l-rN- f(ρhenvlmethoxv)carbonvll-L-leucvll-3-ρvrrolidinone

a) 3-hydroxy-4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]- 1 - pyrrolidinecarboxylic acid l.ldimethylethyl ester

To a solution of 3-hydroxy-4-amino- 1 -pyrrolidinecarboxylic acid, 1,1- dimethylethyl ester (202 mg, 1.14 mmol) in CH2CI2 (5 mL) was added CBZ- leucine (302.9 mg, 1.14 mmol), HOBT (154 mg, 1.14 mmol) and EDC (262.2 mg, 1.37 mmol). The reaction was allowed to stir until complete by TLC analysis whereupon it was diluted with EtOAc and washed sequentially with pH 4 buffer, sat. K2CO3, water and brine. The organic layer was dried (MgSO4), filtered and

concentrated. Column chromatography of the residue (3: 1 EtOAc:hexanes) gave 325 mg of the title compound: MS (ES+) 450.3 (MH+), 472.2 (M+Na).

b) 3-hydroxy-4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]- 1 -pyrrolidine hydrochloride

To a solution of the carbamate (310 mg, 0.69 mmol) in dry EtOAc (5.0 mL) was bubbled HC1 gas for approximately 5 minutes. The reaction was stirred until TLC analysis indicated the complete consumption of the starting material. The reaction was then concentrated in vacuo to give 249 mg of the title compound: MS (ES+) 350.3 (MH+)

c) 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]- 1-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinol

To a solution of the amine hydrochloride from the previous step (249 mg, 0.64 mmol) in CH2CI2 (10 mL) was added CBZ-leucine (170.4 mg, 0.64 mmol), HOBT (86.5 mg, 0.64 mmol), NMM (300 uL) and EDC (147.2 mg, 0.77 mmol). The reaction was allowed to stir at room temperature for 2 hours whereupon it was diluted with ethyl acetate and worked up as described previously. Column chromatography of the residue (3:lEtOAc:hexanes) gave 104 mg of the title compound: MS (ES+) 597.1 (MH+), 619.1 (M+Na).

d) 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]- 1-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone

To a 0°C solution of the alcohol (100 mg, 0.17 mmol) in acetone (5.0 mL) was added Jone's reagent dropwise until the brown color persisted. The reaction was allowed to warm to room temperature and stirred approximately 48 hours whereupon it was quenched with isopropanol, diluted with EtOAc and washed sequentially with sat. K2CO3, water and brine. The organic layer was dried (MgSO4), filtered and concentrated. Column chromatography of the residue (3: 1 EtOAc.hexanes) gave 31 mg of the title compound: MS (ES+) 595.1 (MH+), 617.0 (M+Na).

Compound 2. Preparation of 4-rN-rfphenylmethoxy^carbonvn-L-leucyll-l-NfN- fmethvn-L-leucvm-3-pvrrolidinone

a) 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-l-[N-[(tert-butoxy) carbonyl]-N- (methyl)-L-leucyl]-3-pyrrolidinol

To a solution of 3-hydroxy-4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-l- pyrrolidine (350 mg) was added N-BOC-N-methyl-leucine (222 mg, 0.0.91 mmol), HOBTQ22.5 mg, 0.91 mmol), EDC (208.6 mg, 1.08 mmol) and N-methyl morpholine (0.3 mL, 2.72 mmol). The reaction was stirred at room temperature until complete by TLC analysis. Workup and column chromatography (1: 1

Hex:EtOAc ) gave 480 mg of the title compound which was used in the following reaction: MS (ES+) 477.4, 577.4 (MH+), 599.4 (M+Na).

b) 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]- 1 -[N-[(tert-butoxy)carbonyl]-N- (methyl)-L-leucyl]-3-pyrrolidinone

To a -78°C solution of oxalyl chloride (0.11 mL, 1.23 mmol) in CH2CI2 was added DMSO (0.17 mL, 2.46 mmol) dropwise. The reaction was allowed to stir at -78°C for 20 minutes whereupon a solution of the alcohol (474 mg, 0.82 mmol) in CH2CI2 was added dropwise. The reaction was stirred at -78°C for 30 minutes whereupon triethylamine (0.57 mL) was added in a single portion and allowed to warm to room temperature. Workup and column chromatography (2: 1 hexanes:ethyl acetate) gave 247 mg of the title compound: MS (ES+) 475, 575 (M+H), 597 (M+Na).

c) 4-[N-[(phenylmethoxy)carbonyl]-L-leucyl]-l-N[N-(methyl)-L-le ucyl)]-3- pyrrolidinone hydrochloride

To a room temperature solution EtOAc HCl was added the carbamate. The reaction was stirred until complete by TLC analysis. Concentration gave the title compound: MS (ES+) 475 (M+H, 100%).

Compound 3. Preparation of 4-fN-r( ^" 4-pyridylmethoxy)carbonyll-L-leucyll-l-rN- r(phenvlmethoxv)carbonvll-L-leucvll-3-ρvrrolidinone

a) 3-hydroxy-4-[N-[(4-pyridylmethoxy)carbonyl]-L-leucyl]- 1 - pyrrolidinecarboxylic acid 1 , 1 dimethylethy 1 ester

3-hydroxy-4-amino-l -pyrrolidinecarboxylic acid, 1,1-dimethylethyl ester was coupled with iso-nicotinoyloxycarbonyl leucine in a similar manner as that described above to give 8.5 grams of the title compound: MS (ES+) 451 (MH+, 100%).

b) 3-hydroxy-4-[N-[(4-pyridylmethoxy)carbonyl]-L-leucyl]- 1 -pyrrolidine hydrochloride

The carbamate from the previous step was deprotected with EtOAc/HCl to give 8.4 grams of the title compound after concentration: MS (ES+)351 (MH+, 100%).

c) 4-[N-[(4-pyridylmethoxy)carbonyl]-L-leucyl]-l-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinol

To a solution of CBZ leucinal (155 mg) in CH2CI2 was added triethylamine (0.09 mL) and the amine hydrochloride (200 mg, 0.52 mmol) from the previous step. The reaction was stirred at room temperature for 2 hours whereupon the majority of the solvent was removed in vacuo. The mixture was redissolved in CH2CI2 and sodium triacetoxyborohydride was added. The reaction was stirred at room temperature for 4 hours. Workup and column chromatography (5% methanol/chloroform) gave 200.5 mg of the title compound: MS(ES+) 583 (MH+, 100%).

d) 4-[N-[(4-pyridylmethoxy)carbonyl]-L-leucyl]-l-[N- [(phenylmethoxy)carbonyl]-L-leucyl]-3-pyrrolidinone

To a DMSO (2 mL) solution of the alcohol (50 mg, 0.09 mmol) from the previous step was added triethylamine (0.07 mL, 0.52 mmol) and pyridine/sulfur trioxide complex (41 mg, 0.26 mmol). The reaction was maintained at room temperature until complete by TLC analysis. Workup and chromatography (5% methanol/chloroform) gave 37 mg of the title compound: MS (ES+) 582 (MH+, 100%).

Compound 4. Preparation of f3SV3-rm-benzvloxvcarbonvlVL-leucinvl1amino-l- f 1 -propoxvV 5-methvl-2-hexanone

(3S)-3-[(N-benzyloxycarbonyl)-L-leucinyl]amino-l-diazo-5- methyl-2- hexanone (150 mg, 0.37 mmol) was dissolved in 1-propanol (2.5 ml), then rhodium acetate (2 mg) was added and the reaction was stirred at RT for 2h. The reaction mixture was chromatographed (silica gel, 20% EtOAc/hexanes) to yield the title compound as a white solid (59 mg, 37%). MS(ES) M+H ^* = 435, M+ NH_j ⁺ = 452, 2M+H ⁺ = 869.6.

Compound 5. Preparation of bis-f Cbz-leucinvlV 1 ■3-diamino-propan-2-one Cbz-leucine (500 mg, 1.88 mmol), EDCI (558 mg, 1.88 mmol) was dissolved in DMF (4.0 ml) with l,3-diamino-propan-2-ol (85 mg, 0.94 mmol) and Hunig's base (0.3 ml, 1.88 mmol) and was stirred at RT overnight. The reaction

was diluted with EtOAc (20 ml) and was extracted with water (2 x 20 ml). The combined organics were dried with magnesium sulfate, filtered, concentrated in vacuo. The intermediate was then dissolved in acetone (4.0 ml) and Jones reagent (2.0 ml, 1.5 M) was added dropwise and the reaction was stirred at RT overnight. The excess Jones reagent was then quenched with isopropanol ( 1.0 ml), then the reaction was diluted with EtOAc (20 ml) and was extracted with water (2x 20 ml) to remove the inorganic salts. The combined organics were dried with magnesium sulfate, filtered, concentrated, and chromatographed (silica gel, 2-5% MeOH/ methylene chloride) to give the title compound as a white solid (410 mg, 75%). MS(ES) M+H ⁺ =583, M+Na ⁺ =605.

Compound 6. Preparation of 2-rN-(3-benzyloxvbenzovni-2'-rN'-rN- benzyloxycarbonyl-L-leucinyD1carbohvdrazide

a) methyl 3-benzyloxybenzoate

To a suspension of NaH (0.395 g, 9.87 mmol, 60% in mineral oil) in DMF (20 mL) was added methyl 3-hydroxybenzoate (1.0 g, 6.58 mmol). After stirring for 15 min at room temperature, benzyl bromide (1.1 g, 6.58 mmol) was added. After stirring at room temperature for 3h, the solution was partitioned between ethyl acetate and water. The organic layer was washed with water (2 X 75 mL), saturated aqueous sodium bicarbonate, and brine, then dried (MgSO4), filtered and concentrated to yield an off-white solid (1.013 g, 4.2 mmol). ^J H NMR (400 MHz, CDC1 ₃ ) d 7.67 (m, 2H), 7.48-7.34 (m. 6H), 7.19 (m, 1H), 5.12 (s, 2H), 3.95 (s, 3H).

b) 3-benzyloxybenzoic acid

To a solution of the compound of Example 6(a) (0.400 g, 1.65 mmol) in THF (2 mL) and water (2 mL) was added lithium hydroxide monohydrate (0.076 g, 1.82 mmol). After stirring at reflux for 5 h, the solution was partitioned between ethyl acetate and 3N HC1. The organic layer was washed with brine, dried (MgSO4), filtered and concentrated to yield a white solid (0.355 g, 1.56 mmol). H NMR (400 MHz, CD3OD) d 7.58 (m, 2H), 7.36-7.24 (m. 6H), 7.10 (m, 1H), 5.04 (s, 2H).

c) 2-[N-(3-benzyloxybenzoyl)]-2'-[N'-(N-benzyloxycarbonyl-L- leucinyl)]carbohydrazide

Following the procedure of Example A, below, except substituting 3- benzyloxybenzoic acid for N-acetyl-L-leucine and 2-[N-(N-benzyloxycarbonyl-L-

leucinyl)]carbohydrazide for 2-[N-(N-benzyloxycarbonyl-L-alanyl)]carbohydrazide, the title compound was prepared as a white solid (0.062 g, 25%). MS(ESI): 548.1 (M+H)+.

Example A

Preparation of 2-rN-rN-acetvl-L-leucinvni-2'-fN'-rN-benzvloxvcarbonvl-L- alanvnicarbohvdrazide

To a stirring solution of 2-[N-(N-benzyloxycarbonyl-L- alanyl)]carbohydrazide (0.150g, 0.508mmol) in DMF (2mL) was added N-acetyl-L- leucine (0.092g, 0.534mmol), 1-hydroxybenzotriazole (0.014g, 0.102mmol), and 1-

(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (0.102g, 0.534mmol). After stirring at room temperature for 16h, the solution was diluted with ethyl acetate, washed successively with water, saturated aqueous sodium bicarbonate, and brine. The organic layer was dried (MgSO4), filtered and concentrated. The residue was purified by column chromatography (silica gel, methanol/dichloromethane) to yield the title compound as a white solid (0.028 g,

12%). MS(ESI): 451.1 (M+H)+.

Compound 7. Preparation of ( 1 S N-f2-f( 1 -benzvloxvcarbonvlamino 3- methylbutyllthiazol-4-vlcarbonvn-N'-(N-benzvloxvcarbonvl-L-l eucinvl)hvdrazide

a) N-tert-butoxycarbonyl-(L)-leucinamide

To a solution of N-tert-butoxycarbonyl-(L)-leucine (7.0g, 28.1mmol ) in dry THF (lOOmL) at -40°C was added isobutylchloroformate (3.8g, 28.1mmol) and N- methylmorphiline (6.0, 59mmol). After 15 minutes of stirring, ammonia was bubbled through the mixture for an additional 15 minutes, then warmed to room temperature and allowed to stir for 2 hours. Mixture filtered and filtrate concentrated in vacuo to yield title compound as a white solid (6.5, 28.0mmol). 'HNMR (400MHz, CDC1 ₃ ) d 6.38 (br s, 1H), 5.79 (br s, 1H), 5.04 (br d, 1H), 4.13 (m, 1H), 1.71-1.49 (m, 3H), 1.39 (s, 9H), 0.92 (dd, 6H).

b) N-tt?rt-butoxycarbonyl-(L)-leucinethioamide

To a stirring solution of the compound of Example 7(a) (6.5, 28.0 mmol) in dry THF was added Lawesson's reagent (6.8g, 16.9 mmol) and the mixture was stirred at room temperature under argon overnight. The solvent was evaporated and the residue chromatographed (silica gel, 12% ethyl acetate/hexane) to give the title compound as a white solid (5.4g, 77%). 'HNMR (400MHz, CDC1 ₃ ) d 8.54 (br s,

1H), 7.97 (br s, 1H), 5.28 (br d, 1H), 4.52 (m, 1H), 1.72-1.58 (m, 3H), 1.40 (s, 9H), 0.92 (m, 6H).

c) (1S)-1 -(tert-butoxycarbonyl)amino- l-(4-carboethoxythiazol-2-yl)-3- methylbutane

The compound of Example 7(b) (5.4g, 21.7 mmol) was stirred in dry acetone (lOOmL) under argon at - 10°C. Ethylbromopyruvate (4.7g, 23.9mmol) was added and stirred for lh at -10°C. The solution was poured into a well stirred mixture of chloroform and water and then into saturated sodium bicarbonate solution. The organic phase was separated and the aqueous layer extracted with chloroform. The combined organic extracts were dried over MgSO ₄ , filtered and concentrated to an oil. The oily residue was treated with TFAA (5.0g, 23.9mmol) and pyridine (3.8g, 47.8mmol) in dichloromethane for lh at -20°C. Excess solvent was removed in vacuo and the residue was dissolved in dichloromethane. The solution was washed with saturated aqueous sodium bicarbonate and l.ON KHSO ₄ until pH 7. The solution was dried over magnesium sulfate, filtered and concentrated to an oil which was chromatographed (silica gel, 7.5% ethyl acetate hexane) to give the title compound as a tan solid (4.5g, 61%). 'HNMR (400MHz, CDC1 ₃ ) d 7.98 (s, 1H), 5.04 (br d, 1H), 4.95 (m, 1H), 4.31 (q, 2H), 1.88 ( , 1H), 1.63 (m, 2H), 1.40 (s, 9H),1.32 (t, 3H), 0.85 (dd, 6H).

d) (1S)-1 -(Benzyloxycarbonyl)amino- 1 -(4-carboethoxy thiazol-2-yl)-3-methylbutane

The compound of Example 7(c) (0.250g, 0.731 mmol) was dissolved in TFA (2mL) and stirred at room temperature for 15 minutes when diluted with methanol and concentrated in vacuo. The residue was dissolved in methylene chloride and treated with triethylamine (0.739g, 7.31mmol) followed by benzyl chloroformate (1.2g, 7.31mmol). The solution stirred at room temperature for 2h when partition between ethyl acetate/water. The organic layer was washed with brine, collected, dried (MgSO and concentrated to a residue that was chromatographed (silica gel, 15% ethyl acetate/hexane) to give the title compound as an oil (0.198g, 72%).

'HNMR (400MHz, CDC1 ₃ ) d 8.01 (s, 1H), 7.32 (m, 5H), 5.51 (br d, 1H), 5.14 (m, 1H), 5.10 (s, 2H), 4.37 (q, 2H), 1.93 (m, 1H), 1.81-1.67 (m, 2H), 1.39 (t, 3H), 0.95 ( , 6H).

e) (lS)-N-[2-[(l-benzyloxycarbonylamino)-3-methylbutyl]thiazol- 4-ylcarbonyl]-N'- (N-benzyloxycarbonyl-L-leucinyl)hydrazide

Following the procedure of Example B(a)-(d), below, except substituting (1S)-1 -(Benzyloxycarbonyl)amino- 1 -(4-carboethoxythiazol-2-yl)-3-methylbutane for ( 1 S)- 1 -benzyloxycarbonylamino- 1 -(2-carboethoxythiazol-4-yl)-3-methylbutane in step (c), the title compound was prepared. MS (MH ⁺ ): 10.0

Example B

Preparation of πS.2'RVN-4-frα-benzvloxvcarbonvnaminol-3-methylbutvnthiazo l- 2-ylcarbonyl-N'-2'-fbenzyloxycarbonvnamino-4'-methvlpentanov lhvdrazide

a) N-benzyloxycarbonyl-L-leucinyl bromomethyl ketone l-methyl-3-nitro-l-nitrosoguanidine (6.65 g, 45.2 mmol) in ether (225 mL) is cooled to 0°C. 40% sodium hydroxide is added slowly and the diazomethane is allowed to collect in the ether solution for 30 minutes at 0°C. The ether solution is then decanted and left at 0 °C.

N-Cbz-L-leucine (2.10 g, 7.6 mmol) was dissolved in THF (10 mL), cooled to -40 °C, and 4-methylmorpholine (0.77 g, 7.6 mmol, 0.83 mL) was added, followed by dropwise addition of isobutyl chloroformate (1.04 g, 7.6 mmol, 0.98 mL). After 15 min, the solution was filtered into the previously prepared 0 °C solution of ethereal diazomethane. The resulting solution was allowed to stand at 0 °C for 23 h. HBr (30% in acetic acid) (45.2 mmol, 9 mL) was added and the resulting solution was stirred at 0 °C for 5 min, then washed sequentially with 0.1 N HC1, saturated aqueous NaHCO3 and saturated brine, then dried (MgSO4), filtered and concentrated to give the title compound as a colorless oil (2.43 g, 94%).

b) (1S)-1 -benzyloxycarbonylamino- 1 -(2-carboethoxythiazol-4-yl)-3-methylbutane

A solution of the compound of Example B(a) (1.57 g, 4.58 mmol) and ethyl thiooxamate (0.61 g, 4.58 mmol) in ethanol (10 mL) was heated at reflux for 4 h. The solution was then cooled , concentrated and the residue was purified by flash chromatography on 230-400 mesh sihca gel, eluting with 1:4 ethyl acetate/hexanes, to give the title compound as a yellow oil (1.0 g, 58%). 1H NMR (400 MHz, CDC13) d 7.41 (s, 1H), 7.34-7.31 (m, 5H), 5.40 (d, 1H), 5.10 (d, 1H), 5.05 (d, 1H), 4.98 (q, 1H), 4.48 (q, 2H), 1.80-1.76 (m, 2H), 1.57-1.53 (m, 1H), 1.44 (t, 3H), 0.95 (d, 3H), 0.93 (d, 3H).

c) ( 1 S)- 1 -benzyloxycarbonylamino- 1 -(2-hydrazinocarbonylthiazol-4-yl)-3- methylbutane

A solution of the compound of Example B(b) (0.30 g, 0.8 mmol) and hydrazine hydrate (0.40 g, 8.0 mmol, 0.39 mL) in ethanol (8 mL) was allowed to stir at room temperature for 2 h. The solution was then concentrated to yield the title compound as a white foam (0.28 g, 98%). IH NMR (400 MHz, CDC13) d 8.29 (s, IH), 7.37-7.35 (m, 5H), 5.18 (d, IH), 5.09 (dd, 2H), 4.95 (q, IH), 4.07 (d, 2H), 1.71 (t, 2H), 1.55 (m, IH), 0.96 (d, 3H), 0.94 (d, 3H).

d) ( 1 S,2'R)-N-4-[[( 1 -benzyloxycarbonyl)amino]-3-methylbutyl]thiazol-2- ylcarbonyl-N ^, -2 ^, -(benzyloxycarbonyl)amino-4'-methylpentanoylhydrazide A solution of the compound of Example B(c) (100 mg, 0.28 mmol), N-Cbz-

L-leucine (80.5 mg, 0.30 mmol), l-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (58.2 mg, 0.30 mmol) and 1-hydroxybenzotriazole (7.5 mg, 0.06 mmol) in DMF (0.6 mmol) was allowed to stir at room temperature for 18 h. The solution was diluted with ethyl acetate and washed successively with water, 0.1 N HCl, saturated aqueous NaHCO3 and saturated brine, then dried (MgSO4), filtered and concentrated. The residue was purified by flash chromatography on 230-400 mesh silica gel, eluting with 1:1 ethyl acetate/hexanes, to provide the title compound as a white solid (111.4 mg, 66%). mp 110-112 °C.

Compound 8. Preparation of 2.2'-N.N'-bis-benzvloxvcarbonvl-L- leucinylcarbohydrazide

To a stirring solution of N-Cbz-L-leucine (Chemical Dynamics Corp.) (2.94 g, 11.1 mmol) in 22 mL of DMF was added carbohydrazide (0.5 g, 5.6 mmol), l-(3- dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (2.13 g, 11.1 mmol) and 1-hydroxybenzotriazole (0.3 g, 2.2 mmol). After stirring at room temperature for 22 h, the solution was poured into 500 mL of water. The precipitate was collected by vacuum filtration and washed with water (4 X 150 mL) and dichloromethane (4 X 150 mL), then dried under vacuum to provide the title compound as a white solid (1.49 g, 46%). MS(ESI): 607.1 (M+Na) ^* .

Compound 9. Preparation of 1-N-f N-imidazole acetvl-leucinvlVamino-3-N-(4- phenoxv-phenvl-sulfonvlVamino-propan-2-one

a) l-N-( N-imidazole acetyl-leucinyl)-amino-3-N-(4-phenoxy phenyl sulfonyl)- amino-propan-2-one

Following the procedure of Example C(a)-(d), below, substituting "imidazole acetic acid" for "4-pyridyl acetic acid", the title compound was prepared: MS(ES) M+H ^* = 542.

Example C

Preparation of l-N-( N-Cbz-leucinyl)-amino-3-N-(2-pyridyl-sulfonyl)-amino- proρan-2-one

a) l-N-(N-Cbz-leucinyl)-amino-3-N-(4-phenoxy-phenyl-sulfonyl)-a mino- propan-2-ol

1,3-Diamino propan-2-ol (6.75 g, 75 mmol) was dissolved in DMF (100ml) and Cbz-leucine (20g, 75.5 mmol), HOBT-hydrate (1 lg, 81.5 mmol), and EDCI (15.5g, 81.2 mmol) were added. The reaction was stirred overnight at RT. A portion of the reaction mixture (30 ml) was concentrated in vacuo, then ether (50 ml) and MeOH (30 ml) were added. A IN solution of hydrochloric acid in ether was added ( 1 M, 30 ml) and a white gum formed, which was washed several times with ether. MeOH-acetone were added and heated until the gum became a white solid. The white solid was dissolved in DMF (25 ml) and DIEA (5ml), then 4- phenoxy phenyl sulfonyl chloride was added. The reaction was stirred for 2h, concentrated in vacuo, then chromatographed (silica gel, 1:1 EtOAc: hexanes) to provide the desired product as a white solid.

b) Leucinyl-amino-3-N-(4-phenoxy phenyl sulfonyl)-amino-propan-2-ol l-N-(Cbz-leucinyl)-amino-3-N-(4-phenoxy-phenyl-sulfonyl)-ami no-propan- 2-ol ( 1.0g, 1.8 mmol) was dissolved in EtOH (30 ml), then 10% Pd/C (0.22g) was added followed by 6N hydrochloric acid (2.5 ml), and the reaction was stirred under a balloon of hydrogen gas for 4h at RT. The reaction mixture was filtered, concentrated, and azeotroped with toluene to provide a white glass which was used in the next reaction without further purification.

c) l-N-(N-4-pyridyl acetyl-leucinyl)-amino-3-N-(4-phenoxy-phenyl-sulfonyl)- amino-propan-2-ol

Leucinyl-amino-3-N-(4-phenoxy phenyl sulfonyl)-amino-propan-2-ol (0.36 g, 0.76 mmol) was dissolved in DMF (5 ml), then NMM (0.45 ml, 4 mmol) was added followed by 4-pyridyl acetic acid (0.13g, 0.75 mmol) and HBTU (0.29g, 0.76 mmol) and the reaction was stirred at RT overnight. The reaction mixture was concentrated in vacuo, then chromatographed (silica gel, 5%MeOH: methylene

chloride) to provide the desired product as a white solid (90 mg, MS(ES): M+H+ = 555.

d) 1 -N-(N-4-pyridyl acetyl-leucinyl)-amino-3-N-(4-phenoxy-phenyl-sulfonyl)- amino-ρropan-2-one l-N-(N-4-pyridyl-acetyl-leucinyl)-amino-3-N-(4-phenoxy-pheny l-sulfonyl)- amino-propan-2-ol (45 mg, 0.08 mmol) was dissolved in acetone (5ml), then IN hydrochloric acid (2 ml) was added. The reaction was concentrated in vacuo, then redissolved in acetone. Jones reagent (1.5 M, several drops) was added and the reaction mixture was stirred for 6h at RT. Isopropanol (0.5 ml) was added and the reaction mixture was concentrated in vacuo. The reaction was diluted with pH 7 buffer and then was extracted with EtOAc, dried with magnesium sulfate, filtered, concentrated in vacuo, then chromatographed (silica gel, 5% MeOH-methylene chloride) to give the desired product as a white solid (27 mg, 50%): MS(ES): M+H+ = 553.

B. Crystallization of the protein and protein-inhibitor complexes

Human cathepsin K was expressed in baculovirus cells for the first eight of the nine inhibitors described below. Conditioned media containing expressed pro-cathepsin K was loaded directly onto an S-Sepharose column pre-equilibrated with 25 mM phosphate buffer at pH 8. The column was eluted with a NaCl gradient. Fractions containing pro-cathepsin K were pooled, concentrated to 2.5 mg/ml and activated to mature cathepsin K in 50 mM sodium acetate buffer pH 4.0 containing 20 mM L-cysteine and 1% mature cathepsin K as seed. The activation was monitored using CBZ-Phe-Arg-AMC,as fluorogenic substrate and by SDS- PAGE. When the increasing specific activity reached a plateau (ca. 15 μmol/min/mg), the reaction was stopped by the addition of inhibitor. The inhibited mature cathepsin K was concentrated and dialyzed against 20 mM MES, 50 mM NaCl, 2 mM L-cysteine, pH 6.

Protein preparation for cathepsin K complex with 4-l -f( ^' phenvlmethoxv)carbonvll- L-leucvn-l-NfN-(methvn-L-leucvm-3-pvrrolidinone ( only

Human cathepsin K was expressed in E. coli. The cell pellet from 1 L of bacterial culture weighing 2.35 gm. was washed with 50 mL of 50 mM Tris/HCl, 5 mM EDTA, 150 mM NaCl, pH 8.0. After centrifugation at 13,000 x g for 15 mins,

the washed pellet was resuspended into 25 mL of the same buffer prepared at 4° C and lysed by passage twice through a cell disruptor (Avestin) at 10,000 psi. The lysate was centrifuged as above, the supernatant decanted and the pellet suspended in 25 mL 50 mM Tris/HCl, 10 mM DTT, 5 mM EDTA, 150 mM NaCl, pH 8.0 containing either 8 M urea or 6 M guanidine HCl. After stirring at 4° C for 30 mins, insoluble cellular debris was removed by centrifugation at 23,000 x g for 30 mins and the supernatant clarified by filtration (0.45 um, Millipore).

Varying amounts of the proenzyme form of cathepsin K were refolded by quick dilution into stirring, N2 (g) sparged 50 mM Tris/HCl, 5 mM EDTA, 10 mM reduced and 1 mM oxidized glutathione, 0.7 M L-arginine pH 8.0 and stirred overnight at 4° C. After concentration to ca.l mg/mL using a stirred cell fitted with a YM-10 membrane (Amicon), the sample was clarified by centrifugation and filtration then dialyzed against 25 mM Na2PO4, 1.0 M NaCl, pH 7.0. The dialysate was applied at a LFR= 23 cm/hr to a 2.6 x 90 cm column of Superdex 75 (Pharmacia) pre-equilibrated in 25 mM

Na2PO4, 1.0 M NaCl, pH 7.0. The cathepsin K proenzyme was pooled based upon purity as observed on a reduced, SDS-PAGE gel.

