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2FTD
Asym. Unit
Info
Asym.Unit (78 KB)
Biol.Unit 1 (38 KB)
Biol.Unit 2 (38 KB)
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(1)
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
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: N-[(1S)-1-({[(3S,4S,7R)-3-HYDROXY-... (ILIa)
1b: N-[(1S)-1-({[(3S,4S,7R)-3-HYDROXY-... (ILIb)
View:
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Label:
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
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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Label:
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
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: THIOL_PROTEASE_CYS (A:19-30,B:19-30)
2: THIOL_PROTEASE_HIS (A:160-170,B:160-170)
3: THIOL_PROTEASE_ASN (A:177-196,B:177-196)
;
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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
[
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Exons
(5, 10)
Info
All Exons
Exon 1.5 (A:1-19 | B:1-19)
Exon 1.6 (A:20-92 | B:20-92)
Exon 1.7 (A:93-148 | B:93-148)
Exon 1.8 (A:148-183 | B:148-183)
Exon 1.9a (A:183-215 | B:183-215)
View:
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All Exon Boundaries
1: Boundary 1.4/1.5
2: Boundary 1.5/1.6
3: Boundary 1.6/1.7
4: Boundary 1.7/1.8
5: Boundary 1.8/1.9a
6: Boundary 1.9a/-
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2ftda_ (A:)
1b: SCOP_d2ftdb_ (B:)
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)
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:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2ftdA00 (A:1-215)
1b: CATH_2ftdB00 (B:1-215)
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)
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)
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
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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Show PDB file:
Asym.Unit (78 KB)
Header - Asym.Unit
Biol.Unit 1 (38 KB)
Header - Biol.Unit 1
Biol.Unit 2 (38 KB)
Header - Biol.Unit 2
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