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3KEC
Biol. Unit 2
Info
Asym.Unit (122 KB)
Biol.Unit 1 (59 KB)
Biol.Unit 2 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN MMP-13 COMPLEXED WITH A PHENYL-2H-TETRAZOLE COMPOUND
Authors
:
H. -S. Shieh, A. G. Pavlovsky, B. Collins, M. E. Schnute
Date
:
25 Oct 09 (Deposition) - 10 Nov 10 (Release) - 16 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
S1' Inhibitor; Selective Mmp-13 Inhibitor; S1' Specificity Pocket; No Contact To Zn, Collagen Degradation, Disease Mutation, Disulfide Bond, Extracellular Matrix, Glycoprotein, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted, Zymogen, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
M. E. Schnute, P. M. O'Brien, J. Nahra, M. Morris, W. Howard Roark, C. E. Hanau, P. G. Ruminski, J. A. Scholten, T. R. Fletcher, B. C. Hamper J. N. Carroll, W. C. Patt, H. S. Shieh, B. Collins, A. G. Pavlovsky, K. E. Palmquist, K. W. Aston, J. Hitchcock, M. D. Rogers, J. Mcdonald, A. R. Johnson, G. E. Munie, A. J. Wittwer, C. F. Man, S. L. Settle, O. Nemirovskiy, L. E. Vickery, A. Agawal, R. D. Dyer, T. Sunyer
Discovery Of (Pyridin-4-Yl)-2H-Tetrazole As A Novel Scaffol To Identify Highly Selective Matrix Metalloproteinase-13 Inhibitors For The Treatment Of Osteoarthritis.
Bioorg. Med. Chem. Lett. V. 20 576 2010
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 4-{[({3-[2-(4-METHOXYBENZYL)-2H-TE... (3KEa)
1b: 4-{[({3-[2-(4-METHOXYBENZYL)-2H-TE... (3KEb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
3a: ACETOHYDROXAMIC ACID (HAEa)
3b: ACETOHYDROXAMIC ACID (HAEb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
3KE
1
Ligand/Ion
4-{[({3-[2-(4-METHOXYBENZYL)-2H-TETRAZOL-5-YL]PHENYL}CARBONYL)AMINO]METHYL}BENZOIC ACID
2
CA
-1
Ligand/Ion
CALCIUM ION
3
HAE
1
Ligand/Ion
ACETOHYDROXAMIC ACID
4
SO4
-1
Ligand/Ion
SULFATE ION
5
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(8, 8)
Info
All Sites
1: AC7 (SOFTWARE)
2: BC1 (SOFTWARE)
3: BC2 (SOFTWARE)
4: BC3 (SOFTWARE)
5: BC4 (SOFTWARE)
6: BC5 (SOFTWARE)
7: BC6 (SOFTWARE)
8: BC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC7
SOFTWARE
LYS A:170 , SER B:182
BINDING SITE FOR RESIDUE SO4 A 2
2
BC1
SOFTWARE
HIS B:222 , HIS B:226 , HIS B:232 , HAE B:271
BINDING SITE FOR RESIDUE ZN B 901
3
BC2
SOFTWARE
HIS B:172 , ASP B:174 , HIS B:187 , HIS B:200
BINDING SITE FOR RESIDUE ZN B 902
4
BC3
SOFTWARE
ASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205
BINDING SITE FOR RESIDUE CA B 903
5
BC4
SOFTWARE
HOH B:22 , HOH B:46 , ASP B:162 , ASN B:194 , GLY B:196 , ASP B:198
BINDING SITE FOR RESIDUE CA B 904
6
BC5
SOFTWARE
HOH B:45 , ASP B:128 , ASP B:203 , GLU B:205 , HOH B:277
BINDING SITE FOR RESIDUE CA B 905
7
BC6
SOFTWARE
LYS B:140 , ASN B:215 , PHE B:217 , LEU B:218 , VAL B:219 , HIS B:222 , GLU B:223 , ALA B:238 , LEU B:239 , PHE B:241 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , TYR B:246 , THR B:247 , LYS B:249 , PHE B:252 , HOH B:301 , HOH B:326
BINDING SITE FOR RESIDUE 3KE B 2
8
BC7
SOFTWARE
HOH B:67 , ALA B:186 , GLU B:223 , HIS B:226 , ZN B:901
BINDING SITE FOR RESIDUE HAE B 271
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_073418 (W207G, chain B, )
2: VAR_063434 (H232N, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_073418
W
207
G
MMP13_HUMAN
Disease (MDST)
---
B
W
207
G
2
UniProt
VAR_063434
H
232
N
MMP13_HUMAN
Disease (MANDP1)
---
B
H
232
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (B:219-228)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
MMP13_HUMAN
219-228
1
-
B:219-228
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3keca_ (A:)
1b: SCOP_d3kecb_ (B:)
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Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
Metalloproteases (zincins), catalytic domain
(647)
Family
:
Matrix metalloproteases, catalytic domain
(199)
Protein domain
:
Collagenase-3 (MMP-13)
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
1a
d3keca_
A:
1b
d3kecb_
B:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_3kecB01 (B:112-267)
1b: PFAM_Peptidase_M10_3kecB02 (B:112-267)
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Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-3kecB01
B:112-267
1b
Peptidase_M10-3kecB02
B:112-267
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Chain B
Asymmetric Unit 1
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Asym.Unit (122 KB)
Header - Asym.Unit
Biol.Unit 1 (59 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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