Crystals of mature activated cathepsin K complexed with inhibitor grew to a size of approximately 0.2 mm ³ in about six days at 20°C. The concentration of inhibited cathepsin K used in the crystallization was approximately 8 mg./ml. The method of vapor diffusion in hanging drops was used to grow crystals from the solution of cathepsin K - inhibitor complex. The initial crystal structure to be determined was that of cathepsin K in complex with the cysteine protease inhibitor E64. Crystals of mature activated cathepsin K complexed with E-64 grew to a size of approximately 0.2 mm ³ in six days at 20°C. The concentration of E-64-inhibited cathepsin K used in the crystallization was 8 mg ml. Vapor diffusion was used in hanging drops from a solution of 10% PEG 8000, 0.1 M Na ⁺ /K ⁺ phosphate at pH 6.2 containing 0.2M NaCl. Crystals of the complex are orthorhombic, space group P2,2 ₁ 2 _l , with cell constants of a=38.4, b=50.7, and c=104.9 Angstroms. This crystal form will be referred to as Form II. The crystals contain one molecule in the asymmetric unit and contain approximately 40% solvent with a Vm value of 2.1 A ³ /Dalton. X-ray diffraction data were measured from a single crystal using a Siemens two-dimensional position-sensitive detector on a Siemens rotating anode generate operating a 5 KW. The structure was determined by molecular replacement using X-PLOR. The starting model consisted of all atoms of the main chain of papain and those side chain atoms predicted to be homologous between the two

proteins as determined from sequence alignment. The cross rotation function was calculated using x-ray diffraction data from 10 to 4 A and a radius of integration of 32 A. The highest peak was 6.0 σ. A translation search was carried out using data from 8 to 3.5 Angstroms resulting in the highest peak of 12.5 σ.The resulting model gave an R _c factor of 0.488. This model was refined by rigid-body refinement, and the resulting phases were used to calculate Fourier maps with coefficients IF ₀ -F _C I and I2F ₀ -F _C I, into which the atomic model of cathepsin K was built using the molecular graphics program FRODO. Conventional positional refinement was used to refine the structure during model building. The structure was refined using X- PLOR. The electron density for E-64 was clear in the maps. The inhibitor was built into density and several additional cycles of map fitting and refinement were carried out to a final R _c of 0.191.

Crystallization of the complex of cathepsin K with 3(SV3-ffN-benzvloxvcarbonvn- L-leucinvnamino-5-methyl- 1 -( 1 -propoxv)-2-hexanone

Crystals of mature activated cathepsin K complexed with the inhibitor grew from a solution of 10% isopropanol, 0.1 M NaPO4 / citrate at pH 4.2. Crystals of the complex are tetragonal, space group P43212, with cell constants of a=57.6 A, and c= 131.2 A. This crystal form will be referred to as Form III. Diffraction data were collected as described above. The crystals contain one molecule in the asymmetric unit and contain 36% solvent with a V _m value of 2.3 AVDalton. The structure was determined by molecular replacement using X-PLOR at 2.5 Angstroms resolution. The starting model consisted of all protein atoms of the orthorhombic form of cathepsin K-E64 structure. Molecular replacement was carried out as described above for the cathepsin K-E64 structure determination. The model was refined by rigid-body refinement using X-PLOR, and the resulting phases were used to calculate Fourier maps with coefficients IF ₀ -F _C I and I2F ₀ -F _C I, into which the atomic model of the inhibitor was built using the molecular graphics program FRODO. Conventional positional refinement was used to refine the structure during model building. The structure was refined using X-PLOR. Several cycles of map fitting and refinement were carried out to a final Rc of 0.245.

Crystallization of the complex of cathepsin K with 2-fN-(3-benzvloxvbenzovm-2'- rN'-fN-benzvloxvcarbonvl-L-leucinvnicarbohvdrazide

Crystals of mature activated cathepsin K complexed with the inhibitor grew from a solution of 22.5% PEG 8000, 0.075 M sodium acetate at pH 4.5 containing 0.15 M Li2SO4. Crystals of the complex grew as Form III. Diffraction data were collected as described above. The structure was determined by rigid body refinement with X-PLOR utilizing the previous Form III protein model at 2.4 Angstroms resolution. Fourier maps with coefficients IF ₀ -F _C I and I2F ₀ -F _C I were used to fit the atomic model of the inhibitor using the molecular graphics program FRODO. Conventional positional refinement ( X-PLOR) was used to refine the structure during model building. Several cycles of map fitting and refinement were carried out to a final R _c of 0.237.

Crystallization of the complex of cathepsin K with bis-(Cbz-leucinvn-1.3-diamino- proρan-2-one

Crystals of mature activated cathepsin K complexed with the inhibitor grew from a solution of 10% isopropanol, 0.1 M NaPO4 / citrate at pH 4.2. Crystals of the complex grow as Form IH. Diffraction data were collected as described above. The structure was determined by rigid body refinement of the previous Form IH protein model at 2.6 Angstroms resolution. Fourier maps with coefficients IF ₀ -F _C I and 12F ₀ -F _C I were used to fit the atomic model of the inhibitor using the molecular graphics program FRODO. Conventional positional refinement was used to refine the structure during model building. Several cycles of map fitting and refinement were carried out using X-PLOR to a final R _c of 0.210.

Crystallization of the complex of cathepsin K with 4-fN- r(phenylmethoxy^carbonyll-L-leucyll-l-NfN-(methvn-L-leucvm-3 -pvrrolidinone

Crystals of mature activated cathepsin K complexed with the inhibitor grew from a solution 18% PEG 8000, 0.6 M sodium acetate at pH 4.5 containing 0.12 M Li2SO4- Crystals of the complex grow in Form III. Diffraction data were collected as described above. The structure was determined by rigid body refinement of the previous Form III protein model with X-PLOR at 2.4 Angstroms resolution. Fourier maps with coefficients 1F ₀ -F _C I and I2F ₀ -F _C I, were used to the atomic model of the inhibitor using the molecular graphics program FRODO. Conventional positional refinement was used to refine the structure during model building using X-PLOR. Several cycles of map fitting and refinement were carried out to a final R _c of 0.218.

Crystallization of the complex of cathepsin K with ⁽ lS ⁾ -N-f2-rn- benzyloxycarbonylaminoV3-methylbutyl1thiazol-4-ylcarbonyll-N '-(N- benzyloxycarbonyl-L-leucinyl)hvdrazide

Crystals of mature activated cathepsin K complexed with the inhibitor grew from a solution of 30% MPD, 0.1 M MES at pH 7.0 and 0.1 M tris buffer at pH 7.0. Crystals of the complex are Form π. Diffraction data were collected as described above. The structure was determined by rigid body refinement of the previous Form II protein model with X-PLOR at 2.3 Angstroms resolution. Fourier maps with coefficients 1F ₀ -F _C I and I2F ₀ -F _C I, were used to the atomic model of the inhibitor using the molecular graphics program FRODO. Conventional positional refinement was used to refine the structure during model building using X-PLOR. Several cycles of map fitting and refinement were carried out to a final R _c of 0.211.

Crystallization of the complex of cathepsin K with 2.2'-N.N'-bis- benzvloxvcarbonvI-L-leucinvlcarbohvdrazide

Crystals of mature activated cathepsin K complexed with the inhibitor grew from a solution of 33% MPD, 0.1 M MES at pH 7. Crystals of the complex grow as Form II. Diffraction data were collected as described above. The structure was determined by rigid body refinement of the previous Form II protein model with X-PLOR at 2.2 Angstroms resolution.. Fourier maps with coefficients IF ₀ -F _C I and I2F ₀ -F _C I, were used to the atomic model of the inhibitor using the molecular graphics program FRODO. Conventional positional refinement was used to refine the structure during model building using X-PLOR. Several cycles of map fitting and refinement were carried out to a final R _c of 0.208.

Crystallization of the complex of cathepsin K with 4-fN-

Kphenvlmethoxv^carbonvll-L-leucvn-l-rN-rfphenvlmethoxv^ca rbonvH-L-leucvn- 3-pvrrolidinone

Crystals of mature activated cathepsin K complexed with the inhibitor grew from a solution of 28% MPD, 0.1 M MES at pH 7.0 and 0.1 M tris buffer at pH 7.0. Crystals of the complex Form II. Diffraction data were collected as described above. The structure was determined by rigid body refinement of the previous Form II protein model with X-PLOR at 2.3 Angstroms resolution. Fourier maps with coefficients IF ₀ -F _C I and I2F ₀ -F _C I, were used to the atomic model of the inhibitor

using the molecular graphics program FRODO. Conventional positional refinement was used to refine the structure during model building using X-PLOR. Several cycles of map fitting and refinement were carried out to a final R _c of 0.193.

Crystallization of the complex of cathepsin K with 4-rN-f(4- pvridvlmethoxv carbonvn-L-leucvll-l-rN-r(phenvlmethoxv)carbonvn-L-leucyll-3 - pvrrolidinone

Crystals of mature activated cathepsin K complexed with the inhibitor grew from a solution of 30% MPD, 0.1 M MES at pH 7.0 and 0.1 M tris buffer at pH 7.0.

Crystals of the complex Form II. Diffraction data were collected as described above. The structure was determined by rigid body refinement of the previous Form II protein model with X-PLOR at 2.2 Angstroms resolution.. Fourier maps with coefficients IF ₀ -F _C I and I2F ₀ -F _C I, were used to the atomic model of the inhibitor using the molecular graphics program FRODO. Conventional positional refinement was used to refine the structure during model building using X-PLOR. Several cycles of map fitting and refinement were carried out to a final Rς of 0.267.

Crystallization of the complex of cathepsin K with 1-N-f N-imidazole acetvl- leucinylVamino-3-N-(4-phenoxv-phenvl-sulfonvlVamino-propan-2 -one

Crystals of mature activated cathepsin K complexed with the inhibitor grew from a solution of 18% PEG 8000, 0.6 M sodium acetate at pH 4.5 containing 0.12 M J2SO4. Crystals of the complex are Form IH. Diffraction data were collected as described above. The structure was determined by rigid body refinement of the previous Form II protein model at 2.5 Angstroms resolution.. Fourier maps with coefficients IF ₀ -F _C I and I2F ₀ -F _C I were used to fit the atomic model of the inhibitor using the molecular graphics program FRODO. Conventional positional refinement was used to refine the structure during model building. Several cycles of map fitting and refinement were carried out using X-PLOR to a final R _Q of 0.246. Abbreviations

E-64, [ 1 -[N-[(L-3-trα«-f-carboxyoxirane-2carbonyl)- L-leucyl] amino]-4-guanidinobutane] CBZ, benzyloxycarbonyl

AMC, aminomethylcoumarin MPD, 2 methyl-2,4-pentanediol

PIPES, piperazone-N,N-bis(2-ethanesulfonic acid)

MES, 2-(N-morpholino)-ethanesulfonic acid tris, tris(hydroxymethyl)-aminomethane

PEG, polyethyleneglycol M, Molar

R _C = ΣI(F ₀ - F _C )I / F ₀

F ₀ = observed structure amplitude

F _c = calculated structure amplitude

EDTA, ethylenediaminetetraacetic acid DTT, 1 ,4-dithiothreitol

SDS-PAGE, sodium dodecylsulfate polyacrylamide gel electrophoresis

This invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims.

The disclosures of the patents, patent applications and publications cited herein are incorporated by reference in their entireties.

TABLE I

Table of the orthogonal three dimensional coordinates in

Angstroms and B factors (A ² ) for cathepsin K .

Residue Atom X Y Z B

TABLE I

73 GLN NE2 13.85 45.16 88.80 15.00

74 TYR N 10.54 47.68 84.96 15.00 74 TYR CA 10.04 49.00 84.58 15.00 74 TYR C 8.81 49.41 85.38 15.00 74 TYR 0 8.69 50.56 85.81 15.00 74 TYR CB 9.72 49.05 83.08 15.00 74 TYR CG 8.90 50.26 82.67 15.00 74 TYR CDl 9.48 51.52 82.60 15.00 74 TYR CD2 7.54 50.14 82.44 15.00 74 TYR CE1 8.71 52.63 82.31 15.00 74 TYR CE2 6.77 51.25 82.15 15.00 74 TYR CZ 7.36 52.49 82.09 15.00

74 TYR OH 6.58 53.59 81.84 15.00

75 VAL N 7.87 48.48 85.54 15.00 75 VAL CA 6.65 48.74 86.31 15.00 75 VAL C 7.07 49.05 87.76 15.00 75 VAL 0 6.41 49.80 88.47 15.00 75 VAL CB 5.73 47.48 86.38 15.00 75 VAL CGI 4.32 47.87 86.73 15.00

75 VAL CG2 5.77 46.72 85.07 15.00

76 GLN N 8.18 48.44 88.18 15.00 76 GLN CA 8.71 48.62 89.52 15.00 76 GLN C 9.26 50.02 89.71 15.00 76 GLN 0 8.62 50.86 90.31 15.00 76 GLN CB 9.78 47.57 89.79 15.00 76 GLN CG 10.35 47.60 91.20 15.00 76 GLN CD 11.53 46.64 91.36 15.00 76 GLN OE1 12.17 46.25 90.38 15.00

76 GLN NE2 11.80 46.25 92.59 15.00

77 LYS N 10.43 50.30 89.15 15.00 77 LYS CA 11.04 51.62 89.32 15.00 77 LYS C 10.24 52.83 88.85 15.00 77 LYS O 10.34 53.90 89.44 15.00 77 LYS CB 12.44 51.64 88.71 15.00 77 LYS CG 12.52 51.06 87.30 15.00 77 LYS CD 13.96 50.69 86.97 15.00 77 LYS CE 14.06 49.75 85.79 15.00

77 LYS NZ 15.39 49.07 85.82 15.00

78 ASN N 9.48 52.69 87.77 15.00 78 ASN CA 8.67 53.81 87.31 15.00 78 ASN C 7.51 53.96 88.28 15.00 78 ASN 0 6.94 55.03 88.41 15.00

TABLEI

94 GLU O 7.40 55.80 71.37 15.00

94 GLU CB 4.27 56.10 69.86 15.00

94 GLU CG 3.45 56.13 68.58 15.00

94 GLU CD 1.96 56.28 68.85 15.00

94 GLU OE1 1.48 55.64 69.81 15.00

94 GLU OE2 1.27 57.03 68.11 15.00

95 SER N 6.22 57.71 71.14 15.00 95 SER CA 6.84 58.41 72.26 15.00 95 SER C 6.16 57.91 73.52 15.00 95 SER 0 4.92 57.82 73.58 15.00 95 SER CB 6.63 59.93 72.12 15.00

95 SER OG 5.25 60.23 71.89 15.00

96 CYS N 6.96 57.55 74.51 15.00 96 CYS CA 6.44 57.04 75.77 15.00 96 CYS C 5.44 58.02 76.39 15.00 96 CYS 0 5.84 59.03 76.95 15.00 96 CYS CB 7.59 56.77 76.74 15.00

96 CYS SG 7.00 56.38 78.40 15.00

97 MET N 4.15 57.73 76.21 15.00 97 MET CA 3.06 58.55 76.74 15.00 97 MET C 2.40 58.00 78.01 15.00 97 MET 0 1.16 57.90 78.06 15.00 97 MET CB 1.97 58.73 75.69 15.00 97 MET CG 2.36 59.52 74.45 15.00 97 MET SD 1.29 58.98 73.09 15.00

97 MET CE -0.36 59.43 73.71 15.00

98 TYR N 3.20 57.65 79.01 15.00 98 TYR CA 2.67 57.13 80.26 15.00 98 TYR C 1.93 58.21 81.06 15.00 98 TYR 0 2.48 59.26 81.38 15.00 98 TYR CB 3.78 56.51 81.11 15.00 98 TYR CG 3.32 56.04 82.48 15.00 98 TYR CDl 3.24 56.92 83.56 15.00 98 TYR CD2 2.95 54.72 82.69 15.00 98 TYR CE1 2.81 56.49 84.80 15.00 98 TYR CE2 2.52 54.29 83.95 15.00 98 TYR CZ 2.45 55.18 84.99 15.00

98 TYR OH 2.02 54.77 86.22 15.00

99 ASN N 0.69 57.92 81.43 15.00 99 ASN CA -0.14 58.84 82.20 15.00 99 ASN C -0.54 58.20 83.54 15.00 99 ASN O -1.31 57.23 83.58 15.00

TABLEI

150 TYR N 2.21 19.90 70.99 15.00

150 TYR CA 3.25 20.21 70.03 15.00

150 TYR C 4.60 19.64 70.34 15.00

150 TYR O 5.26 20.08 71.28 15.00

150 TYR CB 3.39 21.72 69.86 15.00

150 TYR CG 4.42 22.11 68.81 15.00

150 TYR CDl 4.39 21.53 67.54 15.00

150 TYR CD2 5.44 23.02 69.11 15.00

150 TYR CE1 5.36 21.85 66.58 15.00

150 TYR CE2 6.41 23.33 68.15 15.00

150 TYR CZ 6.37 22.74 66.90 15.00

150 TYR OH 7.34 23.02 65.97 15.00

151 TYR N 5.03 18.69 69.53 15.00 151 TYR CA 6.35 18.11 69.70 15.00 151 TYR C 7.09 18.15 68.37 15.00 151 TYR 0 6.65 17.56 67.39 15.00 151 TYR CB 6.30 16.68 70.20 15.00 151 TYR CG 7.67 16.22 70.63 15.00 151 TYR CDl 8.45 17.02 71.46 15.00 151 TYR CD2 8.20 15.02 70.17 15.00 151 TYR CE1 9.74 16.65 71.82 15.00 151 TYR CE2 9.50 14.63 70.52 15.00 151 TYR CZ 10.26 15.45 71.35 15.00

151 TYR OH 11.55 15.08 71.70 15.00

152 ASP N 8.21 18.85 68.35 15.00 152 ASP CA 8.98 18.96 67.12 15.00 152 ASP C 10.47 18.82 67.44 15.00 152 ASP 0 11.08 19.72 68.03 15.00 152 ASP CB 8.70 20.31 66.45 15.00 152 ASP CG 9.22 20.37 65.03 15.00 152 ASP OD1 8.48 19.96 64.12 15.00

152 ASP OD2 10.37 20.82 64.82 15.00

153 GLU N 11.03 17.68 67.05 15.00 153 GLU CA 12.44 17.38 67.31 15.00 153 GLU C 13.40 18.37 66.69 15.00 153 GLU O 14.59 18.34 66.98 15.00 153 GLU CB 12.76 15.94 66.86 15.00 153 GLU CG 12.29 15.56 65.44 15.00 153 GLU CD 13.28 15.95 64.33 15.00 153 GLU OE1 14.38 15.36 64.28 15.00

153 GLU OE2 12.95 16.84 63.50 15.00

154 SER N 12.89 19.26 65.85 15.00

TABLE π

Table of the orthogonal three dimensional coordinates in Angstroms and B factors (A-2) for the cathepsin K complex with inhibitor 3(S)-3-[(N- benzyloxycarbonyl) -L-leucinyl]amino-5-methyl-l- (1- propoxy) -2-hexanone.

Residue Atom X B

TABLE II ASP N -44.48 -25.96 66.20 15.00 ASP CA -43.78 -24.69 66.19 15.00 ASP CB -44.75 -23.59 65.74 15.00 ASP CG -44.11 -22.19 65.67 15.00 ASP ODl -42.99 -21.99 66.18 15.00 ASP 0D2 -44.75 -21.27 65.13 15.00 ASP C -43.37 -24.47 67.64 15.00 ASP 0 -44.19 -24.09 68.48 15.00 TYR N -42.10 -24.68 67.95 15.00 TYR CA -41.65 -24.50 69.33 15.00 TYR CB -40.30 -25.18 69.53 15.00 TYR CG -40.41 -26.69 69.53 15.00 TYR CDl -40.91 -27.37 70.64 15.00 TYR CE1 -41.02 -28.74 70.65 15.00 TYR CD2 -40.02 -27.43 68.42 15.00 TYR CE2 -40.13 -28.80 68.42 15.00 TYR CZ -40.63 -29.45 69.53 15.00 TYR OH -40.70 -30.82 69.53 15.00 TYR C -41.62 -23.07 69.82 15.00 TYR O -41.41 -22.81 71.00 15.00 ARG N -41.83 -22.12 68.92 15.00 ARG CA -41.84 -20.72 69.31 15.00 ARG CB -42.00 -19.80 68.09 15.00 ARG CG -40.82 -19.80 67.14 15.00 ARG CD -41.13 -18.98 65.91 15.00 ARG NE -42.05 -19.66 65.00 15.00 ARG CZ -42.68 -19.07 64.00 15.00 ARG NHl -42.49 -17.78 63.77 15.00 ARG NH2 -43.50 -19.77 63.22 15.00 ARG C -43.00 -20.51 70.28 15.00 ARG 0 -42.87 -19.79 71.28 15.00 LYS N -44.10 -21.19 70.00 15.00 LYS CA -45.30 -21.10 70.82 15.00 LYS CB -46.49 -21.67 70.05 15.00 LYS CG -46.76 -21.07 68.69 15.00 LYS CD -48.04 -21.67 68.14 15.00

LYS CE -48.28 -21.36 66.69 15.00 LYS NZ -49.49 -22.07 66.19 15.00 LYS C -45.20 -21.83 72.16 15.00 LYS 0 -46.13 -21.78 72.97 15.00 LYS N -44.10 -22.53 72.40 15.00 LYS CA -43.92 -23.27 73.64 15.00

TABLE IH

Table of the orthogonal three dimensional coordinates in Angstroms and B factors (A- ² ) for the cathepsin K complex with inhibitor bis- (cbz-leucinyl) -1, 3- diamino-propan-2-one.

Residue Atom X Y Z B

W tO tO tO tO tO M W tO tO tO W tO tO tO W t W tO M CO tO tO M

W cn cn w cn cn w uι uι Ui cn in w w w Ln ιπ cπ cπ w cπ -i ιt> ιii '> t> ιt» co co

H H H H H H H H H O O O O O O CO co co co co co Ω Ω < ^* ι κ ^* ι ^ M M M M M CΛ C ^* Λ co co co ? » '-d ϊθ » ^, -θ Hc; ^H <

CO c

CD I I I I I I I I I I I I I I I I I I I I I I I I I I I I I

3 to to to to to to w to M M to to to to to M to to to M M to to to to μ ^j μ ^j rfs μ-> tO tO C μ-> tO U> U> CΛ Ul ιts. Ul CΛ s] rfs UJ Ul ιts U) M tθ μ-» μ ^J O O O OO VD

O CΛ s] C ιtS s] CO rfS |fs. CΛ ιts s] Ui Ul tO VO VO rfs rfs VD Ul CΛ Vθ μ-- CO Ul tO VD rfs sj cΛ vo to o cπ o co μ-N s] uι uι μ-» ui rfs s] cΛ θo μ-» μ-» uι o vo ιt-. cΛ CΛ to o μ-' rπ o I I I I I I I i l l i i i i i i i i i i i i i I x ι_ ₍ _- ₍ -j (_> ι_- ι_i ι_> ₍ _ι _J i ■ — » ■ — » i — » i i to w μ μ μ μ μ μ μ μ μ μ μ μ rπ Ul rf^ rfs Ul Ul W U tO VO O O O VO VO O O VO CO OO OO OO si CΛ sl CΛ CO sJ

=1 K CΛ CO CO CΛ tO CΛ rfs Cπ CΛ IO Ul M Ul CΛ rfs O CΛ CΛ CΛ M VO its Ul rfs CΛ μ^ O

00 CO O Ul O tO CO CΛ UJ CΛ VO rfs tO O ∞ Ul Ul O Co Ul rfs O Ul VO CO tO Ul CO

m Ul Ul Ul Ul Ul Ul Cπ Ul Ul Ul Cπ Ul Ul Ul Cπ CΛ CΛ Cπ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ C ro M tO UI ιts Cπ CΛ s] sl s] CΛ CΛ sl OO OD sl CO tO VO O tO tO ιfs Ui ιls rfs U ⁾ tθ μ ^J p ^J

O)

VO rfs rfs sJ sJ CΛ O l I Ul rfs its CΛ OO VD sl rfs OO Ul sl tO CO Ul its CΛ sl UI CO Ul rfs l μ μ to s] sl U1 00 CX> ιts CO ιf-. ι ^* S O t O tO rfs U1 0 0 CO CO OO VD Ui s] 00

α ι_ ^j _H- ^N i_ ^» H' μ- ^ι μ ^{j j} μ-' μ ^j μ-' μ-' ^j μ ^j μ ^j μ ^j μ ^j μ ^j μ- ^ι μ-' μ ^j ui ui ui ui ui ui ui ui ui ui cπ cn ui ui ui ui ui cπ ui ui ui ui ui ui ui ui ui ui ui

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

CO U) UI UI UI U ^, U> UI UI U) U) UI UI UI U) U) UI U' UI UI UI U) UI U ¹ U) U» U) UI U> vo vo vo oo ∞ oo co ∞ ∞ oo ∞ si si si si sj si si s- si a^ cΛ CΛ CΛ cn cπ cπ cn ui

C C C C C C C C C C C Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω i-d ^ M M M M M M M M C C C C C C C C C C C C C C C C C C co co co G G G G G G G G 2 2 2 2 2 2 2 2 2 « ^* κ' κ' κ-' c_-- c-_ ^* G a G

0 0 2 0 0 O 0 0 0 0 2 0 O 2 0 O 0 O 0 2 0 0 O 2 0 O 0 0 0 W > d d Ω W M M d Ω ro > M M d to μ to μ to μ

μ ^{j j} -» μ ^j μ ^j μ ^j μ ^j - ^{ι j j} μ-' -' μ- ^ι μ-' μ ^j μ-» μ ^j ' μ ^{j j} -' μ ^j μ-'

U1 U1 U1 U1 U1 U1 U1 U1 U1 U1 U1 U1 U1 1 U1 U1 U1 U1 U1 U1 U1 U1 U1 U1 UI U1 U1 U1 U1

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

∞ ∞ ∞ oo co ∞ oo ∞ oo oo CD ∞ rø ∞ _O D _OD cn oo ∞ cn cD rø C _D ∞ ω -O si si sj ω co ω co u ^, to to to w w ^* θ M to μ ^j μ ^j μ-> μ-> μ-> μ ^j μ ^j o o o o vD Vo vo vo

W C C ω rΛ > > > H H H H H H H H Ω Ω Ω Ω | M ω c ω c ω co c c c c c w » &»

"Λ » 'Λ 'Λ ^ ^ 3 ^ ^ O ^t τJ »τJ r _r j M M M M M μN > Ω Ω Ω Ω

O

CO

ID I I I I I I I I I I I I I I I I I I I I I I I I I I I I I CO to to to to to to to μ μ μ to to to to to w to to to to io μ to to to μ μ μ μ it- ui σi ui co co co co co co O P' J-' U' tO tO tO U- tO P' P' VO O O O VD VD OO s

CΛ CO O I-» VO CΛ t CO CΛ s] VO VO rfs θ O s] sl CO rfs rfs U) rfs O (fs rfS sl CΛ

H CΛ tO CO tθ μ-. s] s] VO CΛ Ul Ul VO OO OO VO ιts 00 μ-» sl Ul rfs CO P» O tO Ul CO O rπ

CO I I I I I I I I I I I I I I I I I I I I I I

X μ- ^» μ-> p ^» μ-» p» μ μ to to to to to to tJ to to to tJ tJ to to to co co m Ul CΛ CΛ s] sl VO 00 O s] OO co co o μ μ to to co co to co ιt> t> cπ cfι s! si co to m

ON VO O sl p» sl sl O OO Cθ μ-' tO ιts s] UI CO O ιts sl OO CTl CΛ CΛ VO CO CΛ CΛ sl o uι vo uι ∞ o ω vo si o -o tθ sj vo ιfs. σι ιfs si to μ-» to u> to μ ^j uι cΛ si c r- m s] Cn CD sl sl s] sJ cX> CX» OO sJ sJ s] sl sJ sl sl ssl] ssl] ssll ssJJ ssl] ssl] CαO-) CCDO OC»O OCDO OCXO> OOOO

CO O VO VD CO VO P' O O CD VD C£I CO VO ιts CΛ s] sl Cβ VD CX> VD O O tθ μ ^J U> μ->

Ul its iIS UJ sl O O CΛ M Ul CΛ sl O CO sl μ-' Ul tO ifs rfs VD CΛ sl rfs π CO sl CO ∞ rfs CΛ O VD VO tO O CΛ CD M CΛ VO CO VO sl CO Cπ its U U- Ul itS s VO rfs CO

^α μ ^j H ^, i--' μ-' μ- ^, ' -' μ-' ^ι P ^, μ-' μ- ¹ μ-' ^j μ ^{j j} μ- ^» μ-' μ- ^» μ-' ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui cπ ui ui ui ui ui ui ui ui ui ui ui o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o

TABLE III

110 TYR O -24.44 -37.21 69.43 15.00

111 ARG N -26.34 -36.11 68.92 15.00 111 ARG CA -26.76 -37.08 67.92 15.00 111 ARG CB -28.02 -37.81 68.38 15.00 111 ARG CG -27.81 -38.84 69.48 15.00 111 ARG CD -28.75 -40.03 69.33 15.00 111 ARG NE -28.01 -41.28 69.36 15.00 111 ARG CZ -27.89 -42.06 70.44 15.00 111 ARG NH1 -27.18 -43.18 70.36 15.00 111 ARG NH2 -28.50 -41.73 71.58 15.00 111 ARG C -26.99 -36.46 66.54 15.00

111 ARG 0 -27.67 -35.45 66.41 15.00

112 GLU N -26.41 -37.06 65.50 15.00 112 GLU CA -26.56 -36.57 64.14 15.00 112 GLU CB -25.36 -37.00 63.29 15.00 112 GLU CG -24.03 -36.42 63.76 15.00 112 GLU CD -23.34 -35.56 62.70 15.00 112 GLU OEl -23.95 -34.57 62.22 15.00 112 GLU OE2 -22.18 -35.88 62.33 15.00 112 GLU C -27.86 -37.13 63.56 15.00

