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Title :   CRYSTAL STRUCTURE OF CATHEPSIN K COMPLEXED WITH 7-METHYL-SUBSTITUTED AZEPAN-3-ONE COMPOUND

Authors :   D. S. Yamashita, Z. Baoguang

Date :   24 Jan 06 (Deposition) - 30 Jan 07 (Release) - 28 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Hydrolase, Sulfhydryl Proteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. S. Yamashita, R. W. Marquis, R. Xie, S. D. Nidamarthy, H. J. Oh, J. U. Jeong, K. F. Erhard, K. W. Ward, T. J. Roethke, B. R. Smith, H. Y. Cheng, X. Geng, F. Lin, P. H. Offen, B. Wang, N. Nevins, M. S. Head, R. C. Haltiwanger, A. A. Narducci Sarjeant, L. M. Liable-Sands, B. Zhao, W. W. Smith, C. A. Janson, E. Gao, T. Tomaszek, M. Mcqueney, I. E. James, C. J. Gress, D. L. Zembryki, M. W. Lark, D. F. Veber
Structure Activity Relationships Of 5-, 6-, And 7-Methyl-Substituted Azepan-3-One Cathepsin K Inhibitors.
J. Med. Chem. V. 49 1597 2006
PubMed-ID: 16509577 | Reference-DOI: 10.1021/JM050915U
(for further references see the PDB file header)

Molecule 1 - CATHEPSIN K
	Chains	:	A, B
	EC Number	:	3.4.22.38
	Engineered	:	YES
	Expression System	:	UNIDENTIFIED BACULOVIRUS
	Expression System Strain	:	SF9
	Expression System Taxid	:	10469
	Gene	:	CTSK
	Organism Common	:	RHESUS MONKEY
	Organism Scientific	:	MACACA MULATTA
	Organism Taxid	:	9544
	Strain	:	OSTEOCLAST

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ILI	2	Ligand/Ion	N-[(1S)-1-({[(3S,4S,7R)-3-HYDROXY-7-METHYL-1-(PYRIDIN-2-YLSULFONYL)-2,3,4,7-TETRAHYDRO-1H-AZEPIN-4-YL]AMINO}CARBONYL)-3-METHYLBUTYL]-1-BENZOFURAN-2-CARBOXAMIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ILI	1	Ligand/Ion	N-[(1S)-1-({[(3S,4S,7R)-3-HYDROXY-7-METHYL-1-(PYRIDIN-2-YLSULFONYL)-2,3,4,7-TETRAHYDRO-1H-AZEPIN-4-YL]AMINO}CARBONYL)-3-METHYLBUTYL]-1-BENZOFURAN-2-CARBOXAMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ILI	1	Ligand/Ion	N-[(1S)-1-({[(3S,4S,7R)-3-HYDROXY-7-METHYL-1-(PYRIDIN-2-YLSULFONYL)-2,3,4,7-TETRAHYDRO-1H-AZEPIN-4-YL]AMINO}CARBONYL)-3-METHYLBUTYL]-1-BENZOFURAN-2-CARBOXAMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:19 , GLN A:21 , CYS A:22 , GLY A:23 , SER A:24 , CYS A:25 , TRP A:26 , GLU A:59 , ASP A:61 , GLY A:65 , GLY A:66 , TYR A:67 , ALA A:134 , ASN A:161 , HIS A:162 , ALA A:163 , TRP A:184 , HOH A:392 , TYR B:67	BINDING SITE FOR RESIDUE ILI A 300
2	AC2	SOFTWARE	GLN B:19 , GLN B:21 , CYS B:22 , GLY B:23 , CYS B:25 , TRP B:26 , GLU B:59 , GLY B:65 , GLY B:66 , TYR B:67 , ASN B:161 , HIS B:162 , TRP B:184	BINDING SITE FOR RESIDUE ILI B 301

Asymmetric Unit

No.	Residues
1	A:22	-	A:63
2	A:56	-	A:96
3	A:155	-	A:204
4	B:22	-	B:63
5	B:56	-	B:96
6	B:155	-	B:204

(no "Cis Peptide Bond" information available for 2FTD)

(no "SAP(SNP)/Variant" information available for 2FTD)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CATK_MACMU	133-144	2	A:19-30 B:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CATK_MACMU	274-284	2	A:160-170 B:160-170
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CATK_MACMU	291-310	2	A:177-196 B:177-196