112 GLU 0 -28.64 -37.75 64.27 15.00

113 ILE N -28.13 -36.87 62.29 15.00 113 ILE CA -29.35 -37.38 61.64 15.00 113 ILE CB -30.38 -36.25 61.34 15.00 113 ILE CG2 -31.67 -36.83 60.78 15.00 113 ILE CGI -30.71 -35.45 62.60 15.00 113 ILE CDl -31.50 -36.20 63.65 15.00 113 ILE C -28.85 -37.98 60.33 15.00

113 ILE 0 -27.91 -37.46 59.73 15.00

114 PRO N -29.41 -39.13 59.92 15.00 114 PRO CD -30.48 -39.91 60.57 15.00 114 PRO CA -28.98 -39.77 58.68 15.00 114 PRO CB -30.10 -40.78 58.43 15.00 114 PRO CG -30.41 -41.23 59.83 15.00 114 PRO C -28.87 -38.79 57.54 15.00

114 PRO O -29.84 -38.12 57.20 15.00

115 GLU N -27.67 -38.66 56.99 15.00 115 GLU CA -27.46 -37.74 55.89 15.00 115 GLU CB -26.07 -37.92 55.28 15.00 115 GLU CG -24.92 -37.19 56.01 15.00 115 GLU CD -23.60 -37.16 55.20 15.00 115 GLU OEl -23.65 -37.20 53.94 15.00

μ ^j μ-' μ-> P» -' -' μ-' μ-' μ ^{j j} μ- ^, μ ^j μ- ^ι μ-' -' μ-' ^j μ ^j μ- ^, μ ^j

CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ <"Λ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ uι uι ui ιh ιtN iti ii- ιt» -> ιt» co co co ⁾ u to to to to to w w ιo ιo ιo μ μ μ μ

K ' '-c; w ^, w κ ' ' κ %% £ £ £ £ £ £ H H H H H H H H M H CO CO CO CO

C0 C0 CO C C0 C C0 C0 C CO 2 2 2 2

0 O 2 0 O 0 0 0 O 2 0 O O O 2 O O 2 O O O O O 2 O O O ro > Ω Ω r M d Ω ω > to μ-> ω > o > M to μ-> to to d O c

ID I I I I I I I I I I I I I I I I I I I I I I I I I I I I I

CO CO CO tJ CO CO CO CO tO IO tO tO IO tO tO tO tJ tO tO tO tO M M tO tO tO tO IO M μ ^j to μ ^j co o o ρ» o vo cx> si si rfs uι cn cΛ cπ si cΛ Cπ si cΛ CΛ Ui rfs M co ui ιts c H

VO O CO Ui μ-ι VD tO CO rfs t tθ μ-» CO VD CO CΛ s] Ul tO Ul CΛ ιts O O CO CO μ^ sl rfs

H Ul Ul CXl CO VO Cπ rfs μ-' O OO OO U' M CΛ ifs rfs Ul OO VO CΛ O μ-' 00 sl o ui vo m co x I I I I I I I I I I I I I I I I I I i I I I I I 1 ■ m to w to to to to to to to to to to to to to tθ μ-> μ ^a μ ^j tθ M to M W to t^ rη _ u> u> rfs co o u to u» μ ^j to u co w co to s] si co oo vo o μ-> to μ-» to to o

~* oo t VO CO CO s] tO P» rfs O U- tO O CO O C VO s] ^ VO C its rfs tO tO O OO Ul CO O tO Cπ CO W O UI UI VO W Cπ D O sJ its tO VO CΛ μ^ ∞ U ifs O VO its oo CΛ c * in cΛ CΛ CΛ CΛ CΛ cπ cΛ Ui cΛ CΛ CΛ CΛ CΛ CΛ Ui ui cπ ui cπ ui ui cπ ui cn ui cπ ui rfs CO M tO μ-' VD VO VO O O O O O VO CD CΛ s sl Cπ sl CΛ CΛ Cπ CΛ Ul Ul rfs O tO CΛ tO tO Ul CO CXN CO CΛ VO rfs O O ∞ CΛ Cπ vD CO Vo μ-' if'-. VO CΛ sl lO tO Cn VD CΛ CO

-- Cϊ co cn μ cπ μ (Λ μ co o5 θo μ co si ιt» μ θ θ oi si co to μ ι> oo ιti θi μ ι

μ ^j μ-. ^j _J H-» ^j μ-. μ- ^{ι j j} μ-' μ-' μ ^α μ ^j μ ^j μ ^j -' ^j M P- P' μ-' μ-» μ-' uι uι uι cπ uι uι uι uι uι uι uι uι uι uι cπ uι uι uι uι uι uι uι uι uι uι uι cπ uι

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

w tO M t to to w to io to to to to to u to w to ro tJ to w to to to to to to to to to io to to to to to to io to io to sj si sj si si si si _s i _s i cΛ _C Λ _C Λ _C Λ _C Λ _C Λ _{CΛ C} Λ _CΛ m ui cπ ui cπ cπ cπ cπ cπ ui cπ its rfi

C» sl CΛ Ul rfs C tO O V0 CX) s1 CΛ Ul rfs CO μJ O V0 00 sl CΛ rfs C0 t0 O V0 C» sl CΛ Cπ ιr^ o ^** c o ^* -c o ^* -w o ^** C o ^* i oi ^* c ox ow ow co ^* 4 oc o ^* i o ^* i o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o

CO

CD I I I I I I I I I I I I I I I I I I I I I I I I I I I I I CO co to to μ i i co to μ-> to to I I P» CO Ui P» CO lO CO CO rfs rfs its lO CO t I I rfs LO CO rfs tO rfs

H cπ cn co cΛ si cΛ ifs to vo its O VO OO Ul tO UJ VD p> μ-> vo to o p ^ι o co uι cΛ si si its sl U> Ul rfs rfs CΛ H c co io to io o co ui μ μ ∞ CΛ tO sl o P» tO sl Ul Ul ιts CO CΛ CΛ s] tO CΛ CΛ μ-» W rfs VD CΛ rfs ιfs U1 0 s] CO o ui to CO

H CΛ O O Ul Ul CΛ O rfs CΛ si co si si (Λ cπ to c» vo rfs μ-> co si uι o to ui s] VD Co o oo rfs s oo μ-' uι its VO O CD rπ

CO I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I

X co to to to to μ to co co to co ii- co to to to j- μ i i i i μ μ co μ to μ ιo μ-» μ- ^> p tv) to i μ- ¹ i co to μ-' to t rπ sl tO O O tO M its sl rfs o^ M Cπ CO VO tO tO tO VO OO Cπ OO VO CO OO rfs CΛ sl O cπ CΛ oo rfs sl sl Ul CΛ CO rfs rfs Ui tO

VO sJ ils Ul tO its μ ^J ∞ CΛ itS sJ CO H Ul VO its sl OO O VD Ul O lls tO Ul sl sJ rfS sl O O CO CΛ VD Cπ O CX ⁾ CΛ s CO CO OO U' Ul CΛ μ-' VO sl CX> tO W CΛ CO CΛ Cπ tO OO tO O rfs rfs μ-» O Ul U) o to to o cπ μ-' Co o o cΛ CΛ co si s] P-

31 c r m Ul rfs rfs Ul CΛ CΛ OO sl sl sl sl CΛ CΛ sl sl sl CΛ sl CΛ CΛ CΛ Ul CΛ sl Ul rfs rfs ui ui sl sJ CO sl sl σi CΛ CΛ Ul rfS its OO s ro tO UI OO Ul vO CΛ CO O VO tO O its tO Ul CO sl CΛ o co ui cπ oo o to ui ui cΛ Co vo cπ co μ ^j s μ-' Ui Ui μ-' CΛ Vo vD its v σ>

CO VO VO VO CΛ O sl rfs Vθ CO VO tO VO OO CO Ui CΛ VO sl sl CΛ VO θ μ-' s] tO VD rfs U ⁾ O U ⁾ μ-> CΛ VO s] Ul sJ U ⁾ μ-

CΛ o P" rfs μ-> to cπ O CO OO CΛ tO sl VD I-' OO CΛ O O CΛ CΛ rfs rfS sl o CO CΛ OO OO tO Cπ μ-' O tO VO tO O tO O rf

μ- ^, μ ^{j j} μ-» -> μ- ^, μ-' i-' i-» ^j μ ^j -' μ-' μ-' ^α μ ^j ' μ-' μ ^j μ ^j μ ^j μ ^j μ ^j μ-' μ ^j μ ^j μ- μ μ-> μ ^j -' μ-' μ-

Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul UI Ul Ul Ul Cπ Ul Ul UI Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul Ul U

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

TABLE IV

Table of the orthogonal three dimensional coordinates in Angstroms and B factors (A ² ) for the cathepsin K complex with inhibitor 2 , 2 ' -N,N'-bis- benzyloxycarbonyl-L-leucinylcarbohydrazide.

Residue Atom X Y Z B

CO W ^ CO CO C θ Cθ Nθ CO CO CO CO CD CO CO CO CO CO CO lO CO CO CO CO lO CO CD CO D CD co ro ∞ co cD oo w co cD co ω co i si si si si si si si m m cΛ m m αi cri ^ "^ '- t^ ι^ --3 -- ^** H '-3 ^ 2 S S S S S S S; o θ O O O θ c co co j ^μ < κ< κ ^* κ; κ ^* κ- ^ ^ Hr; ^ ^ H H H w w m W W < ^ κ! --< W

Z Z VO O VO VO VO VO rO V VO VO VO r ri x-i ^ ri ri rS ri in ' Ux- cn M 'n O

O 2 O O O O O O O O O O O 2 O O O C0 O O O 2 C0 O 0 O O 2 O > U! rs ^* W d W d Ω ro > M d Ω Cd O ω > to to μ μ

CO c

CD I I I I I I I I I I I I I I I I I I I I I I I CO μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ P» P» ρ» ρ»

CΛ CΛ ιts U1 00 s] CΛ U1 00 s] CΛ Ul U1 CO ιt-. Ul O O tO tO tO tO tO o * O P'

H C CO tO tO P» s] CO Ul CΛ CO rfs θ O VD s] OO tO UI CO sl Ul rfs Ui μ-» tO lO U> U ⁱ tO H CO CO tO CΛ OO s] O tθ μ-» rfs rfs cπ μ-» co u) uι to μ-' s] U' s] o cπ oo o μ-» CΛ m o x I I I I I I I I I I I I I I I I I rπ μ μ μ μ to to to to tJ to to to μ μ μ μ μ μ oo co co co co u> u> to to μ-» μ-» o cD θo cΛ s] ui rfs rfs Ul CΛ s] s] Ul rη t

-i r→ p" Co u- o co Co cn to rfs ui s] to ui ui to rfs μ-» co CΛ CΛ sl sl CΛ tO Ul Ul

«— . tO si co o cπ cΛ μ-' to co rfs si rfs co cπ o CO rfs 00 Ul o co oo cΛ to μ-' oo o to μ-'

X rπ ro tO P ⁱ O P» μ-> μ ^j O θ ω VO 00 VO CD V0 CX3 O V0 VO s0 sl 0^ Ul rfs CΛ CΛ lts U> ιfs σ»

Ui μ ^j CO CΛ sl O t Ui μ- ¹ ιts CΛ α) U1 0 CΛ CΛ C μJ CD CO C-Λ CΛ sl C» tO s] CD tO

(ji co m oi μ m co o iii 'i Ui m ^ si co w μ m w o o iJi n 'i μ co ui oi

μ-' p- - P- μ-' ' μ-' μ-' μ-' μ-' p> μ ^j μ-' p ^, ι-> μ-> μ-> ρ ^» p' μ-> μ-» μ ^j μ-' p» μ-' p' cπ cπ cπ u ⁱ u ⁱ ui ui ui ui ui u ⁱ ui ui ui ui ui ui ui ui ui ui ui ui ui cπ ui ui ui ui o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o

μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ μ

P' P' P» p ^J P» P» 0 0 0 0 O O 0 O O O O 0 O 0 0 0 0 0 O O O O O O O O O O O -oO VO VO VO OO ro OO OO CXJ ∞ OO CD OO Cn CD sl sl sl

^ β 3 ^ ι-3 ^ -^ ιi «-3 H3 Ω Ω Ω Ω ^ | > > O O O ^{r r} ^ rxl r r rξ r rξ ^ ^ P P P r V O V Vϋ

JO !Λ » ^ ^ » ^ » ^ » ^ H^ μ< ι-< Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω C Cθ to

0 0 0 0 0 0 0 0 0 0 2 0 0 0 2 0 0 0 2 0 0 0 0 2 0 O C0 tC N W > ts ^* w d Ω ro > Ω to d to W μ d μ Ω W > to

I I I I I I I I I I I I I I I I I I I I I I tO M tO tO tO tO tO tO tO tO tO tO tO tO tO W M W tO M W W if-. ifs rf-. rf. UI U' Ui ω sl Ul CΛ CΛ itS its rfs Ui rf O tO CO Ul CO o μ- ^» sl Ul Ul lO Ul O sl UI Ul CΛ Ul CΛ sl Ul CΛ OO vO tO CO CΛ μ- ^» cπ Ul t0 Ul rfs μ-> 00 00 CΛ O tO U1 O s] sl

CO I I I I I I I I I I I I I I I I I I I I I I I I I I I

X Ul UI UI U UJ Ul UI Ui UJ UJ Ui UJ UI UI U' U UI U' Ui UI UI Ui ω ui Ui l

CΛ Ui ui ui cπ rfs rfs rfs it- ui ui ω ui ui ui si ui ∞ vo ∞ si cΛ Cπ cΛ Ui ω to to μ-^ rfs VD Ul CO rfs CO rfs sl tO tO sl VO O CΛ o oo s] o to o ui ui p» p» vo o> si i- ^» rfs rfs CO OO O O Co μ-' CΛ μ-' sl its cΛ 00 00 s] Ul C0 C sJ V0 O V0 rfS s] s] 00

m CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ sl sl s] sl s] s] sl 00 0O 0O 0O 00 s] sl sl s] sl l sl CO CΛ CΛ CΛ sJ sl OO CO OO VD O tO tO CO rfs cπ Ul O μ^ O O O VD sl CΛ CΛ sl CΛ rfs

10 σ> CO O sl lO O VO CΛ tO VO OO VD lO O O rfs tO rfs rfs O Ul μ-» to p» 00 si si ui co to co co co cn oo rfs si its co ui to o CΛ sl O CO tO CO CO Ul sl Ul O O 00 o μ- ^» cπ cΛ

μ ^j H μ-' p ^j p» μ ^{j α j} μ- ^, μ ^{j j} μ- ^, μ ^j p» μ-' ⁱ ui cπ ui ui ui ui cπ ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui cπ cπ ui cπ cπ

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

μ- ^ι i- ^{j j} |- ^j |-- ⁱ |-- ^{N j} μ ^j μα μα μ-ι μ ^j μ ^j μ-' H μ-' - ^ι μ- ^, -' μ ^j μ-' μ-' ^j μ ^{j j} μ ^j

U) U) UJ UJ U' U- U) UI U' W U) U> UI UI UI U- U' UI U> U> U1 UI U> U ⁾ UI UI UI U> UI vO vD CO VO C-O 00 CX) 00 CD 00 sl s] sl s] sJ σi CΛ CΛ CΛ CΛ CΛ CΛ CΛ Cπ Ul Cπ Lπ Cπ

C C C C CO CO CO CO CO CO W W W W W W M M M M G G G G ^** σ ' ^* o ϊt> 'Λ ' ^* ci ^l 2 O c

CD I I I I I I I I I I I I I I I I I I I I I I I I I I I I I

Hi to u to to to to to to to to to to to iO M to to to to to to to to to to co to io to

CD O ∞ 00 CΛ sl Ul Ul CΛ CΛ s] sl C0 00 s] V0 CX) CΛ sJ s ^] s ^] s} C» CΛ sl O C0 O VD c sl p» VO sl O si to w ιt» ^ μ μ w u u '» o iΛ ιb o cn (Λ i uι α) ra CΛ tO VO tO CΛ CΛ P ¹ to O its tO sl rfs CD OO rfs CD tO CΛ tO O M VO VO its tO tO O M m o I I I I I I I I I I I I I I I I I I I I x to p» μ-> to μ ^j μ- ^» μ ^j μ ^j μ-' tO M tO M tO tO tO M M tO M tO tO tO t m o oo sl CO Λ s] O VO ∞ VO sJ VD VO θ μ-> tO M tO CO U ⁱ |ts U ⁾ ιts rfS ιts t U ⁾ Cπ ιts rπ to H M O VO VO Ul sl CO rfs rfs CΛ Cπ OO O UI O CO tO CO rfs its CO tO CΛ rfs O CΛ rfs tO rfs CΛ l to μ-» uι ui si p> ui ιt-. cΛ Co cπ ιts rfs tO CO VO CΛ O CO tO OO CΛ VO VO O OO Ul OO

X c tr m rf it r _f rfs rfs r _f s rf it its it- π cπ ui cπ ui cπ ui il its rfs rfs ui ti cπ ui ui u^ its, Ul Cn O O sl C ^* Λ si OQ VO O O tO -p» O O 00 CΛ CO VO O H CO to il ^* -. tf^

8 rfs rfs OO OO VO tO sl Ul CO tO CΛ Ui CΛ tO μ-' μ ui to oo o Ul rfs μ- ⁱ sl Ul C0 s] 00 C CO CΛ tO tO rfs CD OO sl O O O O Cπ i-' O rfs vo oo to VO UJ UJ tO C» O M C

P' P' P' P ⁱ P ^, P ⁱ P' p- p ⁱ μ μ μ μ μ μ μ μ μ μ H μ μ μ μ p μ μ ui ui ui cn cπ ui ui cπ cn cπ ui ui ui ui ui ui ui ui ui ui ui ui ui cπ ui ui ui ui ui

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

TABLE IV

-33.39 47.92 15.00

-28.29 42.42 15.00 -30.33 50.55 15.00

TABLE V

Table of the orthogonal three dimensional coordinates in Angstroms and B factors (A-2) for the cathepsin K complex with inhibitor (IS) -N- [2-[ (1- benzyloxycarbonylamino) -3-methylbutyl]thiazol-4- ylcarbonyl] -N'- (N-benzyloxycarbonyl-L- leucinyl)hydrazide.

Residue Atom X Y Z B

TABLE V PRO CG ^■ 35.87 -13.15 71.89 15.00 PRO C •34.52 -14.37 68.66 15.00 PRO 0 -33.50 -15.04 68.82 15.00 VAL N -34.82 -13.76 67.52 15.00 VAL CA -33.93 -13.83 66.37 15.00 VAL CB -34.62 -13.31 65.09 15.00 VAL CGI -33.61 -13.11 63.98 15.00 VAL CG2 -35.68 -14.31 64.65 15.00 VAL C -32.68 -13.01 66.64 15.00 VAL 0 -32.76 -11.88 67.11 15.00 LYS N -31.52 -13.61 66.39 15.00 LYS CA -30.24 -12.96 66.58 15.00 LYS CB -29.25 -13.89 67.30 15.00 LYS CG -29.81 -14.64 68.50 15.00 LYS CD -30.24 -13.71 69.61 15.00 LYS CE -30.58 -14.46 70.88 15.00 LYS NZ -31.75 -15.34 70.73 15.00 LYS C -29.67 -12.53 65.23 15.00 LYS 0 -30.20 -12.88 64.17 15.00 ASN N -28.57 -11.79 65.27 15.00 ASN CA -27.90 -11.32 64.06 15.00 ASN CB -28.17 -9.84 63.80 15.00 ASN CG -27.66 -9.39 62.45 15.00 ASN ODl -26.79 -10.02 61.85 15.00 ASN ND2 -28.20 -8.29 61.95 15.00 ASN C -26.41 -11.58 64.19 15.00 ASN 0 -25.74 -11.03 65.08 15.00 GLN N -25.89 -12.42 63.30 15.00 GLN CA -24.48 -12.75 63.31 15.00 GLN CB -24.20 -14.02 62.48 15.00 GLN CG -24.56 -13.94 61.00 15.00 GLN CD -24.28 -15.24 60.27 15.00 GLN OEl -25.14 -15.79 59.60 15.00 GLN NE2 -23.06 -15.74 60.40 15.00 GLN C -23.59 -11.60 62.86 15.00 GLN 0 -22.43 -11.51 63.27 15.00 GLY N -24.12 -10.71 62.03 15.00 GLY CA -23.32 -9.59 61.55 15.00 GLY C -22.33 -10.05 60.49 15.00 GLY 0 -22.59 -11.03 59.78 15.00 GLN N -21.19 -9.38 60.40 15.00 GLN CA -20.18 -9.73 59.39 15.00

TABLE V INH C14 -19.01 -11.83 56.47 15.00 INH C15 -21.22 -11.63 55.23 15.00 INH C16 -22.50 -15.59 56.80 15.00 INH S17 -23.78 -16.32 55.92 15.00 INH N18 -21.80 -16.55 57.50 15.00 INH C19 -22.21 -17.87 57.39 15.00 INH N20 -23.05 -13.25 57.68 15.00 INH C21 -23.27 -17.88 56.55 15.00 INH C22 -21.58 -19.10 58.24 15.00 INH 023 -21.37 -18.39 59.17 15.00 INH C24 -13.79 -23.51 54.96 15.00 INH C25 -14.23 -22.84 56.08 15.00 INH C26 -14.83 -23.54 57.12 15.00 INH C27 -15.00 -24.93 57.04 15.00 INH C28 -14.54 -25.60 55.91 15.00 INH C29 -13.94 -24.90 54.87 15.00 INH C30 -15.72 -25.67 58.14 15.00 INH 031 -17.10 -25.93 57.71 15.00 INH C32 -17.91 -25.03 56.96 15.00 INH 033 -17.69 -24.81 55.77 15.00 INH C34 -19.82 -23.49 57.00 15.00 INH C35 -21.22 -24.12 56.84 15.00 INH C36 -21.92 -24.89 57.97 15.00 INH C37 -21.43 -26.31 58.12 15.00 INH C38 -21.86 -24.15 59.29 15.00 INH C39 -19.87 -22.15 57.76 15.00 INH O40 -19.60 -22.13 58.96 15.00 INH N41 -20.18 -21.00 57.08 15.00 INH N42 -20.20 -19.65 57.78 15.00 INH N43 -18.90 -24.44 57.63 15.00 TRP N -22.80 -21.38 62.25 15.00 TRP CA -22.73 -22.65 62.97 15.00 TRP CB -21.39 -23.33 62.67 15.00 TRP CG -20.19 -22.46 62.98 15.00 TRP CD2 -19.41 -22.45 64.19 15.00 TRP CE2 -18.44 -21.44 64.05 15.00 TRP CE3 -19.43 -23.21 65.37 15.00 TRP CDl -19.67 -21.48 62.19 15.00 TRP NE1 -18.62 -20.86 62.82 15.00 TRP CZ2 -17.50 -21.15 65.06 15.00 TRP CZ3 -18.50 -22.92 66.37 15.00 TRP CH2 -17.55 -21.91 66.21 15.00

TABLEV ASP CB -13.64 -17.12 71.64 15.00 ASP CG -14.11 -15.73 71.18 15.00 ASP ODl -14.12 -15.43 69.96 15.00 ASP OD2 -14.46 -14.93 72.06 15.00 ASP C -12.98 -19.44 71.08 15.00 ASP 0 -11.75 -19.53 71.15 15.00 CYS N -13.79 -20.43 71.47 15.00 CYS CA -13.26 -21.63 72.12 15.00 CYS C -13.13 -22.97 71.41 15.00 CYS 0 -12.36 -23.82 71.86 15.00 CYS CB -13.97 -21.81 73.45 15.00 CYS SG -13.91 -20.34 74.55 15.00 VAL N -13.92 -23.20 70.36 15.00 VAL CA -13.85 -24.48 69.64 15.00 VAL CB -15.13 -24.77 68.83 15.00 VAL CGI -15.08 -26.20 68.30 15.00 VAL CG2 -16.37 -24.52 69.66 15.00 VAL C -12.67 .-24.45 68.68 15.00 VAL 0 -12.73 ^' -^23.82 67.62 15.00 SER N -11.60 -25.15 69.04 15.00 SER CA -10.40 -25.18 68.22 15.00 SER CB -9.19 -25.66 69.02 15.00 SER OG -9.56 -26.66 69.95 15.00 SER C -10.54 -25.93 66.91 15.00 SER O -9.71 -25.75 66.02 15.00 GLU N -11.56 -26.78 66.79 15.00 GLU CA -11.79 -27.55 65.57 15.00 GLU CB -12.53 -28.86 65.84 15.00 GLU CG -11.72 -29.95 66.56 15.00 GLU CD -11.47 -29.63 68.03 15.00 GLU OEl -12.44 -29.48 68.79 15.00 GLU OE2 -10.28 -29.54 68.42 15.00 GLU C -12.51 -26.74 64.50 15.00 GLU O -12.45 -27.06 63.32 15.00 ASN N -13.22 -25.69 64.92 15.00 ASN CA -13.91 -24.83 63.98 15.00 ASN CB -15.29 -24.45 64.49 15.00 ASN CG -16.25 -25.62 64.51 15.00 ASN ODl -17.17 -25.66 65.32 15.00 ASN ND2 -16.04 -26.59 63.62 15.00 ASN C -13.03 -23.63 63.72 15.00 ASN O -12.01 -23.46 64.39 15.00

TABLE V

98 TYR O -14.00 -19.18 81.26 15.00

99 ASN N -16.12 -18.44 81.16 15.00 99 ASN CA -16.24 -18.23 82.58 15.00 99 ASN CB -16.80 -16.84 82.89 15.00 99 ASN CG -16.73 -16.50 84.38 15.00 99 ASN ODl -16.91 -17.36 85.24 15.00 99 ASN ND2 -16.44 -15.25 84.68 15.00 99 ASN C -17.14 -19.31 83.15 15.00 99 ASN 0 -18.33 -19.37 82.85 15.00

100 PRO N -16.59 -20.19 83.99 15.00

100 PRO CD -15.16 -20.25 84.37 15.00

100 PRO CA -17.34 -21.29 84.62 15.00

100 PRO CB -16.27 -21.98 85.47 15.00

100 PRO CG -15.00 -21.70 84.70 15.00

100 PRO C -18.52 -20.82 85.48 15.00

100 PRO O -19.53 -21.51 85.58 15.00

101 THR N -18.37 -19.64 86.09 15.00 101 THR CA -19.42 -19.05 86.93 15.00 101 THR CB -18.92 -17.73 87.61 15.00 101 THR OG1 -17.73 -17.97 88.38 15.00 101 THR CG2 -19.99 -17.15 88.54 15.00 101 THR C -20.68 -18.73 86.12 15.00

101 THR O -21.77 -18.69 86.68 15.00

102 GLY N -20.52 -18.51 84.81 15.00 102 GLY CA -21.67 -18.18 83.97 15.00 102 GLY C -22.36 -19.33 83.25 15.00

102 GLY O -23.34 -19.12 82.53 15.00

103 LYS N -21.87 -20.54 83.47 15.00 103 LYS CA -22.41 -21.74 82.83 15.00 103 LYS CB -21.73 -22.98 83.40 15.00 103 LYS CG -21.93 -24.24 82.59 15.00 103 LYS CD -21.93 -25.43 83.52 15.00 103 LYS CE -20.80 -25.36 84.52 15.00 103 LYS NZ -21.18 -26.01 85.80 15.00 103 LYS C -23.91 -21.86 82.95 15.00

103 LYS O -24.44 -21.97 84.05 15.00

104 ALA N -24.60 -21.92 81.82 15.00 104 ALA CA -26.05 -22.02 81.81 15.00 104 ALA CB -26.65 -20.90 80.97 15.00 104 ALA C -26.59 -23.38 81.35 15.00

104 ALA O -27.77 -23.67 81.53 15.00

105 ALA N -25.72 -24.20 80.77 15.00

TABLEV

132 SER C -29.19 -28.31 62.13 15.00

132 SER 0 -28.82 -29.48 62.02 15.00

133 VAL N -29.40 -27.52 61.08 15.00 133 VAL CA -29.23 -28.02 59.73 15.00 133 VAL CB -30.60 -28.18 58.99 15.00 133 VAL CGI -31.53 -29.06 59.80 15.00 133 VAL CG2 -31.24 -26.84 58.70 15.00 133 VAL C -28.35 -27.10 58.89 15.00

133 VAL 0 -28.22 -25.92 59.20 15.00

134 ALA N -27.74 -27.66 57.85 15.00 134 ALA CA -26.88 -26.90 56.95 15.00 134 ALA CB -25.50 -27.56 56.83 15.00 134 ALA C -27.59 -26.86 55.59 15.00

134 ALA 0 -28.15 -27.87 55.15 15.00

135 ILE N -27.61 -25.69 54.96 15.00 135 ILE CA -28.28 -25.52 53.68 15.00 135 ILE CB -29.64 -24.75 53.86 15.00 135 ILE CG2 -30.59 -25.51 54.77 15.00 135 ILE CGI -29.37 -23.34 54.39 15.00 135 ILE CDl -30.61 -22.47 54.50 15.00 135 ILE C -27.45 -24.69 52.71 15.00

135 ILE 0 -26.36 -24.22 53.04 15.00 136 ASP N -27.98 -24.56 51.49 15.00

136 ASP CA -27.37 -23.75 50.45 15.00 136 ASP CB -27.45 -24.42 49.07 15.00 136 ASP CG -26.86 -23.57 47.94 15.00 136 ASP ODl -26.91 -24.02 46.79 15.00 136 ASP OD2 -26.35 -22.45 48.19 15.00 136 ASP C -28.21 -22.46 50.50 15.00

136 ASP O -29.41 -22.48 50.22 15.00

137 ALA N -27.58 -21.38 50.92 15.00 137 ALA CA -28.23 -20.08 51.04 15.00 137 ALA CB -28.30 -19.68 52.49 15.00 137 ALA C -27.45 -19.04 50.25 15.00

137 ALA O -27.31 -17.91 50.69 15.00

138 SER N -26.97 -19.44 49.08 15.00 138 SER CA -26.18 -18.56 48.22 15.00 138 SER CB -25.05 -19.36 47.56 15.00 138 SER OG -25.57 -20.33 46.67 15.00 138 SER C -26.99 -17.81 47.16 15.00

138 SER 0 -26.48 -16.88 46.52 15.00

139 LEU N -28.23 -18.24 46.97 15.00

TABLE V

149 VAL CB -43.53 -22.90 50.95 15.00

149 VAL CGI -42.55 -24.07 50.90 15.00

149 VAL CG2 -44.47 -23.08 52.14 15.00

149 VAL C -41.69 -21.41 50.01 15.00

149 VAL 0 -41.94 -21.55 48.82 15.00

150 TYR N -40.49 -21.08 50.48 15.00 150 TYR CA -39.31 -20.92 49.63 15.00 150 TYR CB -38.12 -20.36 50.42 15.00 150 TYR CG -36.84 -20.29 49.60 15.00 150 TYR CDl -36.67 -19.30 48.63 15.00 150 TYR CE1 -35.54 -19.29 47.81 15.00 150 TYR CD2 -35.84 -21.25 49.74 15.00 150 TYR CE2 -34.71 -21.24 48.92 15.00 150 TYR CZ -34.57 -20.26 47.96 15.00 150 TYR OH -33.48 -20.27 47.12 15.00 150 TYR C -38.89 -22.18 48.89 15.00

150 TYR O -38.88 -23.28 49.45 15.00

151 TYR N -38.47 -21.98 47.65 15.00 151 TYR CA -37.98 -23.03 46.77 15.00 151 TYR CB -39.09 -23.99 46.35 15.00 151 TYR CG -38.62 -25.09 45.42 15.00 151 TYR CDl -37.92 -26.20 45.91 15.00 151 TYR CE1 -37.51 -27.23 45.06 15.00 151 TYR CD2 -38.89 -25.04 44.05 15.00 151 TYR CE2 -38.49 -26.07 43.19 15.00 151 TYR CZ -37.80 -27.16 43.70 15.00 151 TYR OH -37.46 -28.21 42.87 15.00 151 TYR C -37.35 -22.39 45.55 15.00

151 TYR 0 -37.80 -21.33 45.07 15.00

152 ASP N -36.30 -23.02 45.05 15.00 152 ASP CA -35.59 -22.54 43.86 15.00 152 ASP CB -34.66 -21.38 44.20 15.00 152 ASP CG -34.13 -20.68 42.97 15.00 152 ASP ODl -33.52 -19.60 43.12 15.00 152 ASP OD2 -34.32 -21.20 41.84 15.00 152 ASP C -34.83 -23.70 43.25 15.00

152 ASP O -33.94 -24.27 43.89 15.00

153 GLU N -35.15 -24.04 42.01 15.00 153 GLU CA -34.50 -25.15 41.34 15.00 153 GLU CB -35.16 -25.45 40.00 15.00 153 GLU CG -34.95 -24.38 38.96 15.00 153 GLU CD -35.39 -24.81 37.56 15.00

TABLE V

153 GLU OEl -35.72 -26.00 37.37 15.00

153 GLU OE2 -35.40 -23.94 36.66 15.00

153 GLU C -32.98 -25.02 41.17 15.00

153 GLU 0 -32.30 -26.01 40.92 15.00

154 SER N -32.46 -23.80 41.32 15.00 154 SER CA -31.02 -23.56 41.18 15.00 154 SER CB -30.77 -22.15 40.66 15.00 154 SER OG -31.56 -21.91 39.50 15.00 154 SER C -30.23 -23.82 42.46 15.00

154 SER 0 -28.99 -23.76 42.45 15.00

155 CYS N -30.94 -24.13 43.53 15.00 155 CYS CA -30.35 -24.39 44.84 15.00 155 CYS C -29.60 -25.71 44.92 15.00 155 CYS 0 -30.20 -26.78 44.85 15.00 155 CYS CB -31.43 -24.32 45.91 15.00

155 CYS SG -30.84 -23.76 47.53 15.00

156 ASN N -28.29 -25.64 45.11 15.00 156 ASN CA -27.46 -26.84 45.20 15.00 156 ASN CB -26.08 -26.58 44.61 15.00 156 ASN CG -25.26 -27.85 44.48 15.00 156 ASN ODl -25.77 -28.97 44.56 15.00 156 ASN ND2 -23.96 -27.69 44.26 15.00 156 ASN C -27.33 -27.51 46.58 15.00

156 ASN O -26.74 -26.95 47.51 15.00

157 SER N -27.78 -28.76 46.65 15.00 157 SER CA -27.73 -29.53 47.88 15.00 157 SER CB -28.66 -30.74 47.80 15.00 157 SER OG -28.22 -31.64 46.80 15.00 157 SER C -26.33 -29.97 48.29 15.00

157 SER O -26.16 -30.58 49.35 15.00

158 ASP N -25.34 -29.71 47.43 15.00 158 ASP CA -23.95 -30.07 47.71 15.00 158 ASP CB -23.35 -30.92 46.59 15.00 158 ASP CG -24.02 -32.27 46.47 15.00 158 ASP ODl -24.01 -33.04 47.47 15.00 158 ASP OD2 -24.58 -32.55 45.38 15.00 158 ASP C -23.09 -28.84 47.97 15.00

158 ASP O -21.86 -28.90 47.96 15.00

159 ASN N -23.76 -27.70 48.14 15.00 159 ASN CA -23.08 -26.45 48.42 15.00 159 ASN CB -23.32 -25.45 47.30 15.00 159 ASN CG -22.57 -24.14 47.51 15.00

TABLEV

196 MET N •39.17 -23.23 54.23 15.00 196 MET CA -38.49 -23.84 53.10 15.00 196 MET CB -37.01 -24.08 53.39 15.00 196 MET CG -36.15 -22.83 53.37 15.00 196 MET SD -34.45 -23.19 53.93 15.00 196 MET CE -33.63 -23.67 52.36 15.00 196 MET C -39.17 -25.14 52.72 15.00

196 MET 0 -39.59 -25.89 53.59 15.00

197 ALA N -39.22 -25.41 51.41 15.00 197 ALA CA -39.86 -26.62 50.87 15.00 197 ALA CB -39.64 -26.70 49.36 15.00 197 ALA C -39.42 -27.93 51.53 15.00

197 ALA 0 -38.23 -28.21 51.67 15.00

198 ARG N -40.41 -28.73 51.91 15.00 198 ARG CA -40.18 -30.01 52.57 15.00 198 ARG CB -40.77 -30.03 53.98 15.00 198 ARG CG -40.78 -31.39 54.66 15.00 198 ARG CD -41.18 -31.28 56.12 15.00 198 ARG NE -42.52 -30.73 56.31 15.00 198 ARG CZ -43.63 -31.47 56.40 15.00 198 ARG NH1 -43.55 -32.80 56.31 15.00 198 ARG NH2 -44.80 -30.89 56.62 15.00 198 ARG C -40.74 -31.13 51.71 15.00

198 ARG 0 -41.84 -31.00 51.16 15.00

199 ASN N -39.98 -32.21 51.61 15.00 199 ASN CA -40.35 -33.37 50.81 15.00 199 ASN CB -41.72 -33.92 51.23 15.00 199 ASN CG -41.71 -34.55 52.61 15.00 199 ASN ODl -40.67 -34.60 53.26 15.00 199 ASN ND2 -42.87 -35.01 53.07 15.00 199 ASN C -40.31 -33.04 49.32 15.00

199 ASN O -41.18 -33.43 48.57 15.00

200 LYS N -39.30 -32.27 48.92 15.00 200 LYS CA -39.13 -31.88 47.54 15.00 200 LYS CB -39.46 -30.41 47.32 15.00 200 LYS CG -39.74 -30.07 45.87 15.00 200 LYS CD -41.24 -30.05 45.59 15.00 200 LYS CE -41.92 -28.93 46.40 15.00 200 LYS NZ -43.41 -28.84 46.21 15.00 200 LYS C -37.68 -32.17 47.16 15.00

200 LYS 0 -36.89 -31.26 46.91 15.00

201 ASN N -37.34 -33.46 47.14 15.00

TABLEV

201 ASN CA -36.00 -33.95 46.83 15.00

201 ASN CB -35.78 -34.02 45.31 15.00

201 ASN CG -36.19 -32.75 44.59 15.00

201 ASN ODl -37.20 -32.72 43.87 15.00

201 ASN ND2 -35.40 -31.70 44.76 15.00

201 ASN C -34.84 -33.24 47.54 15.00

201 ASN 0 -33.84 -32.88 46.92 15.00

202 ASN N -34.98 -33.11 48.86 15.00 202 ASN CA -33.97 -32.49 49.74 15.00 202 ASN CB -32.74 -33.42 49.89 15.00 202 ASN CG -31.91 -33.12 51.13 15.00 202 ASN ODl -32.36 -32.48 52.07 15.00 202 ASN ND2 -30.67 -33.60 51.13 15.00 202 ASN C -33.56 -31.08 49.33 15.00

202 ASN 0 -32.39 -30.82 49.02 15.00

203 ALA N -34.51 -30.16 49.36 15.00 203 ALA H -35.31 -30.45 49.85 15.00 203 ALA CA -34.34 -28.77 48.93 15.00 203 ALA CB -35.57 -27.93 49.27 15.00 203 ALA C -33.15 -28.14 49.67 15.00

203 ALA 0 -33.11 -27.98 50.89 15.00

204 CYS N -32.16 -27.74 48.86 15.00 204 CYS CA -30.95 -27.06 49.31 15.00 204 CYS C -30.08 -27.85 50.28 15.00 204 CYS 0 -29.25 -27.26 50.98 15.00 204 CYS CB -31.27 -25.68 49.90 15.00

204 CYS SG -32.21 -24.52 48.84 15.00

205 GLY N -30.24 -29.17 50.32 15.00 205 GLY CA -29.45 -29.99 51.22 15.00 205 GLY C -29.93 -29.89 52.66 15.00

205 GLY 0 -29.14 -30.07 53.60 15.00

206 ILE N -31.23 -29.68 52.83 15.00 206 ILE CA -31.84 -29.52 54.15 15.00 206 ILE CB -33.39 -29.24 54.01 15.00 206 ILE CG2 -34.12 -30.44 53.42 15.00 206 ILE CGI -34.00 -28.84 55.35 15.00 206 ILE CDl -33.66 -27.44 55.81 15.00 206 ILE C -31.57 -30.69 55.11 15.00

206 ILE 0 -31.39 -30.47 56.31 15.00

207 ALA N -31.46 -31.91 54.59 15.00 207 ALA CA -31.21 -33.09 55.42 15.00 207 ALA CB -32.32 -34.12 55.21 15.00

TABLE VI

Table of the orthogonal three dimensional coordinates in

Angstroms and B factors (A ² ) for the cathepsin K complex with inhibitor 2- [N- (3-benzyloxybenzoyl) ] -

2 ' - [N' - (N-benzyloxycarbonyl-L- leucinyl) ]carbohydrazide.

Residue Atom X Y Z B

1 ALA CB -53.28 -28.69 64.46 15.00

1 ALA C -53.74 -30.77 63.13 15.00

1 ALA O -54.17 -31.71 63.79 15.00

1 ALA N -55.61 -29.36 63.92 15.00

1 ALA CA -54.20 -29.34 63.43 15.00

2 PRO N -52.92 -30.93 62.07 15.00 2 PRO CD -52.55 -29.87 61.11 15.00 2 PRO CA -52.38 -32.23 61.65 15.00 2 PRO CB -52.22 -32.03 60.15 15.00 2 PRO CG -51.68 -30.61 60.09 15.00 2 PRO C -51.02 -32.37 62.31 15.00

2 PRO O -50.88 -32.09 63.50 15.00

3 ASP N -50.02 -32.75 61.52 15.00 3 ASP CA -48.67 -32.92 62.02 15.00 3 ASP CB -47.96 -34.03 61.25 15.00 3 ASP CG -48.48 -35.41 61.59 15.00 3 ASP ODl -49.68 -35.69 61.38 15.00 3 ASP OD2 -47.66 -36.24 62.06 15.00 3 ASP C -47.93 -31.60 61.84 15.00

3 ASP O -47.35 -31.34 60.78 15.00

4 SER N -48.02 -30.74 62.84 15.00 4 SER CA -47.34 -29.45 62.82 15.00 4 SER CB -48.32 -28.34 62.42 15.00 4 SER OG -48.91 -28.65 61.17 15.00 4 SER C -46.76 -29.17 64.20 15.00

4 SER O -47.33 -29.58 65.22 15.00

5 VAL N -45.60 -28.54 64.23 15.00 5 VAL CA -45.00 -28.20 65.51 15.00 5 VAL CB -44.16 -29.36 66.11 15.00 5 VAL CGI -42.89 -29.57 65.35 15.00 5 VAL CG2 -43.87 -29.08 67.57 15.00 5 VAL C -44.21 -26.91 65.37 15.00 5 VAL 0 -43.46 -26.73 64.41 15.00

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W S a W W W C C C C C C C C B ffi K K tX a

W M M M M M 2 2 2 2 2 2 2 2 2 M M M M M M M M M M M » 'Λ txl

0 0 0 0 0 2 0 0 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 D tM M M d d Ω ro Ω to μO Ω W > M to μM d Ω W > to μ to μ O

C I I I I I I I I I I I I I I I I I I I I I I I I I I I I I 09 CO UJ U' U) U» UI U) UJ M tO M tO UJ U U) U) UJ UI U) UI U' UJ UI UJ UJ UJ U) U- CO Ul CO ifs its rfs U' tO tO sJ sl sl CO O I-' M ω U tO p- tO tO tO W CO CO Ul it. ω d H OO CO sl Ul Ul rfS sl CΛ CO tO co P' Ui CΛ O CΛ o p» CO CO CO CO P» tO tO t O P» s1 C rfs to co si o cπ vθ sj μ-> VD Ui oo o μ-» μ-' o rfs rfs sl s μ-i CXI sl rfs CO tO H m co I I I I I I I I I I I I I I I I I I I I I P> μ-> μ- ^, - ^ι P ⁱ P' μ-' μ ^{j j j} - ^ι ρ» ρ» μ-» μ-' μ ^{j j j} -» μ-» x to p» p- o tO M tO rfs cO its UI Ul Ul Ul CO ∞ VO sl VO OO CO sl CΛ Cπ Ul sl m c m o to p> co CΛ rfs cπ H o O sl tO C» sl ^ θ ιIS s] O O sl sJ ιtS ιts O O sl CO CD VO rfs rfs cπ o 00 p- rfs O t ifs tO CO CΛ CO O Ul Ul Ul rfs. Ul tO Cθ μ-' Ul W sl rfs c r- m ιts ιt* ιrs ιts rfs ιts cn cn ιt* cπ ιt^ uι uι Ui cπ cπ cπ cπ cπ uι uι uι iΛ Ui ιts ιf^ sJ CΛ sl OO CO CO P ¹ O OO O Vθ O O O O P* O rfs C U ⁾ tO P' O VO CO OO s] cπ

&μ μ u w co si oo co si -i co to tO si o ui ui M co 'i 'i O Ui μ si to '. si io

M ω sl UI U) ∞ CΛ rfs O C ^* 0 P» Ui 00 VD tO ιts VD O U U1 0D sl p^ CΛ CO CΛ V0 VD

μ ^j μ ^{j j j} μ-' μ-' P' * » ρ ^j ρ ^, p' P ⁱ P ⁱ μ-' μ ^j μ-' H M μ ^j P ⁱ cπ cπ ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui cπ cπ cπ cπ ui

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

μ- ^> μ- ^> μ- ¹ μ- ^» P ¹ μ-> p* p» μ-» p> P» μ- ^, μ- ¹ μ ^j O O O O O O O O VO VD Vθ θ θ θ VD VO OO OO CO C» OO CX) CX3 ∞ CO OO C

C H H H H H H H H H H H H H H H H ^ ι-3 --3 ι-3 ι^ 3 ^μ 3 ^μ 3 ^μ 3 ^ ^* ■^ ^■ -< ι- C C C C C C C C C C C C C 'xl » ^, S pci rΛ ^ ^ ^ "Λ ?0 ! ω co c M M M M M M M ^ ^ ^ ^ 'i-i ^ ^ ^ 'ϋ O

0 0 2 0 0 0 0 0 0 0 2 0 0 0 0 O O O 2 0 0 0 0 0 2 0 0 0 0 ro > d ffi N tS M d M M d p> Ωμ-» Ωto ω > dp» Ωμ-> Ωto W > to co to i_i |_i i _J to

CO

C I I I I I I I I I I I I I I I I I I I I I I I I I I I I I 09

9 rfs ιts Ul CΛ CΛ rfs Ul rfs U! CΛ sl s] CO t J O O - ) VO VD VO CO OO CX) sl sl oO CO ∞ C cπ c _{Λ θ} si o vo uι θ rfs M cn c» co vD θ CΛ CΛ si cn ι-' cπ co uι p» oo co cn o to

CO O rO O CΛ sl μJ CΛ sl sl O M sl CO cπ VO VD Ut Ul sl sl UJ sl tO OT CD I

H m co I I I I I I I I I I I I I I I I I I I I - _| -α t _O P _* t _O t _O M t _{O J} U) _U - U t _O t _{O U} I vo vo o vo o rfs w μ-> H> c ω μ-» co u> ι:>. ιf ιt o ρ ^ι o ∞ CD o co

CΛ CO cπ Ul Ul rfs rfs CΛ O OO μ-> CΛ O rfs m cΛ O W CΛ O VO O VO OO O CΛ CΛ U.l. rf _^ s r VO CΛ CO UI tO CΛ tO rfs O s] CΛ CΛ rfs Ul tO rfs CD 00 CO rfs p» Ul Ul CO tO Ul ιts P> p» t c i- m cn cn cn cn cn ui ui ui ui cn ui cn cn cn cn cn cΛ CΛ Ui ui ui ui ui ui ui ui ui ui ui co to p» o o vo oo oo oo o vo μ- ^» o to μ- ^» M P' O VO sl CO OO VO sl cn ul CO sl sl

8 s] rfs U1 Co p> 00 rfs P» CΛ CΛ Ui 00 s] rfs sl CO tO O CO oo ui to co ui ui to cn u μ co co o co si μ-> rfs uι co o

ι_ι ₍ - _{J H} -ι _h -ι -i J H-» ι--. ι--i ι--i H ^» ρ' p* P' P' μ- ^ι μ ^Λ μ ^j μ ^α P- ρ- ρ- p' μ-' ^μ -' ^» p' μ ^j Ui ui ui ui ui ui ui ui ui ui ui ui ui cπ ui ui ui cπ ui ui ui ui ui ui ui ui cπ ui ui o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o

to w to to w to to io M to to to to to to to io io to io io io to u to 'o io io t

P» P' p- p' P ¹ P ^a P ^J P' P' P ⁴ P ⁱ P' P» P' P» |--' p- p' P ^, P ^, H P' P ¹ p- p' P' 0 C U) UI Ui U ^, W M tO t t t t t tO tO t P ¹ P' P ^Λ μ ^j P ¹ O O O O O O VO C 3 »τJ T-J π3 πJ rrJ ι _τ j rrj πj l _τ ) [} πJ hJ ⁱ t) J ^f τJ O C C tfc ^* C

O Vϋ Ovo Ovo Ova vOo Mx Mx xM xM xM xM xM xM xM xM xM mp a-Λ t'Λij M'Λ MtO M C M 'Λ ^ G

O O O O 2 O 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 2 O 2 0

Ώ ro > d N M M D d Ω ro Ω W > w μ to μ

I I I I I I I I I I I I I I I I I I I I I I I I I I I I I to to to to to to to co co w co u u to to to t to to to to to to to to w to to t

∞ CΛ sl CD CO sl CIl O O O O Ca CO CO Ca Ul CΛ sl CO sl sJ CO CO ∞ sl O C μ co co ui o cn μ co tn ui to si -. co co co co si tθ s] to to vo vo uι μ-> sj p» c cn ui to co co cn si si μ ui oo ui co ω ui co oo co P» U) O CO CO CO CΛ Cπ CO P» C

μ-i ι_-i (--ι - ι- ^j (--» ^j μ ^j ρ ^J P ^ι μ ^{j j} - ^ι P ^, ρ- -' P' P» P ¹ P» ' p' μ ^j P ^Λ P» ρ ^j μ cπ ui cπ cn ui ui cπ ui ui ui cπ cπ ui ui ui ui cπ ui ui ui cπ ui ui ui ui ui ui ui ui

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

tJ tO tJ tJ tO IO IO tO IO W t IO M IO tO tO tO tO tO tO tO tO IO M tO tO tO tO C U ^, U' U' U' U) UJ U- t tO t t t tO t tO M M P' H H M H P ⁱ P» P ⁱ μ ⁱ i c Ui ιf w H-ι o 'Λ c*θ s] cΛ cπ ι-s w tθ θ VD θθ sj cΛ Cπ cπ cπ cπ uι cπ c^ t-C ffi K ffi ffi ' K ' ffi ' ffi K W W ' K t ^* -!

O O O O O O O O O O O O O O O O O O O O O O M M M M M M M

X X X X X X X X X X X X X X X X X X X ri r ri rq rq ri ri

O O O O O O O O O O O O O O O O O O O O O O O O O O CO O O s M atO wtO atO aM atO atO aM ^K tO wtO wM aM atO atO ^K tO atO wtO wtO wtO wtO wtO wtO ^* t ^" O ³ ^I-' w o w

CO c

09 I I I I I I I I I I I I l l l i l I I I I I I I I I I CO l lO CO tO tO CO P> C CO rfs ifs h-> to p> -. co i i co co to to co to co to to co d o co o μ-' sj o vo cπ co cπ cΛ Co o ιfS sJ c» rfs UJ U O O I-» V0 O V0 O 0D VD O

H C o o co sj co o to oo o i-' si o Ui ui o o cπ p' cn P ¹ sl CO CO to Λ Ui CO sJ lO si oo o uι uι co o uι ιo o to co cn co μ to μ oo *ι cn si _C Λ vo cπ si oo si CO sJ m i I I l l l l l l l l l I I I I I I I I I I I I x to to i co μ μ co co μ co to to I CO I CO tO l μ to μ ιt> co co co to to co co m tO OO tO O VO VD VO sJ tO CΛ VD P' Ul O Ul rfs to sj O O sl O rfs Ul its OO CO O tO m H c too Cn CD Ul t0 U1 sl p» O C0 t0 C0 its rfs sl tO rfs o^ sJ OO O CΛ P' lO UI CD sl sJ o _r O oo vo cπ vo o to ifs cπ cn co o to o s! OO ιfs p ⁱ sl M sl (TN l UJ s] UJ t U ⁾ CO C»

31

C rr m C» 00 s3 CΛ CΛ CΛ CΛ Cπ cΛ Ul Ul CΛ CΛ CΛ CΛ CΛ sJ sJ uι CΛ CΛ CX) C» sJ sJ s] sJ sJ sl

^■ » cn si w to (n (n to uι o> o oι -i to co cn o μ w '» si μ o co co co co si o)

CO rfs Ul tO CO CΛ si ιfs- ιts, ιfs. rfs _∞ VO rfs |-J _{U1 s} l O CD Ul VO ιts CΛ rfs s] Ul sl CO 00 rfs 00 μ-' oo o μ-' CΛ Oo cΛ to co si si cπ to cΛ to o co vo co si oo

ρ- p' P ^{i i ι} P ⁱ » M P' p' P ^, P' P ^» p ^{» v} ρ» ρ ^j P' μ- ^» - ρ ^j P ^ι P ^ι cπ ui ui ui ui cn ui ui ui ui ui cπ cπ ui ui ui ui ui ui ui ui ui ui cπ cπ ui ui ui ui

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

TABLE Vπ

Table of the orthogonal three dimensional coordinates in

Angstroms and B factors ik ² ) for the cathepsin K complex with inhibitor 4-[N-

[ (phenylmethoxy)carbonyl] -L-leucyl] -1- [N-

[ (phenylmethoxy)carbonyl] -L-leucyl] -3- pyrrolidinone.

Residue Atom X Y Z B

1 ALA CB -46.25 -39.17 62.96 30.60

1 ALA C -47.93 -37.51 63.80 29.74

1 ALA 0 -49.14 -37.57 63.58 32.13

1 ALA N -48.18 -39.83 64.36 28.23

1 ALA CA -47.15 -38.78 64.13 28.86

2 PRO N -47.26 -36.34 63.80 27.19 2 PRO CD -45.94 -36.10 64.40 26.45 2 PRO CA -47.92 -35.06 63.50 27.01 2 PRO CB -47.28 -34.10 64.52 26.65 2 PRO CG -46.25 -34.95 65.31 27.69 2 PRO C -47.73 -34.52 62.09 26.37

2 PRO 0 -46.67 -34.70 61.50 26.53

3 ASP N -48.76 -33.86 61.58 26.63 3 ASP CA -48.73 -33.23 60.26 24.49 3 ASP CB -50.14 -33.03 59.69 23.94 3 ASP CG -50.75 -34.32 59.17 24.73 3 ASP ODl -50.19 -34.88 58.21 31.10 3 ASP OD2 -51.79 -34.76 59.71 23.79 3 ASP C -48.03 -31.88 60.39 24.62

3 ASP O -47.08 -31.59 59.67 23.92

4 SER N -48.55 -31.04 61.28 24.05 4 SER CA -47.98 -29.72 61.55 22.83 4 SER CB -49.04 -28.62 61.52 23.29 4 SER OG -49.84 -28.70 60.36 24.54 4 SER C -47.30 -29.75 62.91 23.31

4 SER O -47.71 -30.51 63.79 26.63

5 VAL N -46.27 -28.92 63.09 24.43 5 VAL CA -45.52 -28.80 64.34 22.41 5 VAL CB -44.44 -29.91 64.50 24.60 5 VAL CGI -43.39 -29.50 65.53 19.58 5 VAL CG2 -45.09 -31.22 64.94 26.54 5 VAL C -44.80 -27.45 64.30 22.72

TABLE VD GLN CB -19.55 -8.58 58.66 13.14 GLN CG -20.40 -7.79 57.65 12.44 GLN CD -20.73 -8.61 56.41 13.48 GLN OEl -19.84 -9.15 55.76 14.90 GLN NE2 -22.02 -8.71 56.08 9.41 GLN C -19.30 -10.83 59.81 15.26 GLN 0 -18.08 -10.64 59.79 16.33 CYS N -19.86 -11.93 60.29 17.72 CYS CA -19.10 -13.04 60.86 16.36 CYS C -19.82 -14.31 60.40 16.07 CYS O -21.05 -14.39 60.44 8.26 CYS CB -19.02 -12.91 62.40 16.53 CYS SG -18.36 -14.33 63.35 15.48 GLY N -19.04 -15.25 59.83 16.86 GLY CA -19.59 -16.52 59.35 14.89 GLY C -19.67 -17.49 60.52 13.50 GLY 0 -18.91 -18.45 60.61 11.64 SER N -20.61 -17.20 61.41 13.66 SER CA -20.82 -17.99 62.61 14.12 SER CB -20.65 -17.10 63.84 17.06 SER OG -21.37 -15.88 63.67 19.58 SER C -22.18 -18.67 62.64 14.42 SER 0 -22.63 -19.12 63.69 15.12 CYS N -22.83 -18.77 61.48 15.74 CYS CA -24.16 -19.38 61.40 12.45 CYS CB -24.61 -19.48 59.92 17.82 CYS SG -23.46 -20.34 58.77 15.84 CYS C -24.23 -20.73 62.12 12.21 CYS 0 -25.27 -21.09 62.66 8.88 INH Cl -26.76 -10.18 57.23 37.63 INH C2 -25.50 -10.64 57.58 37.16 INH C3 -24.85 -11.61 56.79 34.05 INH C4 -25.45 -12.12 55.64 32.87 INH C5 -26.72 -11.65 55.30 36.05 INH C6 -27.38 -10.68 56.09 37.28 INH C7 -24.76 -13.16 54.79 31.70 INH 08 -24.07 -14.24 55.46 33.18 INH C9 -24.20 -15.65 55.36 32.90 INH O10 -24.83 -16.33 56.19 27.65 INH Cll -23.57 -17.64 54.11 33.43 INH C12 -23.56 -17.98 52.63 29.93 INH C13 -24.79 -17.58 51.82 30.09