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CATK_MACMU	133-144	1	A:19-30 -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CATK_MACMU	274-284	1	A:160-170 -
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CATK_MACMU	291-310	1	A:177-196 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CATK_MACMU	133-144	1	- B:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CATK_MACMU	274-284	1	- B:160-170
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CATK_MACMU	291-310	1	- B:177-196

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSMMUT00000000786	1	ENSMMUE00000299516	chr1:129211826-129211722	105	CATK_MACMU	-	0	0	-	-
1.3a	ENSMMUT00000000786	3a	ENSMMUE00000005071	chr1:129210363-129210240	124	CATK_MACMU	1-40	40	0	-	-
1.4	ENSMMUT00000000786	4	ENSMMUE00000005074	chr1:129209777-129209655	123	CATK_MACMU	41-81	41	0	-	-
1.5	ENSMMUT00000000786	5	ENSMMUE00000005078	chr1:129209569-129209414	156	CATK_MACMU	82-133	52	2	A:1-19 B:1-19	19 19
1.6	ENSMMUT00000000786	6	ENSMMUE00000005083	chr1:129207797-129207579	219	CATK_MACMU	134-206	73	2	A:20-92 B:20-92	73 73
1.7	ENSMMUT00000000786	7	ENSMMUE00000005086	chr1:129203234-129203069	166	CATK_MACMU	207-262	56	2	A:93-148 B:93-148	56 56
1.8	ENSMMUT00000000786	8	ENSMMUE00000005089	chr1:129202799-129202694	106	CATK_MACMU	262-297	36	2	A:148-183 B:148-183	36 36
1.9a	ENSMMUT00000000786	9a	ENSMMUE00000005093	chr1:129200410-129199747	664	CATK_MACMU	297-329	33	2	A:183-215 B:183-215	33 33

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:215
 aligned with CATK_MACMU | P61277 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:215
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
           CATK_MACMU   115 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 329
               SCOP domains d2ftda_ A: (Pro)cathepsin K                                                                                                                                                                                             SCOP domains
               CATH domains 2ftdA00 A:1-215 Cysteine proteinases                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh.ee................hhh.eee...eeee....hhhhhhhhhhhh..eeeee...hhhhhh....ee...........eeeeeeeeee....eeeeee...........eeeee....hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA---------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------- PROSITE
           Transcript 1 (1) Exon 1.5           Exon 1.6  PDB: A:20-92 UniProt: 134-206                                  Exon 1.7  PDB: A:93-148 UniProt: 207-262                ----------------------------------Exon 1.9a  PDB: A:183-215         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:148-183            -------------------------------- Transcript 1 (2)
                 2ftd A   1 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with CATK_MACMU | P61277 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:215
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
           CATK_MACMU   115 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 329
               SCOP domains d2ftdb_ B: (Pro)cathepsin K                                                                                                                                                                                             SCOP domains
               CATH domains 2ftdB00 B:1-215 Cysteine proteinases                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhh.............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh.ee................hhh.eee....eee....hhhhhhhhhhhh..eeeee...hhhhhh....ee...........eeeeeeeeee....eeeeee...........eeeee....hhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA---------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------- PROSITE
           Transcript 1 (1) Exon 1.5           Exon 1.6  PDB: B:20-92 UniProt: 134-206                                  Exon 1.7  PDB: B:93-148 UniProt: 207-262                ----------------------------------Exon 1.9a  PDB: B:183-215         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: B:148-183            -------------------------------- Transcript 1 (2)
                 2ftd B   1 APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Papain-like (200)

Protein domain: (Pro)cathepsin K (41)

Human (Homo sapiens) [TaxId: 9606] (40)

1a	d2ftda_	A:
1b	d2ftdb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Cathepsin B; Chain A (207)

Homologous Superfamily: Cysteine proteinases (207)

Rhesus monkey (Macaca mulatta) (1)

1a	2ftdA00	A:1-215
1b	2ftdB00	B:1-215

(no "Pfam Domain" information available for 2FTD)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CATK_MACMU | P61277)

molecular function
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0001968	fibronectin binding	Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0043394	proteoglycan binding	Interacting selectively and non-covalently with a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
biological process
	GO:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	GO:1903955	positive regulation of protein targeting to mitochondrion	Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0051603	proteolysis involved in cellular protein catabolic process	The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
	GO:1903146	regulation of mitophagy	Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
cellular component
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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