TABLE VII TRP C -23.24 -22.55 64.32 19.46 TRP 0 -24.09 -23.21 64.92 24.77 ALA N -22.52 -21.59 64.90 ^* 19.49 ALA CA -22.61 -21.25 66.31 12.94 ALA CB -21.77 -20.01 66.61 12.05 ALA C -24.07 -20.99 66.64 8.35 ALA 0 -24.61 -21.54 67.60 6.75 PHE N -24.72 -20.18 65.80 8.07 PHE CA -26.13 -19.83 65.95 9.51 PHE CB -26.51 -18.67 65.04 7.62 PHE CG -25.96 -17.35 65.48 4.72 PHE CDl -24.74 -16.91 65.01 4.11 PHE CD2 -26.66 -16.56 66.38 2.92 PHE CE1 -24.22 -15.69 65.41 4.53 PHE CE2 -26.16 -15.33 66.79 2.38 PHE CZ -24.93 -14.89 66.31 2.00 PHE C -27.07 -21.01 65.72 10.66 PHE 0 -28.18 -21.04 66.26 14.07 SER N -26.64 -21.96 64.89 10.83 SER CA -27.44 -23.15 64.62 8.54 SER CB -26.92 -23.88 63.37 2.45 SER OG -27.80 -24.93 62.97 2.00 SER C -27.40 -24.05 65.86 7.86 SER O -28.44 -24.46 66.38 6.37 SER N -26.19 -24.29 66.36 5.14 SER CA -26.00 -25.14 67.52 7.65 SER CB -24.52 -25.27 67.84 10.56 SER OG -23.81 -25.61 66.67 14.28 SER C -26.76 -24.61 68.73 6.72 SER O -27.57 -25.32 69.34 8.64 VAL N -26.50 -23.35 69.06 6.44 VAL CA -27.15 -22.71 70.19 6.61 VAL CB -26.73 -21.23 70.25 6.76 VAL CGI -27.74 -20.40 71.03 9.71 VAL CG2 -25.35 -21.14 70.90 2.00 VAL C -28.67 -22.86 70.18 9.86 VAL O -29.25 -23.30 71.17 13.64 GLY N -29.30 -22.56 69.05 12.98 GLY CA -30.75 -22.68 68.94 9.41 GLY C -31.27 -24.10 69.19 10.59 GLY O -32.42 -24.29 69.59 8.20 ALA N -30.44 -25.10 68.91 11.42

TABLEVII LYS N -35.20 -25.71 77.17 26.25 LYS CA -36.59 -25.41 77.47 28.16 LYS CB -37.25 -24.61 76.34 28.65 LYS CG -38.35 -23.65 76.81 27.61 LYS CD -39.60 -24.37 77.25 27.20 LYS CE -40.68 -23.40 77.70 26.81 LYS NZ -41.94 -24.12 78.05 28.10 LYS C -37.37 -26.69 77.76 26.01 LYS 0 -38.28 -26.70 78.60 25.82 LYS N -37.00 -27.77 77.11 26.61 LYS CA -37.69 -29.03 77.34 27.03 LYS CB -37.64 -29.93 76.11 28.30 LYS CG -38.65 -31.06 76.16 29.91 LYS CD -38.79 -31.77 74.82 29.72 LYS CE -37.74 -32.83 74.61 26.31 LYS NZ -38.04 -33.61 73.37 31.45 LYS C -37.09 -29.72 78.56 25.36 LYS 0 -37.81 -30.32 79.35 23.91 LYS N -35.78 -29.57 78.73 25.39 LYS CA -35.06 -30.20 79.84 25.65 LYS CB -33.55 -30.06 79.66 24.57 LYS CG -32.72 -30.84 80.67 20.75 LYS CD -32.89 -32.34 80.50 26.88 LYS CE -31.76 -33.13 81.15 28.72 LYS NZ -31.63 -32.85 82.61 29.46 LYS C -35.50 -29.67 81.19 25.70 LYS 0 -35.92 -30.44 82.06 23.51 THR N -35.42 -28.35 81.34 26.91 THR CA -35.76 -27.67 82.58 25.94 THR CB -34.61 -26.77 83.03 26.05 THR OGl -34.60 -25.58 82.23 27.18 THR CG2 -33.28 -27.49 82.85 28.99 THR C -37.00 -26.78 82.52 25.00 THR O -37.57 -26.43 83.55 28.90 GLY N -37.38 -26.35 81.32 24.41 GLY CA -38.54 -25.48 81.19 21.01 GLY C -38.09 -24.02 81.13 19.83 GLY 0 -38.92 -23.10 81.08 14.91 LYS N -36.78 -23.82 81.15 22.11 LYS CA -36.16 -22.50 81.10 24.14 LYS CB -35.06 -22.38 82.17 26.33 LYS CG -35.61 -22.19 83.60 25.46

TABLE Vπ ASP N -13.67 -23.01 62.46 14.85 ASP CA -12.90 -21.86 62.02 15.28 ASP CB -12.74 -21.86 60.51 21.27 ASP CG -11.30 -22.08 60.07 23.24 ASP ODl -10.60 -21.08 59.84 26.41 ASP OD2 -10.88 -23.25 59.97 20.64 ASP C -13.36 -20.50 62.51 15.18 ASP 0 -12.89 -19.47 62.01 13.47 GLY N -14.26 -20.50 63.48 15.64 GLY CA -14.75 -19.25 64.03 15.74 GLY C -15.68 -18.55 63.07 17.26 GLY 0 -16.72 -19.10 62.72 19.72 CYS N -15.30 -17.35 62.64 19.00 CYS CA -16.14 -16.62 61.70 18.17 CYS C -16.00 -17.19 60.29 19.74 CYS 0 -16.79 -16.86 59.41 22.59 CYS CB -15.85 -15.11 61.73 16.37 CYS SG -16.32 -14.21 63.25 14.06 GLY N -15.00 -18.05 60.09 17.99 GLY CA -14.81 -18.67 58.79 15.84 GLY C -15.66 -19.92 58.60 17.59 GLY 0 -15.50 -20.66 57.63 19.05 GLY N -16.59 -20.15 59.53 18.26 GLY CA -17.46 -21.31 59.44 12.24 GLY C -17.03 -22.45 60.34 10.78 GLY 0 -15.90 -22.47 60.83 9.37 GLY N -17.94 -23.40 60.53 8.77 GLY CA -17.68 -24.56 61.36 8.46 GLY C -18.83 -25.55 61.24 10.14 GLY 0 -19.79 -25.29 60.51 9.60 TYR N -18.69 -26.70 61.88 12.33 TYR CA -19.74 -27.73 61.84 14.13 TYR CB -19.18 -29.12 61.49 14.00 TYR CG -18.53 -29.22 60.13 16.82 TYR CDl -19.29 -29.29 58.96 19.29 TYR CE1 -18.68 -29.37 57.70 19.34 TYR CD2 -17.15 -29.24 60.02 17.85 TYR CE2 -16.53 -29.32 58.77 21.15 TYR CZ -17.30 -29.39 57.61 22.41 TYR OH -16.66 -29.42 56.38 22.94 TYR C -20.44 -27.77 63.20 12.95 TYR 0 -19.80 -27.61 64.23 14.93

TABLE Vπ

93 GLU C -12.31 -13.29 67.71 24.19

93 GLU O -11.61 -12.31 67.45 24.56

94 GLU N -12.28 -13.94 68.87 23.61 94 GLU CA -11.38 -13.58 69.96 24.32 94 GLU CB -12.02 -12.55 70.90 22.62 94 GLU CG -12.23 -11.20 70.27 23.90 94 GLU CD -12.86 -10.23 71.21 24.44 94 GLU OEl -12.18 -9.26 71.60 29.56 94 GLU OE2 -14.04 -10.43 71.57 23.54 94 GLU C -10.99 -14.84 70.73 23.80

94 GLU O -11.64 -15.89 70.59 21.98

95 SER N -9.95 -14.73 71.55 20.75 95 SER CA -9.47 -15.86 72.36 19.71 95 SER CB -8.26 -15.46 73.19 20.00 95 SER OG -8.57 -14.41 74.09 24.28 95 SER C -10.60 -16.38 73.25 20.63

95 SER O -11.48 -15.60 73.65 22.33

96 CYS N -10.56 -17.66 73.58 17.74 96 CYS CA -11.60 -18.26 74.42 18.66 96 CYS C -11.59 -17.72 75.85 19.92 96 CYS O -10.58 -17.79 76.56 21.50 96 CYS CB -11.51 -19.78 74.41 16.39

96 CYS SG -12.75 -20.61 75.44 19.58

97 MET N -12.72 -17.14 76.26 17.89 97 MET CA -12.88 -16.59 77.60 18.67 97 MET CB -12.86 -15.07 77.57 17.60 97 MET CG -12.76 -14.43 78.94 18.29 97 MET SD -11.15 -13.66 79.17 26.40 97 MET CE -9.99 -15.01 78.76 19.16 97 MET C -14.18 -17.09 78.20 21.66

97 MET O -15.07 -16.31 78.52 25.61

98 TYR N -14.30 -18.41 78.29 23.47 98 TYR CA -15.49 -19.06 78.83 23.75 98 TYR CB -15.58 -20.50 78.30 21.70 98 TYR CG -16.39 -21.46 79.13 18.51 98 TYR CDl -17.74 -21.64 78.90 18.20 98 TYR CE1 -18.49 -22.49 79.70 19.99 98 TYR CD2 -15.80 -22.16 80.17 16.39 98 TYR CE2 -16.53 -23.01 80.97 12.68 98 TYR CZ -17.87 -23.17 80.74 16.90 98 TYR OH -18.60 -23.99 81.57 22.57 98 TYR C -15.48 -19.01 80.37 26.07

P» P ¹ P» P» P ^» . ρ- μ ^j μ ^j ρ» ρ ^, μ ^j P ^j -' μ-» μ-' -» ρ ⁱ P- p ^, P' μ-' P ⁱ P' p' ^ι p- p» P' μ-' p- ' μ-' p- ρ- P' ' p' p ^» ' to to to to t ^* oo ttoo p» p ^, μ- ^{ι j} P- μ-» ρ- μ-' P- ρ ^j P ^> P ^ι P' P' p' P ¹ -» μ-' μ- ^, μ-' - ¹ P ^ι μ-' μ-' P ^Λ P ^{> i} P' P ^ι P' o o o o o co co a w co co w w io oo co co oo co αi oo oii cD ^ i si si si si si si in oi oi oi ui ui ui ui ui ui

^ lr ⁱ t ⁱ tr' t* ^ t ^t t ⁱ t ⁱ Ω Ω Ω Ω Ω Ω O Ω Ω > > > > > > > Ω Ω Ω Ω O Ω Ω Ω Ω Ω j h κ ^{* j} Hc; κ' hci κj μ< t- ^, c c c c c c c c co co ω co co co co co c c c c c c c c c c co co co co co co co co ω G G G G G G G G G 2 2 2 2 2 2 2 2 --< κ; f G G G G G G

2 O 0

I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I -_ *- its J Co co u co u co co co co co co co co co co co co co co co co co co co to to to to to μ μ o Φ α) si θ3 si si si oi si oι ui ιtι -i i- cn uι co co ιo co to μ o o co uι uι ui si CO rfs tO CO OO VO O Ul CΛ tO P' CO tO Cπ CΛ UI sl co μ o si co cn oi ui to μ μ cn to M si o Ul OO CD CO VO CO tO sl itS sl its sl sl CΛ CΛ _s l CO tO tO co CO O tO tO VO rfs CO O Ui μ-> ι|s U> rfs

to p> μ μ μ co io to to μ μ μ to μ to to to to μ μ μ μ μ μ μ μ to μ μ to to to co co co tj rfs O rfs to μ -- co uι ω ^ co (D si co co oo uι uι μ to uι uι uι co si co o to o cn sJ rfs CO CO P' O O rfs ifs rfs co

O CO CO CO rfs rfs 00 cπ p» oo o to p» tO rfs CΛ tO CO CO tO VD CO cπ sl rfs p» CO O to CO O vo o tO rfs cπ cD to cn cπ CO CΛ rfs Ul O CO CO si oo co co cn p' CO O CΛ CO rfs O rfs CO CO P' P' O O O CΛ CO sl Ul sl Ul Ul sl sl CD sl tO cπ

TABLE Vπ

126 ALA C -41.59 -34.41 67.50 28.51

126 ALA 0 -42.22 -33.91 68.43 29.45

127 ARG N -40.60 -35.30 67.68 27.15 127 ARG CA -40.20 -35.80 69.01 26.50 127 ARG CB -39.52 -37.17 68.92 25.80 127 ARG CG -40.36 -38.31 68.39 29.17 127 ARG CD -41.39 -38.82 69.38 30.20 127 ARG NE -42.01 -40.06 68.90 31.67 127 ARG CZ -43.14 -40.57 69.38 31.87 127 ARG NH1 -43.62 -41.70 68.87 32.34 127 ARG NH2 -43.80 -39.97 70.36 33.34 127 ARG C -39.30 -34.88 69.83 26.63

127 ARG 0 -39.61 -34.54 70.98 29.49

128 VAL N -38.13 -34.58 69.27 24.07 128 VAL CA -37.14 -33.75 69.93 20.27 128 VAL CB -35.74 -33.96 69.29 17.18 128 VAL CGI -34.73 -33.00 69.87 16.62 128 VAL CG2 -35.27 -35.40 69.51 16.17 128 VAL C -37.51 -32.28 69.92 19.91

128 VAL 0 -38.00 -31.75 70.91 21.31

129 GLY N -37.26 -31.63 68.79 21.40 129 GLY CA -37.56 -30.22 68.67 18.08 129 GLY C -36.62 -29.60 67.67 17.76

129 GLY 0 -36.22 -30.27 66.71 14.46

130 PRO N -36.25 -28.33 67.86 18.11 130 PRO CD -36.68 -27.44 68.96 20.59 130 PRO CA -35.35 -27.64 66.94 17.36 130 PRO CB -35.03 -26.36 67.70 17.67 130 PRO CG -36.33 -26.07 68.41 19.12 130 PRO C -34.10 -28.47 66.69 18.18

130 PRO O -33.43 -28.92 67.63 21.49

131 VAL N -33.81 -28.71 65.41 14.71 131 VAL CA -32.66 -29.47 64.99 10.15 131 VAL CB -33.09 -30.69 64.16 13.09 131 VAL CGI -31.88 -31.39 63.55 14.17 131 VAL CG2 -33.88 -31.63 65.02 19.95 131 VAL C -31.80 -28.60 64.10 10.57

131 VAL O -32.33 -27.86 63.27 13.19

132 SER N -30.49 -28.71 64.25 7.45 132 SER CA -29.59 -27.93 63.42 7.72 132 SER CB -28.23 -27.81 64.07 9.68 132 SER OG -28.37 -27.45 65.44 20.96

TABLE VC

180 ILE 0 -36.73 -19.88 59.76 18.36

181 LYS N -35.50 -21.05 61.27 9.02 181 LYS CA -35.06 -19.88 62.03 6.93 181 LYS CB -34.92 -20.19 63.52 8.20 181 LYS CG -34.55 -18.99 64.39 4.18 181 LYS CD -34.21 -19.41 65.80 5.00 181 LYS CE -33.83 -18.23 66.69 2.00 181 LYS NZ -33.38 -18.69 68.03 2.00 181 LYS C -33.71 -19.45 61.47 6.56

181 LYS 0 -32.76 -20.23 61.51 9.50

182 ASN N -33.63 -18.25 60.93 6.31 182 ASN CA -32.38 -17.79 60.36 7.51 182 ASN CB -32.62 -17.18 58.97 12.34 182 ASN CG -31.37 -17.16 58.12 13.66 182 ASN ODl -30.38 -17.83 58.43 13.80 182 ASN ND2 -31.40 -16.41 57.03 14.20 182 ASN C -31.67 -16.80 61.27 8.95

182 ASN 0 -32.29 -16.18 62.12 9.35

183 SER N -30.37 -16.65 61.07 12.23 183 SER CA -29.55 -15.74 61.87 12.33 183 SER CB -28.41 -16.50 62.54 11.14 183 SER OG -27.51 -17.06 61.60 2.83 183 SER C -29.03 -14.56 61.05 17.18

183 SER 0 -27.84 -14.23 61.12 14.11

184 TRP N -29.92 -13.92 60.30 20.03 184 TRP CA -29.59 -12.77 59.45 17.75 184 TRP CB -29.94 -13.03 57.99 17.44 184 TRP CG -28.96 -13.87 57.26 11.74 184 TRP CD2 -29.09 -14.40 55.93 10.49 184 TRP CE2 -27.91 -15.11 55.65 11.82 184 TRP CE3 -30.09 -14.34 54.96 7.76 184 TRP CDl -27.75 -14.27 57.71 13.64 184 TRP NE1 -27.11 -15.01 56.76 18.22 184 TRP CZ2 -27.70 -15.76 54.44 8.06 184 TRP CZ3 -29.88 -14.99 53.75 8.86 184 TRP CH2 -28.70 -15.69 53.50 6.44 184 TRP C -30.30 -11.51 59.91 18.70

184 TRP 0 -30.21 -10.47 59.27 18.61

185 GLY N -31.05 -11.62 61.01 19.92 185 GLY CA -31.75 -10.48 61.55 17.99 185 GLY C -33.25 -10.62 61.47 21.34 185 GLY 0 -33.78 -11.41 60.68 24.20

TABLE Viπ

Table of the orthogonal three dimensional coordinates in

Angstroms and B factors (A ² ) for the cathepsin K complex with inhibitor 4-[N-[(4- pyridyl ethoxy)carbonyl] -L-leucyl] -1-[N-

[ (phenylmethoxy)carbonyl] -L-leucyl] -3- pyrrolidinone.

Residue Atom X Y Z B

TABLE IX

Table of the orthogonal three dimensional coordinates in

Angstroms and B factors (A ² ) for the cathepsin K complex with inhibitor 4-[N-

[ (phenylmethoxy)carbonyl] -L-leucyl] -1-N[N- (methyl) -

L-leucyl) ]-3-pyrrolidinone.

Residue Atom X Y Z B

TABLE IX ASP N -44.64 -25.95 66.33 15.00 ASP CA -44.10 -24.60 66.28 15.00 ASP CB -45.17 -23.57 65.90 15.00 ASP CG -44.59 -22.26 65.40 15.00 ASP ODl -43.41 -21.95 65.68 15.00 ASP OD2 -45.34 -21.52 64.73 15.00 ASP C -43.52 -24.32 67.66 15.00 ASP 0 -44.20 -23.78 68.53 15.00 TYR N -42.27 -24.69 67.85 15.00 TYR CA -41.62 -24.50 69.13 15.00 TYR CB -40.20 -25.08 69.12 15.00 TYR CG -40.20 -26.58 69.20 15.00 TYR CDl -40.68 -27.24 70.33 15.00 TYR CE1 -40.76 -28.62 70.38 15.00 TYR CD2 -39.81 -27.36 68.11 15.00 TYR CE2 -39.89 -28.74 68.15 15.00 TYR CZ -40.37 -29.36 69.29 15.00 TYR OH -40.51 -30.72 69.31 15.00 TYR C -41.63 -23.07 69.62 15.00 TYR 0 -41.57 -22.84 70.83 15.00 ARG N -41.74 -22.11 68.70 15.00 ARG CA -41.77 -20.68 69.08 15.00 ARG CB -41.86 -19.77 67.84 15.00 ARG CG -40.77 -19.98 66.80 15.00 ARG CD -41.01 -19.12 65.58 15.00 ARG NE -42.34 -19.33 65.02 15.00 ARG CZ -42.70 -18.96 63.80 15.00 ARG NH1 -41.83 -18.36 63.00 15.00 ARG NH2 -43.94 -19.18 63.38 15.00 ARG C -42.94 -20.39 70.02 15.00 ARG 0 -42.79 -19.67 71.02 15.00 LYS N -44.10 -20.98 69.72 15.00 LYS CA -45.29 -20.80 70.53 15.00 LYS CB -46.53 -21.26 69.78 15.00 LYS CG -46.84 -20.43 68.56 15.00 LYS CD -48.15 -20.86 67.92 15.00 LYS CE -48.39 -20.11 66.62 15.00 LYS NZ -49.58 -20.62 65.88 15.00 LYS C -45.18 -21.53 71.85 15.00 LYS 0 -45.95 -21.29 72.77 15.00 LYS N -44.18 -22.40 71.95 15.00 LYS CA -43.99 -23.17 73.16 15.00

TABLE IX LYS CB -43.71 -24.63 72.80 15.00 LYS CG -44.67 -25.19 71.78 15.00 LYS CD -44.34 -26.64 71.49 15.00 LYS CE -44.42 -27.48 72.76 15.00 LYS NZ -45.74 -27.26 73.43 15.00 LYS C -42.92 -22.65 74.11 15.00 LYS O -42.70 -23.25 75.15 15.00 GLY N -42.24 -21.57 73.73 15.00 GLY CA -41.21 -21.00 74.58 15.00 GLY C -39.83 -21.65 74.47 15.00 GLY O -38.92 -21.31 75.21 15.00 TYR N -39.68 -22.56 73.52 15.00 TYR CA -38.41 -23.26 73.31 15.00 TYR CB -38.63 -24.56 72.54 15.00 TYR CG -39.27 -25.70 73.30 15.00 TYR CDl -40.37 -25.50 74.13 15.00 TYR CE1 -40.97 -26.57 74.82 15.00 TYR CD2 -38.78 -27.00 73.17 15.00 TYR CE2 -39.37 -28.07 73.84 15.00 TYR CZ -40.45 -27.85 74.66 15.00 TYR OH -41.02 -28.91 75.33 15.00 TYR C -37.36 -22.43 72.56 15.00 TYR 0 -36.22 -22.86 72.46 15.00 VAL N -37.76 -21.27 72.03 15.00 VAL CA -36.86 -20.43 71.23 15.00 VAL CB -37.38 -20.33 69.78 15.00 VAL CGI -36.34 -19.72 68.89 15.00 VAL CG2 -37.75 -21.69 69.26 15.00 VAL C -36.62 -19.00 71.75 15.00 VAL 0 -37.55 -18.32 72.18 15.00 THR N -35.38 -18.53 71.67 15.00 THR CA -35.04 -17.18 72.11 15.00 THR CB -33.58 -17.11 72.54 15.00 THR OG1 -32.76 -17.76 71.55 15.00 THR CG2 -33.39 -17.76 73.88 15.00 THR C -35.25 -16.15 70.99 15.00 THR O -35.59 -16.51 69.86 15.00 PRO N -35.10 -14.85 71.31 15.00 PRO CD -35.02 -14.21 72.63 15.00 PRO CA -35.29 -13.83 70.27 15.00 PRO CB -35.03 -12.54 71.03 15.00 PRO CG -35.58 -12.84 72.37 15.00

ιt_ co uJ Ui U) U> uι uι ui u> U) ω uJ U' U' U ⁾ u> u ⁾ UJ U' U' u> u> uι uι uι uι uι u> U) u> uι U ⁾ Ui uι uι uι uι uι uι uι uι o vo vo vo vo vo vo vo vo vo c ^* o oo oo cD C» c» oo co sj sj sj s si s] s] si si cΛ CΛ CΛ CΛ m m m m m m m m rfs

C C C C C C C C C C C C C C C C C C Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω C C - - KJ KJ J - K- KJ M W W W W W W W C C C C C C C C C w w to w w w w w co cn G a G G G G G G 2 2 2 2 2 2 2 2 2 H. G G G G G G G G G G G

2 0 0 0 2 0 0

I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I co to co rfs rfs CO U> U> U) U> Ui U> Ul U) Ui UI Ui Ui Ui U) U> UI Ui UI U' U> UI Ul Ui Ui U> U> U> tO U' Ui Ul UI U> Ui UI Ui cn . cn μ o ιo oo c. oι ιt» ι. co μ. o μ μ to to co co ιfι co co ιo to co u uι ^ ". ω co to co μ o o μ μ o o o

Ul sJ OO p- Ul O CO CO P ¹ sj to co o cΛ si m cΛ s] to tθ s_ uι to o to co ,fs. ,ts co μ-* cΛ co si tθ ιfs. cn m it to o cn co vo si to co oo ui s] ∞ sl rfs ∞ p- sl tO lO O ∞ tO ∞ its O sl UI Ul Ul sl cn OO CO O rfs VO CO OO o co oo o

CO I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I W tO tO tO tO tO M tO tO tO W M tO W tO tO tO tO tO tO W i sJ CΛ CΛ CO U) UJ rfi rf-ι m m cΛ CΛ tθ m ιt-» ιt-s CΛ CΛ CX _. s] p» P» P» O VO C» sl CΛ CΛ m ιts rfs ι^

H 5. rfs rfs. tO VD CΛ rfs lO |-> ιts. Ui o 00 o tO CO tO OO CΛ VD tO Cn O tO CO ifs Ul sJ UI itS sl μ ^J VD O VD P' O its tO OO Ul co co co si co oo co cn cn to co o tO it ui ι. co μ μ cn o co co μ μ co to uι co co μ ιo ι. co ι. oo cn to ι. μ μ uι

sl CD -O VD CD CO sl sl OO sl VO CXl VO O VO CD CD CΛ sl CΛ tO CO UI m itS its its ω c (Λ OJ rfs. s tO tO O O OO OO sl CO iti m tO P' C-O its CΛ sl CO OO CΛ OO μ-' tO sl tO O tO O its P' CΛ CD VD CΛ tO O CO tO m O VO ifs. ∞ O m ∞ μ-' its CO Ul tO CO

μ ^j ρ» P ^Λ P ¹ P ⁱ P» μ- ¹ P ^J P ¹ P ^J P* p- p* P ¹ ι-- ^, '- ⁴ H' p- ρ- p' P» P» ρ» μ-' p- ρ* H P' P' p ^, p- p ^, μ-' ^» H P- ρ* ρ ^j ' P ^ι m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o

TABLE IX LYS CA -37.20 -28.78 77.78 15.00 LYS CB -36.83 -29.73 76.64 15.00 LYS CG -37.74 -30.93 76.59 15.00 LYS CD -37.39 -31.91 75.51 15.00 LYS CE -38.47 -32.98 75.42 15.00 LYS NZ -38.17 -34.02 74.40 15.00 LYS C -36.89 -29.42 79.13 15.00 LYS 0 -37.79 -29.93 79.80 15.00 LYS N -35.62 -29.36 79.53 15.00 LYS CA -35.17 -29.95 80.79 15.00 LYS CB -33.65 -30.16 80.81 15.00 LYS CG -33.08 -30.87 79.59 15.00 LYS CD -33.91 -32.09 79.21 15.00 LYS CE -33.34 -32.77 77.99 15.00 LYS NZ -34.29 -33.81 77.44 15.00 LYS C -35.59 -29.16 82.02 15.00 LYS O -36.42 -29.61 82.81 15.00 THR N -35.01 -27.98 82.17 15.00 THR CA -35.26 -27.11 83.32 15.00 THR CB -34.10 -26.13 83.49 15.00 THR OG1 -34.11 -25.20 82.40 15.00 THR CG2 -32.77 -26.87 83.51 15.00 THR C -36.58 -26.34 83.35 15.00 THR 0 -36.92 -25.75 84.37 15.00 GLY N -37.30 -26.30 82.24 15.00 GLY CA -38.56 -25.58 82.19 15.00 GLY C -38.44 -24.08 82.03 15.00 GLY O -39.45 -23.39 81.86 15.00 LYS N -37.22 -23.56 82.10 15.00 LYS CA -36.96 -22.13 81.97 15.00 LYS CB -36.42 -21.56 83.28 15.00 LYS CG -37.47 -21.47 84.38 15.00 LYS CD -36.85 -21.18 85.72 15.00 LYS CE -36.08 -22.36 86.23 15.00 LYS NZ -37.00 -23.52 86.37 15.00 LYS C -35.99 -21.90 80.82 15.00 LYS 0 -35.12 -22.73 80.57 15.00 LEU N -36.16 -20.79 80.10 15.00 LEU CA -35.31 -20.46 78.95 15.00 LEU CB -36.19 -20.14 77.73 15.00 LEU CG -35.60 -19.92 76.34 15.00 LEU CDl -35.30 -21.23 75.64 15.00

TABLE IX CYS CB -13.84 -21.68 74.32 15.00 CYS SG -14.09 -20.14 75.26 15.00 VAL N -14.06 -22.83 71.15 15.00 VAL CA -14.11 -24.04 70.33 15.00 VAL CB -15.47 -24.21 69.61 15.00 VAL CGI -15.58 -25.61 69.01 15.00 VAL CG2 -16.61 -23.97 70.58 15.00 VAL C -12.98 -24.06 69.30 15.00 VAL 0 -13.18 -23.78 68.12 15.00 SER N -11.80 -24.45 69.76 15.00 SER CA -10.60 -24.55 68.94 15.00 SER CB -9.45 -25.07 69.79 15.00 SER OG -9.53 -24.53 71.10 15.00 SER C -10.73 -25.37 67.67 15.00 SER O -9.99 -25.17 66.72 15.00 GLU N -11.61 -26.36 67.70 15.00 GLU CA -11.83 -27.23 66.55 15.00 GLU CB -12.73 -28.41 66.92 15.00 GLU CG -12.20 -29.30 68.03 15.00 GLU CD -12.38 -28.71 69.41 15.00 GLU OEl -13.54 -28.51 69.82 15.00 GLU OE2 -11.37 -28.43 70.06 15.00 GLU C -12.41 -26.48 65.37 15.00 GLU O -12.37 -26.95 64.23 15.00 ASN N -13.03 -25.34 65.65 15.00 ASN CA -13.65 -24.52 64.62 15.00 ASN CB -15.10 -24.18 64.99 15.00 ASN CG -16.04 -25.37 64.87 15.00 ASN ODl -17.24 -25.24 65.03 15.00 ASN ND2 -15.49 -26.53 64.55 15.00 ASN C -12.83 -23.26 64.38 15.00 ASN O -11.82 -23.03 65.05 15.00 ASP N -13.28 -22.43 63.44 15.00 ASP CA -12.56 -21.22 63.09 15.00 ASP CB -12.53 -21.05 61.57 15.00 ASP CG -11.12 -20.82 61.03 15.00 ASP ODl -10.18 -20.65 61.83 15.00 ASP OD2 -10.96 -20.82 59.79 15.00 ASP C -13.09 -19.95 63.76 15.00 ASP O -12.67 -18.85 63.43 15.00 GLY N -14.00 -20.09 64.72 15.00 GLY CA -14.55 -18.91 65.36 15.00

TABLE IX THR CB -20.66 -32.20 65.31 15.00 THR OG1 -19.57 -31.77 64.48 15.00 THR CG2 -21.84 -32.58 64.45 15.00 THR C -19.91 -30.70 67.18 15.00 THR O -19.94 -31.00 68.37 15.00 ASN N -18.92 -30.00 66.64 15.00 ASN CA -17.77 -29.54 67.42 15.00 ASN CB -16.75 -28.84 66.55 15.00 ASN CG -15.86 -29.80 65.85 15.00 ASN ODl -15.33 -30.72 66.46 15.00 ASN ND2 -15.68 -29.61 64.55 15.00 ASN C -18.17 -28.63 68.60 15.00 ASN 0 -17.53 -28.66 69.66 15.00 ALA N -19.20 -27.82 68.40 15.00 ALA CA -19.67 -26.91 69.44 15.00 ALA CB -20.66 -25.91 68.86 15.00 ALA C -20.33 -27.72 70.55 15.00 ALA O -20.26 -27.37 71.72 15.00 PHE N -20.96 -28.83 70.16 15.00 PHE CA -21.61 -29.70 71.13 15.00 PHE CB -22.57 -30.66 70.43 15.00 PHE CG -23.73 -29.98 69.79 15.00 PHE CDl -24.28 -28.84 70.36 15.00 PHE CD2 -24.29 -30.48 68.63 15.00 PHE CE1 -25.35 -28.21 69.79 15.00 PHE CE2 -25.37 -29.87 68.04 15.00 PHE CZ -25.91 -28.72 68.62 15.00 PHE C -20.59 -30.46 71.96 15.00 PHE O -20.79 -30.69 73.15 15.00 GLN N -19.48 -30.82 71.33 15.00 GLN CA -18.43 -31.54 72.03 15.00 GLN CB -17.46 -32.17 71.04 15.00 GLN CG -16.71 -33.36 71.59 15.00 GLN CD -16.83 -34.56 70.67 15.00 GLN OEl -17.35 -35.61 71.07 15.00 GLN NE2 -16.37 -34.41 69.44 15.00 GLN C -17.70 -30.62 72.99 15.00 GLN O -17.18 -31.07 74.02 15.00 TYR N -17.64 -29.34 72.65 15.00 TYR CA -16.96 -28.38 73.52 15.00 TYR CB -16.74 -27.03 72.81 15.00 TYR CG -16.38 -25.93 73.78 15.00

s] _s ] sl _s l _s ] _sl sj _s j _s ] _s l _s ] _s l _s ] _{sl s} j _s l _s l _s ] _{s3 s} ] _sl sj _s l _s l _{sl sl s} l _s l _s l _s l vo c-o cn oo oo oo oo _o cx) sj s_ sj sj s_ sj sj sj sj _ _. c _. cΛ _C Λ _C Λ CΛ CΛ CΛ m m m > C C C C Ω Ω Ω Ω Ω Ω Ω Ω Ω <! < w ω rΛ fΛ M ω ω M W Hϊ ^μ < κ^ ^ ; - H^ c c c c ^ ^ > Ω 2 2 2 2 2 2 2 2 rΛ W ω fΛ ω w cΛ w 2 2 2 2 2 2 2 2 2 C C C

2 0 0 2 0 0 0 0 2 0 0 2 0 0 0 0 0 2 0 0 2 0 0 0 0 0 2 O O O 5 d Ω W N M d Ω td > M M d Ω W > Ω to p to μ to

CO c α I I I I l l l l l l l l l I I I I I I I I I I I I I I I I

9 P» p* p» p» P- P' P' P' P' P' P' P' μ μ μ μ μ μ μ to μ μ μ μ μ μ μ M sl CΛ CΛ CΛ tfs- m cΛ m rf m rfs c to t _> f- c _. cn si si co o _ _θ Cθ - Nθ . co μ

= ^■ ? c cn ιt» CΛ m rfs cn O s_ o_ rf_. to μ-» 0 0- O rfs UI OD VO VO O. si cn m cn co J 00 sj to

H CO CΛ rfs sj CD rfs m c vD cΛ CΛ μ-' θ sj u) ui si p ^» CΛ θ O sj rfs sl CO sl CO Ui rfs rπ co I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I

X M to io to to to to to to co ω . co co co co ω co co co co co co co co ω to to to m vo si co ιt_. cn uι o. oo vo o o o o o o μ-> μ-> μ-> p' P ¹ m m m u> to μ-> o oo vo cΛ

■f . to co o rfs μ^ ui co cn s o tθ ιt_. co u vD tθ m m ιts. si m M _Λ θ vo m ιts p ^» VD θ ^* o rfs cn ui vo cn si rfs to vo o _. to o μ- ^ι cxι c μ ^j _C Λ m c» co cπ cx> to m

30 c r m-

00 CO CX) sl sl sl s] sl sJ sl sJ sj sl sJ s, s_ sl s] sl sl sl sl sl s] s] sl sl sl s4 sl

Si O P» O VO --O VD OO VD OO VO OO M tO Ul Ul cn s_ CΛ CD sl ιts cπ m CΛ CΛ CΛ CΛ C» CΛ ιt-» p» to to P» rfs o to o to rfs VD 0. O 00 rfs Cn C0 00 CΛ C0 tfs. Ul C. O C0 t0 P» 00 CΛ CΛ CΛ rfs O o sl l to VD O sl p» sl o. CO its VO OO C-. p' OO tO I-' sl O _. O sl sl

-> -' -' ' P' p- p ⁱ H P ^ι μ-» p- p» P' μ-' P' μ-' -' -' p ^, p» P' P' » P» P» P» P* P» m m m m m m m m m ui cn cπ tn ui cπ cn cπ m m m m m m m o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o

TABLE IX

79 ARG CA -18.61 -29.26 81.22 15.00 79 ARG CB -17.95 -29.71 82.54 15.00 79 ARG CG -17.19 -31.05 82.52 15.00 79 ARG CD -18.12 -32.28 82.55 15.00 79 ARG NE -18.94 -32.34 83.76 15.00 79 ARG CZ -20.14 -32.92 83.84 15.00 79 ARG NH1 -20.69 -33.51 82.78 15.00 79 ARG NH2 -20.82 -32.88 84.99 15.00 79 ARG C -19.47 -28.02 81.44 15.00

79 ARG O •19.86 -27.74 82.57 15.00

80 GLY N -19.75 -27.27 80.38 15.00 80 GLY CA -20.58 -26.08 80.52 15.00 80 GLY C -20.38 -24.97 79.49 15.00

80 GLY O -19.36 -24.93 78.78 15.00

81 ILE N -21.37 -24.08 79.41 15.00 81 ILE CA -21.35 -22.92 78.50 15.00 81 ILE CB -22.14 -23.20 77.17 15.00 81 ILE CG2 -23.59 -23.57 77.46 15.00 81 ILE CGI -22.11 -21.97 76.25 15.00 81 ILE CDl -22.75 -22.19 74.90 15.00 81 ILE C -22.00 -21.76 79.25 15.00

81 ILE 0 -22.86 -21.98 80.11 15.00

82 ASP N -21.56 -20.54 78.96 15.00 82 ASP CA -22.09 -19.34 79.61 15.00 82 ASP CB -21.08 -18.20 79.59 15.00 82 ASP CG -19.89 -18.44 80.48 15.00 82 ASP ODl -18.82 -17.87 80.21 15.00 82 ASP OD2 -20.03 -19.18 81.47 15.00 82 ASP C -23.40 -18.85 79.02 15.00

82 ASP 0 -23.89 -19.36 78.02 15.00

83 SER N -23.96 -17.84 79.68 15.00 83 SER CA -25.19 -17.20 79.27 15.00 83 SER CB -26.03 -16.83 80.49 15.00 83 SER OG -25.19 -16.35 81.52 15.00 83 SER C -24.76 -15.96 78.49 15.00

83 SER 0 -23.59 -15.58 78.53 15.00

84 GLU N -25.68 -15.29 77.81 15.00 84 GLU CA -25.29 -14.13 77.03 15.00 84 GLU CB -26.39 -13.59 76.13 15.00 84 GLU CG -25.83 -12.69 75.03 15.00 84 GLU CD -24.85 -13.42 74.11 15.00 84 GLU OEl -25.26 -13.79 72.99 15.00

OO OO OO CO OO ∞ OO OO OO -O CO CO OO ∞ OO CO CD OO CO CO CXJ CXJ CO OO ∞ ∞ CO CO

- ι vo vo vo vo D vo t-o α3 θo oo cx) co c_) sj s_ sj s_ s] si sj si sj si s] si cΛ CΛ (Λ »- ι- -- ) ^, ι. ^, ι- ^|i - '- 'fl ^, tJ -- H H '- . ι- ^ ι- t- H >- . rξ rξ r r<i r rξ r π O O O VO VO r r<l r4 r4 r<! x r4 r<i r<l r4 x r4 vo vo vo vo vo vo vo o o o o o o o vo vo vo vo vo vo vo vo vo vo vo vo

0 0 0 0 0 0 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 O 0 O d M d Ω W > Ω W d t-. tsι W d W d Ω ω > to μ μ to to p μ ro

CO c

00 I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I CO t tO t t tO tO P ^J tO t tO M t tO tO P ⁱ P ^J P ⁱ P ^J P* tO tO P ^J t M d to μ ^j to tθ H μ ^j vo ρ ^ι P ^Λ P ^ι P* o H P ^J o ιt uι o^ s cΛ s cx) vo o μ-' VD θ t to

H C OO O rfs CO sl Ul CO CO cn cn si cn o M oo _- -θ ι ^* s. s] ui sj co s p» -o o3 V£) co to

H tO sj vo cΛ m m m o CD tO P> sl m OO sl O VO tO rfs OO VD rfs Oo μ-' CO CΛ O O m co I I I I I I I I I I I x I I I I I I I I I I I ρ> p ^» p ^» p* μ-* p> m P ^» I I p- p ^» ρ» ρ- ρ» ρ» ρ» ρ» P ^ι ι- ^, P' p' p» p» ρ ^, P ^ι P ^ι P ^> μ co co to μ μ p ^» μ-> VD VO O u- m m c. cΛ rfs its ut ui co uj u' U- its ui rη

H to co ιt p> o Λ W m w cn s_ p» ιo ∞ vo to ιo c» oo cΛ m co ιt-. μ-> si cn π ,is c^

— - Cl CΛ sJ |-- ^ι Js pι μ- ^ι tθ μ-' UI C» tO VO Oθ μ-' VD O tO VO OO O VO UJ VO tO CΛ tO sJ

30

C rr m cn CΛ CΛ _CΛ l sl sl s sJ sJ sJ s] s] sl sl sl sJ sJ s] sl sJ s] sl sJ sJ sl O0 OO OO 0O CO CO VO VO o p» co rf_. rf sj cn m _s i cΛ. c _Λ c _Λ sj n Λ _s i _s i co co o o p' p'

Si CO O M il^ CO sl μ-' O its O m OΛ C^ OO sJ rfs VO sJ lO OO i's P^ OO O O αJ lO CΛ M

_. to <_. oo s ^] ιts rf_. o m vo o ιfs. u] ιt-. cΛ io to oo tθ rf^ m vo cn o ω

H-' P' P' P' P- P' P' P- P- P' P' P' P' P' P' P' P' P' P' P' P- P' p- m m m m m m m m m m m m m m m m m m m m m m m m m m m m o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o

μ-> μ- ¹ p- μ-»

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O c* _{. Λ CΛ} C _{Λ CΛ} cΛ m m m rf ιts ιfs rfs ι co uι u> u) U) UJ U- uι u ^, t t t tθ

C C C C C C C C C C Ω Ω Ω Ω ^ -

K ^* Kj K ^* K ^* κ< C κ! κj κ! ι< ι< κ! ^ κi ^ t _ t ^*, t ¹ tti w cn ω co. co co > W W W W W W W fΛ tΛ Hj Kj ^ ^H ^ IΛ

O O O O O 2 O O O O 2 O O O 0 2 0 O 2 0 0 O 0 0 2 0 0 0 2 0 w d Ω ω > ω > ro > N W d Ω ro >

CO c CD I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I

9 to M to to w to to to to to to to to to M w to to to to w w to to 'i -i i. ui co ui o. o. -i si o. cn cn 'i. i. co co 'o μ io μ tj μ co to μ o μ c =i to m o si cn m vo _^ si si m m ω m uι oo rfs o m M cn co oo to to oo cΛ co

OO C-i m sJ Ul t P^ O CΛ s] O CΛ m sJ <^ p ⁱ sl U» VO t sl O tO t m s] Oo m rfs tO ι

H πt co I I I I I I I I I I I I I I I I I I I I I I I I I I I I I x lo to to to M to to to w to to to to to M to M to to to w w w m o ∞ co vo co sj uι cΛ ιt-» ιf^ co u> to o μ- ^ι P ⁱ P ⁱ P ⁱ m m ιts u' to H θ θo oo si c» oo m 4s -i t

- ifs VO O. tO to s! O CΛ VO s] t>O CD rfs s] O _. I ιts rfs rfs CΛ tθ m tO P» s]

CΛ CΛ m CO CΛ to to m cΛ CΛ tθ s] oo rfs. m m o m m to to σ θ3 to o

3-0» °°

C tr m OO OO OO OO OO OO OO OO sl OO OO OO OO OO ω Φ OO OO O OO OO OO OO OJ OO OO CO OO OO OO to to to p' o o o o oo o o p- μ-' p-- t ιfs UJ U> U> m rf» U ⁾ Ui U' 0 U ⁾ ιts ui sl

OO OO OO CΛ U> ιti O tO VO C VO sJ OΛ CΛ tO M |--s W CΛ sl O ∞ m tO VO VO sl Ul C θ VO O U) ιf^ CΛ O VO ιt^ l-' sl IO tO s] C» ιts m m θ VD I- ^J CΛ lO P' Cn ιfi sl Oθ m sl c

_(- _ ^ μ_ ₍ __ ι-_ μ_ μ-ι μ_. » H ^ι P ^α P- μ ^j μ ^j P ⁱ P ^, P» ρ ^» μ ^j P' R p' p- μ ^j μ ^j μ ^j P ⁱ m m m m m m m m m m m m m m m m m m m m m m m m m m m m m

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

TABLEIX

209 LEU N -27.08 -32.00 57.36 15.00

209 LEU CA -26.10 -31.82 58.42 15.00

209 LEU CB -25.07 -30.77 58.03 15.00

209 LEU CG -23.69 -31.04 58.63 15.00

209 LEU CDl -23.08 -32.21 57.88 15.00

209 LEU CD2 -22.82 -29.81 58.52 15.00

209 LEU C -26.77 -31.46 59.73 15.00

209 LEU 0 -26.25 -30.66 60.51 15.00

210 ALA N -27.91 -32.08 59.97 15.00 210 ALA H -27.81 -31.90 59.38 15.00 210 ALA CA -28.67 -31.80 61.19 15.00 210 ALA CB -29.27 -31.17 61.33 15.00 210 ALA C -28.06 -32.58 62.37 15.00

210 ALA O -27.58 -33.69 62.23 15.00

211 SER N -28.08 -31.93 63.53 15.00 211 SER CA -27.60 -32.53 64.76 15.00 211 SER CB -26.07 -32.52 64.86 15.00 211 SER OG -25.53 -31.21 64.89 15.00 211 SER C -28.25 -31.80 65.93 15.00

211 SER 0 -28.68 -30.65 65.78 15.00

212 PHE N -28.44 -32.51 67.03 15.00 212 PHE CA -29.04 -31.94 68.23 15.00 212 PHE CB -30.53 -32.29 68.37 15.00 212 PHE CG -30.81 -33.77 68.41 15.00 212 PHE CDl -31.04 -34.48 67.24 15.00 212 PHE CD2 -30.85 -34.45 69.62 15.00 212 PHE CE1 -31.30 -35.84 67.27 15.00 212 PHE CE2 -31.11 -35.82 69.67 15.00 212 PHE CZ -31.33 -36.51 68.48 15.00 212 PHE C -28.22 -32.41 69.43 15.00

212 PHE O -27.54 -33.43 69.36 15.00

213 PRO N -28.19 -31.63 70.50 15.00 213 PRO CD -28.56 -30.21 70.63 15.00 213 PRO CA -27.41 -32.07 71.65 15.00 213 PRO CB -26.98 -30.75 72.28 15.00 213 PRO CG -28.17 -29.90 72.06 15.00 213 PRO C -28.21 -32.91 72.65 15.00

213 PRO O -29.45 -32.81 72.72 15.00

214 LYS N -27.50 -33.77 73.38 15.00 214 LYS CA -28.12 -34.59 74.42 15.00 214 LYS CB -27.50 -35.97 74.52 15.00 214 LYS CG -28.01 -37.00 73.53 15.00

TABLE X

Table of the orthogonal three dimensional coordinates in Angstroms and B factors (A*--) for the cathepsin K complex with inhibitor 1-N- (N-imidazole acetyl- leucinyl) -amino-3-N- (4-phenoxy-phenyl-sulfonyl) - amino-propan-2-one.

Residue Atom X Y Z B

1 ALA CB -8.26 15.35 87.29 15.00

1 ALA C -6.43 14.73 88.90 15.00

1 ALA O -6.17 15.27 89.97 15.00

1 ALA N -8.92 14.74 89.58 15.00

1 ALA CA -7.91 14.50 88.49 15.00

2 PRO N -5.47 14.25 88.09 15.00 2 PRO CD -5.62 13.29 86.98 15.00 2 PRO CA -4.05 14.45 88.44 15.00 2 PRO CB -3.32 13.49 87.50 15.00 2 PRO CG -4.27 13.38 86.30 15.00 2 PRO C -3.55 15.87 88.27 15.00

2 PRO O -4.33 16.79 88.21 15.00

3 ASP N -2.23 16.02 88.20 15.00 3 ASP CA -1.59 17.30 88.03 15.00 3 ASP CB -0.07 17.14 88.15 15.00 3 ASP CG 0.45 17.62 89.50 15.00 3 ASP ODl -0.04 17.07 90.52 15.00 3 ASP OD2 1.29 18.57 89.55 15.00 3 ASP C -1.90 18.00 86.73 15.00

3 ASP O -1.71 17.44 85.64 15.00

4 SER N -2.32 19.26 86.85 15.00 4 SER CA -2.67 20.16 85.75 15.00 4 SER CB -3.63 19.49 84.75 15.00 4 SER OG -4.80 19.03 85.40 15.00 4 SER C -3.32 21.45 86.30 15.00

4 SER O -3.83 21.46 87.42 15.00

5 VAL N -3.30 22.53 85.53 15.00 5 VAL CA -3.93 23.80 85.94 15.00 5 VAL CB -3.00 24.65 86.90 15.00 5 VAL CGI -1.73 25.13 86.17 15.00 5 VAL CG2 -3.76 25.89 87.45 15.00 5 VAL C -4.21 24.62 84.69 15.00 5 VAL O -3.43 24.58 83.75 15.00

TABLE XI

Table of angles between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 3(S)-3-

[ (N-benzyloxycarbonyl) -L-leucinyl]amino-5-methyl-1- (1-propoxy) -

2-hexanone.

Atom 1 Atom 2 Atom 3 Angle Atom 1 Atom 2 Atom 3 Angle

TABLE Xπ

Table of angles between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor bis- (Cbz-leucinyl) -1,3-diamino-propan-2-one

Atom 1 Atom 2 Atom 3 Angle Atom 1 Atom 2 Atom 3 Angle

TABLE XIII

Table of angles between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 2,2'-N,N' bis-benzyloxycarbonyl-L-leucinylcarbohydrazide.

Atom 1 Atom 2 Atom 3 Angle Atom 1 Atom 2 Atom 3 Angle

M M M M M M M M

03 00 W CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ W W W W CΛ CΛ CΛ CΛ CΛ CΛ CΛ w w W W W W M it* its CD D C W W W W W W W W W m m m M to W W W W m m m m m m m vo

2 2 2 2 O O O O O O O O O O O O O O O 2 co co o co o co co o

W W W W Ω Ω > > M M ro ro ω ω cd ω d d Ω Ω Ω Ω Ω Ω Ω d w w ω M w w w w w w w w w w w w w w w w w w w w w w w w W W W w w w w w w w m m m m m cπ m m m m m m m m m m n n cn cn m m m m m m tn

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 w w w w M M M M M M M M M M M M M M M M M o o o o CO CD VO VO vo vo vo VO VO vo CO VD VD VO CD CO CO VO VD VD VO VO VO VD vo vo VO VO VD VO 00

vo M 00 rfs rfs rfs CO w o CO w 00 it* si μ-ι it* CΛ M rfs O sl VO CO OO W M lO O CO it* it oo w oo σι to CJ CΛ M O co m CO CΛ co oo CΛ s CO CΛ 00 M m O O lO CΛ sl Ul W CO Ul its W OO OO sl co m oo to

M

W CΛ σ. CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ W w w w w w w W CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ W CΛ w CO CΛ CΛ CΛ CΛ OS m m m m cn cn cn m m m m CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ M co o o o o o o O O O O O O O O O O O O O O O O O O O O 2 2 2 2 2 2 2 2 O o O

> > > > > > d d d d d d d d ω

w w W W W W w w w w w w w w w w w W W w w W W W W w t W W W m m m m m m m m m m m m m tn m m cn m m m cπ cπ cπ m m

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

CO CO CJ to to co to co co to to to CO Ul O CO CO to co co to co co to ui ui C to CO O O

CD VO VD VD CO CD co co vo vo vo VD CD CO CO VD VD vo vo CO CD CD VO VD VD VD VO O VO OO 00 00 00 w w w w w CΛ CΛ w w W CΛ CΛ W W CΛ w CΛ CΛ w w w w CΛ W w w CΛ W CΛ CΛ W W CΛ CΛ W CΛ w CΛ

CΛ CΛ m CΛ CΛ CΛ it* m OS CΛ CΛ CΛ It* m CΛ CΛ O tO CΛ CΛ CΛ CΛ CO m CΛ m CΛ CΛ CΛ CΛ m CΛ m it* m

CO O o o o 2 O O O O 2 O O o O O 2 o O 2 O 2 O O O O O O 2 o o o o 2 O 2

C ω d W Ω tC w Ω t M ω d M Ω > Ω tc w w w w w 09 CO d 00 CΛ sj 00 CΛ 00 m m si sl m W 00 CΛ CΛ w co m ιt* CΛ M ιt* m CΛ m W to m CΛ ιtS ||S s] CO VO rfs 00 to O m its m its CΛ co to o en si μ-> ιo CΛ m oo vo CO O it- W W UI sl W rfs OO Ul sl sJ W O CO CΛ

m m o o to o CΛ to o to o sl sj CO CΛ O s] to to to w rfs 00 Ul to Ul CΛ 00 M sl W CΛ W sl cn o vo m c M m W W CΛ w w CO CΛ rfs O t m O 00 CΛ CΛ it* M o cπ vo rfs CΛ o co o m C

TABLE XIV

Table of angles between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor (IS) -N- [2-[ (1-benzyloxycarbonylamino)-3-methylbutyl] thiazol- 4-ylcarbonyl] -N'-(N-benzyloxycarbonyl-L-leucinyl)hydrazide.

Atom 1 Atom 2 Atom 3 Angle Atom 1 Atom 2 Atom 3 Angle

M M M M M M M M M M M M M M M MM MM

Cn CΛ CΛ CΛ CΛ CΛ W W W W W W W CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ W W W OO W W OO OO W W M M M M M M M M M M M

W W W W W W cπ cπ Cπ Ul Cπ UI Cn Ww W W W W W W W M W W WW rfs O O OO rfrfss iitts _* W W VO VO VO VD VO VO VO VD CO CO VO

O O O O O O cn w cn n n tn n 2 2 O O 2 O O O 2 2 0 0 0 0 0 0 0 0 0 0 2 2 2 w w w W ro W Ω Ω Ω Ω Ω Ω Ω d d > d W W W W W Ω Ω Ω Ω Ω W W W

M M M w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m ui cn cπ cπ 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 0w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w w2 w2 w2 2 2 2 _, ,_. [_. w w w 2

( w cn M M M M M M M M M M O O O O O O O O O O O O O O O O O O O O O c ro M M M M M M

CO 00 CΛ M M W O. CΛ M CΛ C . CΛ Cn 00 0O CΛ M M W CΛ W M W W M M W M 0O W W M W 00 M W W W W M W 00

9 ifs rfs W CO VO m W M VO W W M W it* rfs W CO VO m W rn tO M M VO VO W VO ifs M W CD W it* CO W W VO W rfs

O 2 O O 2 o o o o o s. -o.. 2 -, Ω 2 2 0 0 0 Cn Ω Ω Ω Ω 0 Ω Ω Ω Ω 2 Ω Ω O O 2 o o o

H .. ts M .. w ω a > to w w ts w ro w ω Ω Ω ω > > ω ω ω d ω d C M W W W ω ω

M M M W W W M M -I m cn if* cn M sl rfs Ul sl sl OO CΛ OO sl OO CΛ CΛ M CO CΛ m M sJ Oo m W CΛ CΛ CΛ sl x CΛ CO rfs 00 rfs VO 00 CΛ CΛ to cπ sl en w m O m VD OO tO CΛ M sJ CΛ m W CO O CΛ M CΛ CO CO CΛ it* VO VO 00 M OO OO sl cπ cΛ rfs OO it* to o si _M co vo m Cn sl sl OO M M CΛ OO W CΛ O M C O OO ιts O OO O. CΛ Ul CΛ M tn ιt* sJ ιt* O ιt* ιt* C0 CΛ W CΛ O Ui s] 00 W CΛ sl s] 00 CΛ 00 CΛ Ul lO s] CΛ W M VO O VO O W s] rf* CΛ lO VO sl OO CO O ιt* VD W O O Ul Ui W M W VO it* VO m UI M rfs

.2 CΛ 30 sj c --J r- i-> t-* *-> \-> -> \-> M M M M M M M M M M M s CΛ O. CΛ CΛ CΛ CΛ CΛ W W W W W W CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ 0O W W W 0O W W 0O W W W M M M M M M M M M

W W W W W W W Ul Cπ Cπ Ul Ul Ul W W W W W W W W ifs W W W rfs O O rfs W W W VO VO VO VO VO VO VO VO VO VO

8 Ω Ω Ω Ω Ω Ω Ω W W to ω w cn 2 2 2 2 2 ^: -3 2. § r_ Ω 2 2 Ω Ω Ω 2 0 0 0 0 0 0 0 Ω O 0 0 2 2 ro W W ro M W W Ω Ω Ω Ω Ω Ω d d d d d d d d W d W ro W W Ω Ω Ω Ω Ω W M

M M M M M M M M M M M M M M M W M M M M W w

W W W W W W W W W W W t W W W W W W W W W W W W W W W W W W W W W W W W W W W W W m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m cπ cn cn cn

Ow 0w 0w 0w 0w 0w Ow Ow Ow Ow Ow 0w Ow Ow Ow 0w 0w 0w 0w Ow Ow 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w 2w w2

M M M M M M M M M M M M M M M M M M M M M O O O O O O O O O O O O O O O O O O O O O

M M -^ r-^ M -^ ^

CΛ CΛ CΛ . M C _Λ. C_Λ. C-Λ.. C_I.. C_Λ. .M M -W_ C _Λ. C _Λ. C _n. CΛ M CΛ O. CΛ CΛ M M M W 00 W W 03 M W W OO OO W OO W CO OO 00 w

W W M VO W W W W W VD VO m W W W M VD W W M W VD VO VO W rfS M w it* VD W O it* it* W it* W its rfs VD rfs w

2 O o o o o o o o d O Od 0 Or 0 O 2 2 0 0 O 2 o o o o o o d ro 2 O o.. o o o o O O O O 2 O O 2

W o Ω W W roW Mw ω Ω dw d > ω ro ro ω ω ww row ω M d ro d ro w w

W M w w

oo w co m cΛ cn co co sl O0 W 00 σ. M sl 00 ιt* lO 03 VO CΛ CΛ W W CO rfs M M CΛ m rfs si oo si cπ cΛ to co si Ul sJ CO sl CΛ rfs M M it* sJ Ul W m OO O OO CO OO 00 M CO lO VO sJ O lO lO CO sJ CΛ CΛ CΛ O its sl sl sl o CΛ m CD O O O CΛ m M m θO O CD rfs CO OO ιts O lO ιts uι cΛ sl o CD OO O O W M O m M O W OO O rfs sl M O VO ιt* W ιt* rfS M W VO CO CO rfS s] C OO CΛ CΛ OO VO VD M VO -O M W U> M m m θ O ιo oo o. co vD M θ ιt _* uι cn oo cn

CΛ CΛ Cn CΛ CΛ CΛ CΛ CΛ CΛ W μ-i M W W W W P' M M W W W W W W W W W W W W W W W W W W W W M M M fi W ιfr ^ μ μ ι|_ ti |t> . - - « W m m ω U - _ _ ω U ιJ ι^ fk ^ ι^ ι> fc ^ ιl» ι^ ι|i W I. W I _. Ui ω «) iO

0 0 O O 0 0 0 0 0 0 0 0 O O 2 2 0 _d 0 _d 0 _d 0 0 2 2 2 0-.. 0-.. 0--. 0-.. O--. 0 0 O O O O_ 0_ 0 0 O 2 2 2 d d W M > > > > >.. >.. .. > W W W

M M w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W c m m m m m m rfs co uι uι uι uι u) uι u uι uι uι uι u> u) uι uι uι uι u) uι uι uι uι uι U) U) uι uι uι u) uι uι uι

M

CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ W W W CΛ M CΛ M w w w w W W M W ._ W ._ M . W W M - W- - W- W CΛ W W W CΛ M W M Ul U1 UI M ιt* M rfs M ιt* rf rf-s. Ww Ww CoO w VO it* w m it* rfs CΛ VO CΛ U1 VO C W VO CΛ W it* W VO CΛ W it* W VO CΛ 0 2 2 0 0 0 0 0 0 0 0 0 2 0 o O O O O O O O O O O 2 O 0 2 O ~ O 0 2 o O 2 0 2 d Ω Ω d 5 W ro d d d d M > M d ro

M M

sj M M CO M CΛ CΛ rfS 00 s] ^s J s] s] 00 CO O. CΛ s] sl CΛ VO VO sl w m CΛ sJ CΛ sl s] rf sl W CΛ CΛ lO VO lO sl W VO m si rfs w w en o rfs VD W m OO rfs cΛ rfs W VO rfs CO sl rfs O OO VD OO m M rfs CO s) CΛ rfs M W sl M M CΛ OO CΛ s] cn

Cθ m cΛ W Cθ m ιt* O O. Vθ m θO W M VO VO ιt* ιt* M O ιt* CΛ lO CO CΛ vo ^j o. o tn M si tn M si si 00 to s] W VD M O s] 00 rfs. V0 0 _. ιt* W θ sl cπ ιt* rfs C0 00 sl CO CΛ VD W sl OO W OO VO W VO sJ lo m OO M sj CO s sl

CΛ

00

CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ W M W W W W W M M M W W W W W W W W W W W W W W W W W W M M

It* .. M it* it* W CΛ VO U1 U1 CΛ CΛ CΛ VO VO VO W W CO U1 CO ιt _* ιt _* ιt _* ιt _* ιt _* ιt _* ιts ιt _* m m m m m vD vo vo o O O O o o o o o o o 2 2 2 0 0 o 0 0 2 2 2 O O O O O O O O O O O O O ^' 2 2 ^' 2 Ω > d d w d d d > > > ^* > ro w w

M M w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w tn m m m m m m m m co uι uι uι uι uι uι u) uι to u) U) uι co u» uι uι uι u) uι u) uι uι uι uι uι uι uι uι uι u) uι uι

M M

CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ W W CΛ W W W W W CΛ M W W M W M W W M W W W W W M W W W W M W W W W m m M m m m it* rf w ** CΛ ιt* CΛ Ul W VO CΛ W vD W vD W W vD CΛ W rfs CΛ m vo to lt> CΛ Ul VO ιts rfs W Ul O 2 o o 2 0 2 0 O o 2 O O o o 2 O O O o o o 0 2 0 o O O O 2 O O O O O O O O

Ω Ω > > d d d d d d d d d >

M w w

M

rfs cΛ CΛ CΛ CΛ CΛ M t CΛ CD m ιfs. U ⁾ U1 t Ul M O. M VD M ιt* M CD CO Cπ θO O. m Ul rfs CΛ OO CO CΛ M CΛ CΛ CΛ Ul OO

CΛ ιfs oo w m m oo cΛ m vD ιt* vD co uι oo co o. ιt _* m m ιt* vo m co o oo cΛ W sj cΛ ιt _* o co rfs w oo cn io M cn co M

M CO CD O W m m θ 00 M M m 03 rfS ^s J C0 sl CD ιfs sl 00 0. C0 Ul sJ s] O s) W V0 O VD ιts VD C0 W C0 W O 00 rfs C O M CX) sl sl lΛ C0 σN O CΛ O W M C» ιt* sl ιfs ιt* 00 O CΛ UJ O M m CΛ M C0 s] Ui sl M M Uι V0 VD 00 V0 m sl CΛ

TABLE XV

Table of angles between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 2-[N-(3- benzyloxybenzoyl) ]-2 '- [N'-(N-benzyloxycarbonyl-L- leucinyl) ]carbohydrazide.

Atom 1 Atom 2 Atom 3 Angle Atom 1 Atom 2 Atom 3 Angle

TABLE XVI

Table of angles between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 4- [N- [ (phenylmethoxy)carbonyl] -L- leucyl] -1- [N- [ (phenylmethoxy)carbonyl] -L-leucyl] -3- pyrrolidinone.

Atom 1 Atom 2 Atom 3 Angle in degrees

- ⁱ ^ - ⁱ ^ i- ⁱ i-' t- ^k r- ^t M M M M M M M M M M M OO OO OO OO OO OO OO OO OO OO OO OO M M M M ∞ CO OO OO CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CXJ CO OO CO CD ∞ CO CX- OO CD OO rfs rfs rf rfs rfs. rf . rfs rfs rfs rfs rfs CD VO VO VO rfs rfs rfs rfs W W W W W W W W W W W rfS _| fS ιt* ιts rf_. rfs rfs rfs rf* ιfs rfs

2 2 2 2 2 2 2 2 2 2 2 o o 2 2 0 0 0 0 0 0 0 0 0 2 2 d 2 d2 0 0 0 0 0 0 0 0 0 0

W W W W W W W W W W W W M W

M M M y-^ t-^ ^ ^ ro w d d d d ro w ro w M d d

W W M M M t-^ t-> -^ M M M M roW ro 0 W roW roW roW roW wW tWsi fWsi NW tWsi w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m cn O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

M M M M M M M M vO VO VO VD VO VO VD VO CO VD VD VO vD VO VO VD VD VO VD VO VO VO VO VO VO VO VO VO VO VO c

CD o o O O O O O O O O O cn

00 CO OΛ OΛ M M CO M M OO M M M CO OO M M M O _O_ O_Λ-. O_O M. M M O _O O_Λ. O_Λ. C_O M. M 00

H it* its W W O VD it* CO VO VO rfs CO VO CO rfS it* V _O. v_O. V_D_ rf_s. W_ rf_s. C_O V_O V_O_ rf_s W_ W__ rf_s V„O V ₀ D rf ₀ s

C O O 2 O O 2 O O O 2 o o O 2 O O O O 2 O O O O 2 O O 2 O O H K d W Ω X d M W X d o W W d W d X d M d m w w w w W M W W ro w d x d M W d w r

M W M W M W M M W w W cn x m m m M OΛ o s vo M CΛ rfs W CΛ VD VO M M W rfs _ CΛ CΛ ιt* cΛ m s] s cπ s] s] M si σ. vD m oΛ co oo cπ s m sJ CD O its m iO O CΛ VD its o M OO CΛ W OO OO CO OO rfs VD W CΛ sl OO CΛ M H O CΛ CO M W O W rfs CΛ CO sl O rfs rf

CΛ tO rfs CΛ CO CΛ O m sJ O M CΛ M sJ tO CΛ O VD M OO Oo m O CO W O OΛ rfs CO M O M sl rfs cπ tO OS OO sl its rfs rfS

X to to rfs M VO O lO W lO VD W tπ OO CΛ Ul W VO CO VO sl lO sl Ul lO sl W vD sl its W VO rfs VO rfs W sl O rfS M OO VO M VD

C co r ^* m ι* σ>

M t ιf* rfs rfS 00 sl Ui lO lo rfs

O O O O O d d d EC w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m cn O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O c M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M r-^ MY- ⁱ Mr- ⁱ M- ⁱ M- ¹ Mr- ⁱ Mr- Mr- ¹ M- ⁱ M M M M M M M it* rf rf it* it* rfs it* rf rf rf rfs it* rf its rf rf rfs rfs rfs rfS rfS rfS rfS co ιo ιo ιo ιo ιo ιo to ιo co ιo ιo u> ιo co ιo

CD cn i-> i-> r-> i-* t-> -> i-> M ^ |__ H» M M M M M M M M M M

H CO CO IO CO CO CO CO rfs CO UJ Ul rfs 00 CO CO it* 00 CO Ul Ul Ul it* 00 CO OO tO tO CΛ CO CΛ CO CΛ CΛ lO OO Ui CΛ OO CΛ CΛ rfs Ul

H 00 00 00 sj 00 00 sl CO CO 00 s] CO rfs sl CO rfs s CO 00 sl co it* rfs sl sl W sl W sl sl it* sl W if* CO sl

C O 2 O O 2 O O O 2 O O O O o o o 0 2 0 0 0 0 0 0 0 0 0 0 0 0 o o O O O O O 2 o H > > > d > d X d X X o > ro > > x > ω x Ω W m w w w w > r w w w n x m m W sl OΛ sJ oo VO CΛ CΛ W CO M Ul Ul VO -O OO M sl si α. s] sJ Ul OO CΛ OΛ sl oO ifs CΛ CΛ rfs OO CΛ m oo si oo rfs VD OΛ OO W tO Ui sl C CΛ m its VD OO m O W OO tO W CO O sj io vo vo W si αo vD o rfs w rfs co M 00 M to as it _* si VD

VO M CO O O sJ Cl _. CO cn m iO M Ui m W ιfS ||_. m -Λ ιts VO CΛ W O sJ CΛ CO l W m M O OO UJ ιts sJ C Cθ W M W CO co M Oo oo cn n cΛ sj sl W sl CO W CO CΛ OO M OΛ W lO W CΛ CO W OO CO O O sl l O M W VO its OO VO m sl cΛ OO sl

C o r~ m s.

M M M M M M M M M M M M M M M M M M

CO U UI U) U) UI UI CΛ OΛ CΛ CΛ CΛ CΛ CΛ CO UI UI U» U) UI UI UI U1 UI U1 U1 UI U1 U1 U1 U1 U) UI UI UI U1 U1 U1 U1 U1 U1 U1 sl sl sl sl sl sJ sl M t-* r-> * t-* * sl sl sl sl sl sl 00 00 00 0O -0 00 00 CO 0O 0O 00 sslj ssli ssli ssli ssli ssli ssli ssl, ssli ss]i o o o o o o o o o o o o o o O O O O O O O O O O O O O O O O O O O O O O O O O O O t Ω Ω Ω Ω Ω Ω Ω ω ω ω ω ω ω ω ω ω ω ω w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m

M CΛ

w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m ui cn ui O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O cn -^ -^ -^ M M M M M M M M M M M M M M M M M M M M cΛ CΛ cn cΛ CΛ en cΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ m m m m m m m m m m m m m m m m m m m m m m m m m m m m

CD cn M M M M M M M M M M M M M M M M M M M M M M M \-> -^ r-' r-' -^ ^ -"

CΛ CΛ CΛ CΛ W CΛ CΛ CΛ CΛ Cn W CΛ CΛ CΛ CΛ lO CΛ Ul Ui CΛ UI CΛ CO rfs CO UJ rfs I OΛ UI CΛ CO IO IO CΛ CΛ CO IO CO IO CΛ CO

H M w to * ιn __ι M __ι tN_ w _π M W W M M 0_o0 M 0_o0 0_o0 M 0_0θ M O 0O0 CO CO 00 to OO M OO sl OO M M OO sj 00 sl M 00 -H C o o o ω o o 2 o o co o -o 2 O o O O O O 2 0 0 2 O O O O O O O O O O 0.. 0 2 0 0 H ω Ω > Ω ω Ω > Ώ ω d Ω 8 Ω W Ω w ω ω Ω ω ro Ω ω w w m cn x m it* m M ifs rfs tO sl M CΛ CO sl rfs sJ lO U1 00 it* VO 00 00 VO CO 00 M lO Ul s] sl 00 ^s j oΛ to cΛ CΛ to m co αo m vo si m co m ιo co to w sj w ιt» w m uι cΛ ιt* o w co rfs w co M CΛ m ιt* vo m m sj t _N O M M CO W O W CO VD it* O M

Z _n OS rfs o tn o oo to oo m ιt _* w cΛ ιt* co m m oo O rfs CO O rfs VO W M CO CΛ Oo cn m oo oΛ CO M vo m w OΛ m o m CΛ

3 ^ω sl OΛ UI CΛ M rfs CΛ W M ifs VD O OO CO OO m O VO rfs VO rfs W OO rfS it* M m vO VO CΛ CΛ O M w to m 00 rfs CΛ s] o c ts 1- m

10

W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W t m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m 0 0 0 2 2 2 2 2 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 to w fΛ fΛ tΛ w ^* Λ Cn ω tΛ fΛ _ 0 > m ω ω ω W rø to to W to « to Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω Ω w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m c cn ow ow ow ow ow ow ow wo ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow wo ow ow ow ow ow ow ow ow ow

W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W M

CD cn M M M M .

H W W W W CΛ W W W CΛ W M W W W W W W CΛ CΛ W W W CΛ W M W W W W CΛ CΛ W CΛ W W CΛ w w w w w O Ul Ul cn to it _* en w rf rfs ui ui ui m CΛ to w it _* m en w rfs Its Ul Ul CΛ CO W it* cn cΛ W rfs co cπ ui cπ ui O O O O 2 O O 2 O 2 O O O O O O O 2 2 O 2 O 2 O 2 O O 0 2 2 0 2 0 2 0 0

> d > > d > > d > d > > d W > w ω m M M w

CO CO CO UI VO W IO CO VO m rf* cΛ ^sj uι w co m ^{sj s} co ιt* m m _Λ _o w ιts oo w rfs co oo rfs rfs ui ^sj co ιt* s ^j to vo sl OO W CO W VD M sl OO m M m en CO tO ιf* CO rfs Ul M sl CΛ CΛ ιI^ m tO tJ. W M tO sl M O sl cn CX> CD OO O ιt* 00 sl O OΛ OO O CO sl sl Ul cn sl sl cn -^ in M OΛ m m θ O rfs W OO ^s l M m sl M ιt» M lO CΛ OO CΛ VD OO CΛ -sl CΛ CΛ vO VO sJ W OΛ rfs its tO VO Ul rfs VO rfs w vo to o w m t-J M ^sj io to si o co w o co to vo o oo w m o M rfs m ifs en vo

m m m m m m m w w w w w w w w w vD vo vo vo vo vD vD tn m m io rf _.. . |f_ rfS if* if* 0 0 0 0 0 0 0 2 0 0 2 o o o o o w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow ow wo ow ow ow ow ow U U] UI UJ Ul UJ UJ UJ UI U> UI UI U) UJ UI Ui CO Ul Ul UI Ui Ui UI Ui Ul UI Ul Ui Ui Ui Ui U>

M W CΛ W W W W W W W W W CΛ W W W CΛ W W CΛ W W W W CΛ W w w cn m w ιo w c _Λ m _t o w w w c _Λ m w w _ιf* w w c _Λ m to w w o o 2 O O 2 O 2 O 2 O O O 2 O o o O 2 O 2 ro w > ro M cn x rn m CO m m cΛ ιt _* vo vo si M M M VD C» M w m m m m m rfs oo vo si cΛ si vo oΛ CΛ vo oo oo s] cπ oo M sl to U) sl s]

H its co w io vo w M W vo tn m m m rfs to vo sj ui vo oo vo m its o it _* o M o o s s] to ui m ui M s] rfs 00 CO VD w

1 VO M M Cn cn θ VO UJ M CΛ M lO s] C» lt» ιt* M m θO M CO C» CΛ CD tO O M C» s] C» Ui UJ UI Vθ M CD t O W C» O UJ O lO ∞ ιls CD M θ m CD m ιtS sJ W VO lO CΛ m VO lO lO tX) VO rfs W CΛ l OO ιt* CΛ r* £ m oi

CΛ CΛ Cn CΛ CΛ CΛ CΛ CΛ CΛ Cn cn CΛ Cn cn CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ Cn CΛ CΛ CΛ CΛ tΛ CΛ CΛ CΛ C^

CΛ cn cΛ m m m m m m m m m m m m m m m m m m m M rfs rfs cπ ui ui o o O O CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ it* 2 2 2 0 O O O O O O O O 0 O O O 0 0 0 0 0 O O O O O O O O O 0 0 0 0 0 0 2 2 2 2 2 0 d > > > >

w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m cn O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w c sJ sl sl sl sJ sl sl sJ sl sl s] s_ s] s] s] sl sl sl s] sl sl sl CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ Cn CΛ CΛ CΛ CΛ CΛ CΛ CΛ

CD cn

H CΛ CΛ CΛ CΛ CΛ Cn CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ Cn cn CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ C^ ιt* m en CΛ M M CΛ M rfs m CΛ CΛ CΛ M M CΛ M rfs m CΛ CΛ m θ O M O M rfs O M ιt* m θ ιt* m θ O rfs m θ CΛ M c 0 0 0 0 0 2 0 0 0 0 0 2 0 0 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

H > d to > d to > > d > d > d > > > > d m W W t- ¹ \-^ ^ M n x m cn eo W m vθ m m CΛ M lO W CΛ sl UI CΛ rfs ul tO ιts tO M CD VO CΛ C» CD W M CΛ C» CD s] ιts _Λ CΛ m U s^ rn oo w w M M m w w o oo oo o en w cΛ W m co w ιt _* m co co oo cΛ CΛ M tθ sj cn oo ιt _* cΛ vo cΛ VD vo o m co tO cn M CXJ rfs Ul W CO VO W M m CO OO rfs CO Ui W W sl CO OΛ sl sl W OO W W OO W its CΛ CO VO o o to cn w o W _f x M CΛ CΛ VD OΛ sl CΛ OO W sJ CΛ VO CO CΛ CO OO W O VD m m vO OO sl W sl M VO W W tO O rfs VO OO m VO CΛ CO VD M f c sj r- m

TABLE XVπ

Table of angles between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 4-[N-[(4- pyridylmethoxy)carbonyl]-L-leucyl]-1-[N-

[ (phenylmethoxy)carbonyl]-L-leucyl] -3-pyrrolidinone.

Atom 1 Atom 2 Atom 3 Angle Atom 1 Atom 2 Atom 3 Angle

w w W CΛ CΛ CΛ CΛ OΛ OΛ CΛ CΛ CΛ CΛ W W W W CΛ CΛ w w CΛ CΛ CΛ W w w CΛ CΛ OΛ W co to co CO CΛ ON CΛ CΛ OΛ cπ cπ ui ui cπ ui n ui CΛ CΛ m CΛ CΛ CΛ CΛ CΛ cn CΛ CΛ m O O O O 2 2 2 2 2 Ω Ω Ω Ω O fΛ t_ c/- 0 O O O O O O O O o o O __ ' > Ω Ω Ω Ω G ° d d ro ro ro > Ω

w w w w w w w w w w w w w w w w w w w w w w W W w w w w cn cn cn m m m m m cn n cn n cn cn m m m m m m m m m m 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 O O O O O O O O O O O

M M M M M M M rf rfs its it* it* rfs rf rfS rfS it* rfS rfs rfs its its rfs lO lO lO CO CO CO CO lO CO lO lO CΛ CΛ tn CΛ O O

M to

w O O co co cn w W CΛ w w W CΛ w w W CΛ CΛ W w w CΛ W W W CΛ W CΛ W CΛ W CΛ W W CΛ w W W CΛ m CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ co m m co CΛ CO CO CΛ CΛ CΛ CΛ m CΛ m cn CΛ CΛ CΛ cn o Ω o CΛ CΛ CΛ CΛ CΛ CΛ O O 2 O O O 2 O O O O 2 O O O 2 ro d ro d Ω ² G O O O O 2 > Ω Ω 9 O 2 O O

> °d ^a G O

> d ω d > ui ui cn co cn io co cn n oo ifs sj oo M Cn

CΛ rfs O O M VO its rfs M sl sl lO CO sl OΛ O rfs OΛ CO VO W tO O W W m Ui VO sJ Ui Ul sl rfs O W rfs M W Ul Ul CΛ lO CΛ its sl rfS rfs ui

C cO

CD CO

w w M W M w w to to CΛ CΛ w w W W w tn CΛ ON CO OΛ CΛ CΛ CΛ W W CΛ CΛ CΛ w o t o o M W m CD VD m m m w W W O M M w cπ w w w cn cn n

O O O O O O O O to to to 2 O O O 2 O O o o to to ω > X X w w ro Ω Ω Ω d ro ro ro ω ro > Ω Ω Ω w w w w w M M M w w w w w w w w w w w W W w w w w w w w w W W W W W W W W w w w m m m m m m m cn m m n ui cπ cπ tn cn cπ ui m m m m m m m m m

O O O O O o o o o O o o O 0 0 w w w w w w w w w w w w w w w 2w 2w 2w 2w 2w 2w 2 2 2 2 2 2 2 2 2 2 2 w w w w w w w w w w w m m rfs rfs rfs it* rfs rfs It* rfs It* rfs rf CO CO CO Ul U) Ul lo io co co io io co co Ul Ul Ul

M M M M M M M M M M M

CO w w OΛ CΛ w w tn w W M OΛ W CΛ CΛ CΛ W CΛ w CΛ CΛ CΛ CΛ W en CΛ en en Λ c w w to to w W M co vo M m m vo M m w W W m w cπ w W W w m w w w w

CD 2 ω O O O O O O O O to 2 O O 2 2 O O O O O O O O O CO Ω Ω > ω tβ Ω W W d Ω ro Ω ro W ^Z G Ω ro 9 > ° W ro

HI w w M

H

C H m M 00 OΛ s m sl s] J rfs m si m OΛ CΛ rfs rfs 00 oo sl sl rfs vo M sl CO sj CO M CO M rfs rfs. s sj CO rfs O rfs it* it* vo w CO vo o m M vo CΛ W vo w m en M m M o co m to ui M OΛ m CΛ s s as oo rfs, o

00 vo w oo to CΛ CJ m s to cπ vo m m oo to w w o oo OO VD rfs VO M m rfs W CO O VD rfs oo cπ CO M W rfs O M M O CO o o to CO it* o vo o M sj w sl rfs M rf* CO OΛ CΛ Cπ ιt* M UI CO W lO M l VO O

TABLE XVπi

Table of angles between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 4-[N- [ (phenylmethoxy)carbonyl] -L-leucyl] -1-N[N- (methyl) -L-leucyl) ] -3- pyrrolidinone.

Atom 1 Atom 2 Atom 3 Angle Atom 1 Atom 2 Atom 3 Angle

TABLE XViπ

w W wWw ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww ww w w w w w m in cujii ucni tmn ui imn tmn mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm min ui cn mui cn min mui m m cn ui cπ o o o o O O O O m om mo om om om om om o _ι ts or _f oιfs oιf oιf orf oιt orf orfs orf oιt* or _f s oιts oιts oιt oιt* o O m m om om om om m om o ι _f oιts oιt* or _f rf rfs rf , rf rf

CO c M M

M w W W W M M M M w w oo oo w w w w W w W W W 00 00 00

CD co o O !- ^■ M CO CO VO O o VD VO rfs rf M M VO 00 O VO 00 M VO M M o rfs rfS to 00 vo rf CO O O 2. o o 2 o o 2. O O 2 O _ O O O o 2 o o 2 O O 2

H p O O O O O O O 2 2 _, _

Ω > ro d d Ω w w w d ro ro > W d d W Ω W d d W

H w w w w M M w d w w w W M C H rn co 00 W W VD W sl C» M m W CΛ m cn ^s J cπ sl W 00 sl VO 00 W ιt* W m sl M ^s J 00 sl ιfs VO CΛ M W sl M W s] CΛ m M w cΛ _O M vo m oo m vo m w oo si m M M M m m w cD si oo oo cx-i w m vo M O M M OΛ m oo o it _* sl O CO CΛ CO x m OO O OO CO O rfS OO O sl M CΛ its W CO CO OO O M 00 M W CO rfS CO sl cπ W CO m tO VD M OΛ M O O rfs CΛ en m CO to m sj oo o VO CO W Cπ rfS sJ CO CO Ul M Ul W rfS sl O rfs OO CO W CD VO OΛ CΛ rfs cD O m rfs M sl OΛ O it* M M O VO sl CΛ

30 c oo t r- m ro cn w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m o m o om om om om om o om om om o om om om om om om oιfs, oιi. orf oιfs oιf oιts orf oιts orfs, orfs oιts orfs orfs orf orf oιts orfs orf orfs orf oιt* oιfs. orf ιots

m vo sj cπ rfs co cπ ui oo m rfs to cΛ Oo w cΛ it* cπ to oo vo do en M oo m vo OΛ si rfs ^s J VD M tO OO m OΛ OO m W M VO m co w m m cΛ co m oo oo m vo si its rfs cΛ it _* Ul sl o sl i w rfs M W W OΛ M sl CΛ OO VD CO W CO W Ui OΛ rfs O

O OO W tO CΛ W W W OO M lO VO m M VD OO ιt» OΛ VO W M V0 OΛ CΛ CΛ W 00 ιt* m CO 03 0Λ ιt* W W m m M C0 0Λ W vo vo oo si ui vo rfs sj o oo o o _Λ vo oo co cn 00 rfS 00 CΛ C0 O M O C0 θ m 00 t0 Cπ CO O ιt* M O CΛ s] 00 VD W O

w w w M M W w w rfs rfs. it* M M M _ ,_, ,__ M M M M M M M 0 _0- 0 —0 . M M M M M rfrfs irfts* rfrfss W W W W W o o W W OO OO OO OO OO OO OO OO VO OO OO VD VD VD VO VD VO VD VO rfs rfs VO VO VO VO OO OO OO W W W M M M M M

2 2 O O O O O O O O O O O O " ^{^} O O O O O Ω 2 2 2 ro ro ro d d d d d d 2 Ω ^{O Q} o o ϋ tn a > W d ^O d ^O d ^O d ^O Ω ^O Ω Ω ro 0 ro ⁰ X 2 2 2 2 2 w w w M M M M w w M M w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o tn oΛ cn cn oΛ CΛ CΛ CΛ CΛ CΛ CΛ cΛ CΛ m m m m m m m m m m m m m m m m m m m m m m m m m m m m m

w w w M

W W rfs rfs rfs V-^ ^ ^ ^ i-* ^ 00 t θ i- ^χ - ^χ t- ^χ y- t- ^χ t-> t- ⁱ ts) o W W W OO CO OO OO OO OO OO OO rfs CD OO M M VO VD VO VO VO VO VO m 2 O O O O O O O O O O O O O 0 0 0 0 0 0 2 2 2 ro ro r r d d d d d d d d Ω d d ro ro n w ow ow M w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m o en ocΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ om om om om om om om om om om om om om om om om om om om om om om om om om om om om om w M M M M M M M w M it* W M OO CO M OO M OO M W OO OO OO W W M M o 00 ** M OO rfs CO VO rfs VO frs OO O CO tO rfs M M VO CO O 2 O 2 2 0 2 0 O O 2 2 0 0 O O O O d ro d W Ω Ω d Ω W d > d

W W W W M M W

rfs θΛ m s] ιts VD m cθ CO s] OO CO CΛ lt* sJ CD . VO _ 0_0_ 0_0_ 0_0_ C_Λ_ CO rfs CO rfs O OO OΛ to m m sj sJ rfs CO sl rfs rfs rfs sl CD lO rfs rfS M 00 sJ M 00 Ui s] rfs ιt* W W m W ιt* ιts W CΛ VO VD 0Λ rfs O sJ t W CO O sl VO CO rfs rfs W sl OO VD O s] CD

CΛ CB W CΛ lO CO VO CΛ sJ ifs OΛ sl M ∞ sJ UI U VO CO CΛ VO W M its m vO ifs U CΛ ∞ sJ rfS M sJ M w sl cn o m θ C0 t M m UJ cn Cn W sJ W W M W ιts σN 00 CΛ ιfs W CΛ W sJ CΛ rfs UJ rfs tJ. W W M C0 O 00 M rfs CO rfs

0 -O W M _r M ₀₀ M _∞ M ₀₀ M _O - ₎ M w it* O _- W W W W W W W M M O_ O_ O_ o_ O_ O_ M O_ _{∞ ∞ or} M _{∞ o O} - ₎ o o o o O O O O O O O O O 2 2 2 O O O O O O 2 2 2 2 d > > > d d d d Ω Ω Ω Ω Ω Ω w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m O O O _O O O _O O O _O O O O _{O O} O O O O O O O O O O O O O O O O O O O O O O O O O O O

CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ <n σ> CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ

30 -si M M M M M M M M M c o M M M 00 CO 00 00 00 00 M M M M w W W OO OO OO OO W W W W W W W W M M M M M M M M M M M W W w r <* ^» VO VO VO ifs. rfS rfs rfs rfs rfs. VO VO VO VO M O - O - it -* rfs rfs it* O O O O O O O O OO OO OO OO OO OO OO OO CD OO OO O O m 0 2 2 0 0 0 0 0 0 0 0 0 0 2 O O O O O O _O O _O O Ω Ω Ω Ω 2 2 __ 2 _. 2 Ω Ω Ω Ω O Ω 2 2 § ro W Ω Ω > > > Ω Ω Ω Ω W d d d d cn w > > > d d d d d Ω Ω Ω Ω Ω Ω

M M M M W W W W W w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m cπ i o CΛ oCΛ oCn oCΛ oCΛ oCn oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCn ocn oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oCΛ oen oCΛ oCΛ o o o o o w M w w

00 rfs M 00 0O M 0O M 0O 0O M 00 C0 M M M CD M 00 03 00 00 M w rfs M M W rfs 00 W W 00 M 03 M 00 M 00 M w co rf CO CO rfs CO rfs CO rfs rfs VO rfs rfs CD VD CO rf CO rfs rfs rfs CO VO rfs CO VD O rfs VO rfs o lO VO rfs VO rfs OO lO VO M o o 0 0 3 ⁽ ^ ⁽ ^ ^!2 ! 0 0 0 0 0 0 O O O 2 O 2 2 O O O O o o o o O 2 O O O O 2 2 ro w w ro ro ω > Ω W ω w ro ro Ω ro ώ w > Ω Ω d w w w w w w M w w

OΛ VO CO ιt* W 00 m VD M m UI 00 s] 00 rfs θΛ M CD lO rfs CO CO sl cπ rfs CO OΛ W m sl VO VO CΛ CΛ rfs CO OO CD W sl CO OO CO UI M CΛ sl W its its CO lO OO Ui CΛ sl M its it* M CO O rfs Ul to m W M CΛ M CΛ M CΛ M CΛ CΛ sl CΛ sJ VD O M sl o rfs O it* VO W CO rfs lO CD VD Ul W to M m sj Ul rfs W M lts CO VD O tO its lO OO CO CO Ui ifs OΛ 00 sl M M 00 O O W sj Ul Ul CΛ sl OO rfs OO rfs W sJ M w O CΛ 00 rfs si w w co m cΛ rfs m cΛ m rfs ιt _* si uι oo uι oo

W W W W W W W W OO OO W W W W W W W W W OO M W W o o o o o o co vo

O O O O O O O O O O w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m ui cj. cn o sJ osJ os] os] osJ os] osl osl osJ os] osJ osl osl osJ os] osJ os] osJ osl osl osJ osl osJ osl osJ osJ osl oOΛ oCΛ

w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m cn cn o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o o

W W W W 0O W W W W W W O3 W W W W 0O M 0O W 0O W W W W W W M W 00 M W W M W W W W W oo o O O rfs o M rfs O O rfs CO rfs O rfs W W O O W CO O it* VO W W VD o o M W VD VO rfs O 2 O O O o o o o O O O 2 O O 2 O O 2 O 2 2 o o O 2 O o o 2 o O O O 2 > d > ro > d > > > d W W > d > W W > d w d > w w M M M M W M M > d Ω W

C sl CXJ VO rfs rfs M m cΛ sJ W M ^s J CΛ CΛ CXJ ^s l W CΛ C» m θo m M tO cn ιts tXJ CΛ m tO ^s J l ^j l W M CO CΛ t Ul C» C^ CD O Cn M tO UJ sJ IΛ CO O VO CΛ O CΛ it-s CΛ M ∞ sl W its lJI CO Ul M O W VD M lO O CO m M VD O CΛ M CΛ tO CΛ W sJ M VD tn CΛ rfs CΛ ιt* m sJ 00 m CΛ W CΛ VO CΛ W CD M W ιts rfS 00 W sl O V0 m VD M ιt* V0 CΛ W V0 CΛ C0 m C0 sJ UI vo co sj M θo o rf , ιt^ ιt* s] m o M tn oo o vo tj m o t o w eΛ e» s] t ιt* cΛ CΛ sj M s uι u ^, ιts uι W sj

-^ ^ ¹ ,-> ^ \-* -> -> > i-> M M M M

OΛ OΛ CΛ CΛ CΛ M 00 CΛ CΛ CΛ 00 OΛ 0O M M CΛ CΛ M CΛ CΛ CΛ CΛ 0O O0 00 0O M M M M M M M CO OO OO OO OO OO OO OO

W W M M VO rfs W W W rfs W rfs ω vO W W VO W W W W ιfs rfs rfs rfs VO vO VO VO vO VO VO VO ιts ιt» ιts rfs rfs rfs rfs. ιts. O O O 2 o .. o O 2 o o o 2 o o o o o o o o o o o o o o o o o o o o o o o o d d d W tM ro W d Ω Ω M w w w d ^" d ^" d ^{" "} d d d d W W W W tSl tM IM IM W W W W

M M w w w w w M M w M M M M M M M M M M W W W W W W W W w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m o _(-J o _(- _ oμ ^j oμ ^j o_ι o ₍ _- o ₍ _- o|__ o^ o|_. o ₍ _- o|_- o_» o|-_ o|-_ o|-_ oM oM oM oM oM oM oM oM oM oM oM oM oM oM oM oM oM oM oM oM oM o oM oM oM oM CO UI UI UI UI M M M M M O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O 00 CO CΛ rfs W VD VO rfs rfs W W it* rf W

w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w tπ ui cπ m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m cπ O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

₍ _. _| _, _(- _ . |-_ _(- _ l_- >_» _> _» |__ (_- |-_ M M M M M M M M M M M M M M M M M M M M M M M M M M M M

CO IO IO CO CO W M M M M M O O O O O O O O O O O O O O O O O O O O O O O O O O O

M M M I-* M M M M M M M M M M M M M M M M μ_ ,__ ,_, M M M CΛ CΛ tO Cn CΛ Cn CΛ CΛ CO M OΛ OO OO CΛ CΛ CO CΛ CΛ CΛ OO OO OΛ OO CΛ M M 0O 0O OΛ CΛ 00 0θ σ. CΛ oo oo cn M 00 00 OΛ

W M W M M W W s C s s W W it* W W W rfs rfs W rfs W CD VO rfS ifs W W rfs rfs W W VO rfs W VO rfs It* w O O O O O O O O 2 2 0 0 2 0 2 Ω 2 o o o o o O O O O O O o o ω ro Ω Ω Ω Ω W r W d Wo d d Ω Ω W Ω d W Ω d

W W w d ro d w w w w M w w w M M w d

W W M M W W M

CO m OΛ its M m m W rfs sJ M CΛ M CΛ CO VO W OO OO CΛ sl M M CΛ m oO OO VO OO sl sl OO OΛ m M CO OΛ CO W M s] M Ul CO sJ Ul W CO OΛ sl rfs OO OΛ OO O rfs CD VO tO ∞ m CΛ U' CΛ VO VO W sl iti rfs W if^ OO CΛ VO sl tO M VO CO O sl

M W W O m CΛ W W m CΛ tO UI M W rfs CO m O OO O sl sJ rfs O sl O W Ul M CO Ul OO M VO M VO VO VD VO Cπ O CO CO M O O CO tO ifs rfS sJ Ui Ul M M OΛ O O Ui VD sl rfS its Ul CO sl tO rfs M VO W M rfs Ul sJ sJ M W M M OO O

w w w w w w w w w w w w w w w w w w W OΛ CΛ W W W W W CΛ CΛ OΛ W W W W W W W y-^ y-> t-^ M w m m m m cπ ui ui ui ui cπ cπ cπ ui ui vo r _f ._s. t _ _N j. w_ . m._ m.- rf._. r _{f 1} (s r _f rfs. κ j tJ o θΛ θ _s rf—s - it*-* rf *-s vo to vo vo

O O O O O 2 2 2 2 2 2 2 co co co cπ to O O ^ O O O O O O O 2 2 2 2 2 2 2 2 2 2 2 O to to ro ro ro Ω Ω Ω Ω Ω W > W W W W M W

M M M w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w iΛ m m m m m m m m m m m m m m m m m m m m m m m m m m m m π n tn O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w _l o io io io ω io ui io co co co ui io io co co co io w w w w w w w w w w w w w w w w w w w w w w w w

CO M c en w M w W W W w w W OΛ W W W M M M CΛ W M W W M W W M. OΛ W W M

CD w m co it* rf to n co it* m rfs it* w m ιt» Ul CO CO VD M m VO rfs m vo en m cΛ vo w it* CΛ VO CO 2 O O O o 2 O O O O O O O O O o o o 0 0 0 0 0 2 0 0 0

-J W > W d W ro > d d

M w w 2 O

M d

H

C H m CO OΛ OΛ 03 co w si co w m si 00 it* it* vo t M si ui sj oΛ m co si oo oo m M o si si w OΛ m vo sj co W CO sl OΛ O CO sj sl M OO rfs sJ Ui m rfs OO s] rfs co ιts ιt* co oo s ^j co s] θ si s ^j oΛ θΛ si oo w ιt* s cπ m co o x m O M O W m OO VO sl OO O rfs m m rfs M cn M to uJ ui w ui cn cn w co its si w o tO sl its rfs o W M VO m M M m CO OO its Ui OΛ Ul sl sl W CΛ O Ul Ul O Ui Ul VD M m rfs W θ m θ O OO ιt* lO CΛ VO s] o W O CΛ Ul tO lO UI CO CO

H

3 sj c W W W W W W W W W W W W W W W W W W W W W CΛ W W W W W W CΛ CΛ W W W W W W W r .3 m m m m m m m m m m m m m m m m m m m rfs its w m m m rfs its rfs w w cΛ CΛ CΛ CΛ its rfs rf m O O O O O 2 2 2 2 2 2 2 2 2 C0 to to C0 C0 Ω O Ω O O Ω Ω O Ω 2 2 2 2 2 2 2 2 to ro ro ro ro w Ω Ω Ω Ω Ω W d cn w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m cn cn O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w lo io io ω co io io co ω io co co co co io io io co ui w w w w w w w w w w w w w w w w w w w w w w w

rfS ιt* m ∞ W VO VO l tX3 ^s l M ^s J sl Ui m m C» m s] CΛ rfS ιtS sJ in sl CΛ M ιfs m M C» ιts VO ιtS s] M CO M m ∞ m eX3 W VD sJ M rf^ tO CΛ W m CΛ CΛ M W M tO ιfs Ul CO CO M ιf-s C» VO lO VO O sl tn VO M CΛ tO O sJ rfs W sl O M

CXI CΛ m W O CΛ ιfs W M M ιt^ ιf-* ιf-* ιfs M sJ ^s l VD CΛ s] CO M Ui M CO M M CO CΛ m M m rfs W VD VO M OO M CΛ m rfs e» M m W CΛ VO ιt* O W m CO VD m CO CD VO sl VO VD CΛ VO s] CΛ W OO lO sJ Ul M O sl OΛ W sJ sJ CO sJ M W Ul rfs Ul

M M M W W W M t- ¹ -^ r-^

W W CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ en CΛ CΛ Ui Ui m - m~ c-Λ -CΛ c-n c-Λ c-n c-Λ c ₀ Λ < ₀ n c-n c-Λ s-i o o rfs ιt* s] O o rfs O O M M M M O O O O o

CO to 2 2 2 2 O O O O O O O O O O O O O O O O O O O 2 2 O O p Q O O O O O o

Ω Ω d to ro w > >

M rø ro ω d W d W d W w M w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w c_n i_n c_n. c_n. _. m m m m m m m m m m m m m m m m m m m m m m m m m m cn π i cπ O O O O _{O O O O O O} O O _{O O} O O O _O O O O O O O O O O O O O O O O O O O O O O O Ω O

CO UI UI UI UI UI UI UI UI UI UI W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W O O O O O O O O O O O VD VO VO VD VD VO VD VD CO CXJ OO OO OO _s l _s l _s l sl - _s l _s l _s l _s l _s J _s l _s l sl _s J _s l _s l _s l _s l s]

3 w r- ¹ r-^ -^ M M M M M c Λ CΛ CΛ CΛ CΛ CΛ CΛ C cn o CΛ CΛ CΛ CΛ tO CΛ CΛ Cn CΛ CΛ CΛ CΛ CΛ C

O s] O O rfs O en M \-^ t- ¹ ^ i-> ^ O O O O oΛ

CO CO 2 2 2 2 0 0 0 0 0 O O O O O O O o o o o 2 2 O O O O O O O O O o Ω Ω O d d ω w ω ω

M M w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m ui o CO oIO oIO oIO oIO oIO oIO oIO oIO oCO oCO oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW oW O O O O O O O O O O O CO VO VO VO VO VO VO VD VO OO OO OO OO OO sJ sJ sj' sj , s ^. ]- s ^. j ^. s ^. ] ^. s ^. j, s ^. j ^. s ^. j, s] s] s] s] sj s] sj

OO sl C» M M ιt* C» m M m C» sJ M ιfs C ιts. CD sJ VO VD ιfs M M W M tn sl CO VO tO ιfs. M sJ UJ t tO W s^ ui oo m m cΛ m cΛ si w ifs w so oΛ co w m o oo o rfs cΛ rf M vo M o cΛ m m sj co o M O sj it o m vo

M W to o m rfs M W ui oo io m m m si o W OO tO rfs W sJ OΛ M VD OO eΛ rfs rfs m sl ui CΛ sl ui J VO CΛ sl O W sJ Ui M rfS sJ O OO O W Ui OΛ sJ M sl W CD to m θ sj o ιf- _* ιts. w m vo W si w oo m tn vD s] rfs uι co oo M rfs co

WW WW WW WW WW WW WW WW WW WW WW WW WW WW WW WW WW WW CCΛΛ CCΛΛ CCΛΛ CCΛΛ WW WW WW WW WW WW WW WW WW WW WW WW WW WW WW CCΛΛ CCΛΛ CCΛΛ CΛ CΛ

L mn imπ imn icoo icoo iuoi uuii uuii uuii uuii uui uuii cmπ m cmπ mm mm mm tuoi coΛΛ mm mm m mm mm mm ccΛΛ CCΛΛ CcnΛ ccnn ccΛn ecnn ccΛn ttoo uuii uuii uuii ccΛΛ CCΛΛ CCΛΛ C enΛ m m 2 2 2 0 0 0 0 0 0 0 ' O^ ' O ^* ^ to to r ton totn t ton t ton r ton a 2 o0 o0 o0 _2. _2- O0 O0 _2_ __ - 2. Z 2 O O O O O o O o O O O __ - . __ 2 O Ω Ω Ω Ω Ω Ω W W d d d >

M M w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m

0 0 0 0 0 0 0 0 O 0 O O O O 0 0 0 O 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 to ui ui ui ui ui ui ui ui Ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui UJ Ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui

CO CO tO Ul Ul Ul Ui Ui UI Ul Ui Ui UJ UI Ul Ul Ui Ul W W W W W W W W W W W W W W W W W W W W W W W W CΛ W W W CΛ W W W mcΛ ιmn ccΛΛ tcoo co 0~ "2 "20 ^" ~ o -

VO its CΛ CD CO CO rfs oΛ CD sJ sJ M m ifs M O W CO OO sJ M VD W OO CΛ rfs CD rfs W O

W W W W CΛ CΛ CΛ co ui u ⁱ ui cΛ CΛ CΛ 0 O O O 2 2 2 w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m ui 0 IO 0UI 0UI 0U) 0UJ 0UI 0UI 0UI 0UI 0UI 0UI 0UI 0UI 0UI 0UI 0UI 0UI 0U ⁾ 2U1 2UI 2UI 2UI 2CO 2CO 2UI 2UI 2UJ 2U ^I 2UI 2UI U2I 2UI U2J U2I 2UJ 2UJ U2I 2UI 2UI 2UJ 2UI 2UI CO Ui Ui UI UI Ul Ul Ui Ul Ui UI UI Ul UI Ul UJ UI Ul W W W W tO W W W W W W W W W W W W W W W W W W W

M M

W W W W en W CΛ W W W W W W W W W W W W W tn W W CΛ W W W W CΛ W W CΛ W W W CΛ W W W CΛ W W ιt** m m cΛ m cΛ θΛ CΛ ι ^* s. m m cΛ m cΛ en ιf ^* * m cΛ to cΛ UJ CΛ Ui uι uι cΛ m cΛ CΛ m ιo cΛ m cΛ CΛ m m cΛ CΛ m cΛ io 2 0 > O to 0 O 0 2 O to O 0 0 > 2 2 O > O« 2 P> 2 O O ω 2 0 0 2 O O 2 0 0 2 O 0 2 2 0 O O 0 0 O 2 0 Ό

M > ω ω ω ω ω d M ω

rfs W tO sJ CΛ VO sl VO m VD OO VO CΛ si cD co rfs oΛ OO si co cΛ rfs co cΛ s ^j co ui i ui m m its sj cπ sj rf cπ M sj oΛ O O VO CO Ul sl sl rfs OΛ OΛ VO W OO sl itS its rfS sl W OO W m M O OΛ W O O rfs to m sl rfs W CO OΛ CΛ tO UI CO OO si oo m w M M o m oo to o CΛ M O W m M rfs rfs Ul OO sl cΛ s Ul O tO sl CO VO OΛ O rfs sj CO M W M 00 O m m OO O CΛ sJ Ui W rfs o OO CO oo co vo m rfs ifs si m oΛ M oo oo m sl sl CΛ ifS its O M its Ul W CO Ul l M rfs

W W W CΛ CΛ CΛ CΛ CΛ W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W m m m m m m m m m m m to ui ui ui ui ui m m m m m m tΛ CΛ CΛ cn cΛ CΛ cΛ CΛ CΛ CΛ CΛ CΛ CΛ CΛ m m m m 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 2 2 > > > > > > ω ω ω ω ω ω d d d d d d d d w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O lO UI UI Ul Ui UI Ul Ul UI UI UI Ui Ul UI UI UI UI UI UI UI Ul UI Ul Ul Ui UI UI UI UI Ui UI UI UI Ui UI Ul Ui UI UI Ui Ui Ul co ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui co ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui ui W

M CO

"°

3 C v _o W W W W OΛ CΛ CΛ CΛ W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W W w r m m m m m m m m m m m m m co ui ui u ⁱ u ⁱ u ⁱ m m m m m cΛ CΛ CΛ CΛ CΛ CΛ CΛ OΛ CΛ CΛ CΛ CΛ CΛ cΛ CΛ m m m 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 2 2 g > > > > > > > ω ω ω ω ro d d d d d d d d r- ⁱ i- ^k t- ⁱ t- ⁱ t- ^{i Λ} t- ⁱ - ⁱ w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m m ui tπ cπ O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O

CO UI UI UI UI UJ UI UI UI UI UI UI UJ UI UI UI UI UI UI UI UI UI UI UI UI UI UJ UJ UI UI UI UI UI UJ UI UI UI UI UI UI UI UI U1 UI UI UI UI UI UI UI UI UI U1 U1 UI U1 U1 U1 U1 UI UI UI UI UI U1 UI U1 UI UI UI UI UI U1 UI U1 UI U1 U1 U1 U1 U1 U1 U1 U1

CΛ W W W W W W W W CΛ W W W W W W W W W W CΛ W CΛ W W W W CΛ W CΛ W W W W W W W W m rf tJ C cn ιt* m rf m ιts u rfs. m m cΛ t cΛ ιt^ m m c cn c ιf^ m m cΛ C cn ιfs m cΛ c t cΛ

0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 2 0 2 0 0 0 0 2 0 0 0 0 2 0 0 0

> > Ω W > ω > > > > Ω > > Ω > ω > to > > Ω

M

sl lJ1 CΛ s ^] M C» sJ CΛ CD m sJ lO W OO tO M rfs VO sl CΛ VO VD sl W VD M OO ιts sl CO lΛ ι ^* S ιt* ιt* tO OΛ CΛ ∞ m "^ O ιt* CΛ C» CΛ VD m W M tO M U) W VD VO O C» sl W cn ιfs W Cθ m C» sl sl U sl CΛ CO in M VD W lO CO VO CO rfs CO M M m O W OΛ sl W rfs O M CΛ tO W en OO M W sl in its cΛ OO sl O O CΛ O 00 00 rfs O Ul CΛ M O rfs CΛ Ul s] 00 it* O CΛ CΛ O m tO CΛ tO M M Ui W W sl CΛ CO m CΛ CO rfs O O tO O OO O CO M rfs to Ul O OO VD M tO O O OO CO

TABLE XIX

Table of angles between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 1-N- (N- imidazole acetyl-leucinyl) -amino-3-N- (4-phenoxy-phenyl- sulfonyl) -amino-propan-2-one.

Atom 1 Atom 2 Atom 3 Angle Atom 1 Atom 2 Atom 3 Angle

CO c

CD CO

H

H C HI m

CO x m m

H

1 r- s " ^"" m cn

M \-> i-* ^ w w W M OΛ M w w W CΛ CΛ W W w w w w w w w w os as os m m m vo M CO to ui CO W W Ul Ul m m m m m m M M M o co o 2 2 O O O O O O O O O O O 2 2 2 2 2 2 2 2 O O O

Ω Ω Ω W W d ° G > > > > > > > W W W W w w w w w w

VO VO

co rfs 00 W m oo W 00 OΛ OΛ to M 00 m cn oo s 00 M W CO rfs M M VD OΛ m rfS CD to x sl it* CO CO rfs sj rfS CO s] vo m m 00 sl O its oo m CD W 00 VD CO 03 00 00 CΛ W CΛ m m

H sj

CO m J

IO cn

OΛ VO VO sl OΛ CO rfs W OΛ rfs CO CΛ O rfs CO w sl tO M O OΛ W CO rfs cΛ rfs to w exj vo m si o oo m co CO 00 W CO O to it _* en m co vo it* m rfs CΛ w m M O CΛ lO OO lO OΛ VO O OO ^s l M VO rfs iπ OO Ul sJ OΛ M

M CD m vo w w sl CΛ M CO VO m rfs M s] sl Ul w CO CO OΛ CO rfs OΛ W sl ON tO M CΛ rf VO sl 00 CΛ rfs rfs sj CΛ o M VO sl sj O CO rfs OΛ sl 00 CO to o m co m oo M to CΛ w 00 W M OΛ 00 s] oo Ul rfs Ul M VO CO sl rfs rfs sj o CΛ to en W Ul M W O VO Ul VD O ifs rfS sl sj rfs cπ co O M si rfs s sl Ul W M CO VO CΛ CO sj W CO CΛ 00 to co m m co M vo oΛ m oΛ its ifs W

3 si t-x μ_ι _ X-Λ j. ^c CΛ en CΛ W W w w cn CΛ CΛ CΛ CΛ CΛ CΛ r* !c-nt» CΛ Cn W W CΛ CΛ CΛ W CΛ W CΛ en CΛ M m m m M M W CO CO W in cn r-^ t-^ r-^ m w to M m O O O CO O to to O O O 2 2 2 2 Ω Ω Ω Ω Ω C0 C0 O O O 2 O O O ro Ω Ω Ω Ω Ω - Ω - > > cn w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m m m m m m m m m m m m m m m m m m m m m m m m m m m O 2 2 2 2 w w w w w 2 2 2 w w w 2 2 S 2 2 2 2 2 O O O O O O O O O O O O O w w w w w w w w w w w w w w w w w w w w w to ui CO Ul Ul Ul w w w w w w w w w w w w w w w M M

Cn CΛ W CΛ CΛ sl OO CO M OΛ sj Ul W rfs M CO M CΛ UI VO W sl rfs OΛ CO m W sl M rfs W VO CO OΛ CΛ CO W W it* O OΛ CΛ VO OΛ ^sj w m io m co its M W M vo m rfs vo rfs co

W CO W rfs M sJ M O s] to Ul M VO it* 00 rfs CO VD OΛ CO rfs CO OΛ M CΛ OO W M M M O rfs m its rfS sl cπ O _l ts CΛ VO M VO tO VD s cn m O VO OΛ 00 O sl M CΛ M w vo o o ^sj rfs w cπ oo cn cn w cΛ o cn cΛ its

^ y- t-~ ^ M M M as as as os CΛ CΛ CΛ CΛ CΛ CΛ cn cn CΛ CΛ CΛ CΛ CΛ CO OΛ CΛ CΛ OΛ OΛ OΛ OΛ OΛ OΛ CΛ OΛ OΛ OΛ CΛ CΛ CΛ OΛ CΛ CΛ

O O O O M M O O M M o o M M M ON OΛ rfs CO sl sl sj s] s] s] 00 00 00 sl sl sj sj 00 00 00 CΛ ON

O O O O 2 O O O O O O O O O O 2 O O O o o O O O O 2 2 2 2 2 2 2 o o O O o

> > > to to o ω to w ro W

W W W W W w w w w w w w w w w w w w w w w w w w w w w w w W W w cn cn cn n n cn cn cn cn cn cn m m m m m m m m m m m m m m m m m cn O O O O O O O O O O O O 2 2 2 2 2 O O O O O O O O O o o O O O O O

CO Ul Ul l Ul to ui ui ui ui to ui CO to o co to w w w w w w w w w w w w w w w w W W W W M - t-' i-' t-^ - ¹ o o O O O CO VO VO VD VO VD VO VO CO CD VO VD VO VO VD VD CO vo

o m sj to sj rf oo o CO M o o w s] CO CO rfs CΛ CO CD 00 O rfs. sj CΛ rfs CO Ul OO O UI VO IO OO OΛ W W to CO 00 s] oo n rfs rf rfs CO sj w sj CΛ 00 w M CD m vo M 00 M CΛ VD sl o ^s i oo oo ^sj ui cn vo rf ^s io

TABLE XX

Table of distances in Angstroms between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 3 (S) -3- [ (N-benzyloxycarbonyl) -L-leucinyl]amino-5- methyl-1- (1-propoxy) -2-hexanone.

Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist.

w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w m m m cπ cπ cπ cπ cπ π ui cn m cn cn cn cn cn cn in in in cn cn cn cn cn cn cn in cn in in cn cn cn O O O O O O O O O O O O 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 w w w w w w W W W W W W W W W W W W W W W W W W W W W w w

CD 00 00 00 sl sj sl j sj s oΛ OΛ CΛ CΛ OΛ CΛ m m m m m m rf rf rf co w M o o vo co vo

M

CΛ CΛ CΛ CΛ W W W W W W W CΛ W M W M W M OΛ W W M W W OO CΛ OO OΛ CΛ CΛ W W CΛ W W

M m o ui OΛ OΛ Ui cn oΛ cn cn w w vo cπ vo co co w rt* rfs vo m m it _* w rfs M to m w m ui

0 0 2 0 0 0 0 0 0 2 CO o O O O O O 2 2 O O O O o O O co O 2 O

> Ω to > d Ω W > d > W > to d w w Ω W

M w w M M W β

CO rfs rfs to rfs rfs ιt* U> W ιts rfs rfs U U W ιt* ιts ιfS. rfS |fs UJ UI |ts rfs U ⁾ ιfs rfs _l t* ιfs rfS ιts rfs rfs

C CD CO co to oo sj CΛ o o oo cn m O O CO Ul M rfs cn it* rfs co rfs. co

H CO W ui M CΛ rfs 00 o O OΛ M

H C w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w w H cn cn cn m m m m m m m m m m m m m m m m m m Ui cn cπ cπ cn cπ cn cπ cπ ui cn rπ O O O O O O O O O O O O O O O O O O O O O O 2 2 2 2 O O O O O O O co w w w w w w w w w w w w w w w w w w w w w w w w w w w M M x 00 00 00 03 sl sj sl sl sj s] sj OΛ OΛ OΛ OΛ CΛ CΛ en uι cπ u. cπ uι ui rfs ιt* rfs rfs W W O o CO CO CO m m M w w CΛ CΛ CΛ ON ON w w OΛ W W W W W W W w tn en w cΛ W W oo 00 O C W cn en M m CΛ M rfs CΛ m co w m it* rfs to m m

39 sl O 2 O O O 2 O 2 2 O O O O o O O O O o 2 2 O 2 c OO to > > ω Ω W r m-

OΛ rfs rfs tθ rfS ιt* rfS ιt* rfs tO Ui rfs rfs rfs Ui Ui W W rfs ifs rfs ui lO its rfs rfs CO its W ifs rfS its rfs rfs

VO OO m W W sl sl CΛ M o OΛ co m co o o ₀ 0 CO sj ui to co tn oo m M rfs ui oo io cπ ui co vo W Ul Ul sl CO OO W lO Ul M rfs ui cπ co to m rfs w co O M CO 00 W M rfs VO VO rf M W OO CO O VO OO tO sl rfs O Cπ rfs OD cn CΛ to in sl s] ui w 00 sl o w rfs si w m si W O OO OΛ CO O W s]

TABLEXXI

Table of distances in Angstroms between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor bis-(Cbz-leucinyl) -1, 3-diamino-propan-2-one.

Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist.

TABLE XXπ

Table of distances in Angstroms between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 2,2 '-N,N'-bis-benzyloxycarbonyl-L- leucinylcarbohydrazide.

Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist.

TABLE XXiπ

Table of distances in Angstroms between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor (lS)-N-[2-[ (1-benzyloxycarbonylamino)-3- methylbutyl]thiazol-4-ylcarbonyl] -N'- (N-benzyloxycarbonyl-L- leucinyl)hydrazide.

Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist.

TABLE XXIV

Table of distances in Angstroms between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 2-[N- (3-benzyloxybenzoyl) ]-2 '-[N'-(N- benzyloxycarbonyl-L-leucinyl) ]carbohydrazide.

Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist.

ι*o n

TABLE XXIV

N40 161CA 3.804 25N40 160C 4.036 25N40 161N 4.304 N40 162N 4.578 25N40 660 4.918

TABLE XXV

Table of distances in Angstroms between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 4- [N-[ (phenylmethoxy)carbonyl]-L-leucyl] -1-[N- [ (phenylmethoxy)carbonyl] -L-leucyl]-3-pyrrolidinone.

Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist.

TABLE XXVI

Table of distances in Angstroms between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 4- [N-[ (4-pyridylmethoxy)carbonyl]-L-leucyl]-1- [N- [ (phenylmethoxy)carbonyl] -L-leucyl]-3-pyrrolidinone.

Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist.

TABLE XXVπ

Table of distances in Angstroms between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 4-[N-[ (phenylmethoxy)carbonyl]-L-leucyl] -1-N[N- (methyl)-L-leucyl) ] -3-pyrrolidinone.

Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist.

TABLEXXVffl

Table of distances in Angstroms between atoms of the inhibitor and protein for all protein atoms within 5 Angstroms of the inhibitor 1-N-(N-imidazole acetyl-leucinyl) -amino-3-N- (4- phenoxy-phenyl-sulfonyl) -amino-propan-2-one.

Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist. Atom 1 Atom 2 Dist.

TABLE XXIX

Active site amino acid residues for Cathepsin K