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3WV3
Biol. Unit 3
Info
Asym.Unit (126 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (60 KB)
Biol.Unit 3 (119 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-13 COMPLEXED WITH N-(3-METHOXYBENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE
Authors
:
H. Oki, Y. Tanaka
Date
:
12 May 14 (Deposition) - 24 Sep 14 (Release) - 24 Sep 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Mmp-13, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Nara, K. Sato, T. Naito, H. Mototani, H. Oki, Y. Yamamoto, H. Kuno, T. Santou, N. Kanzaki, J. Terauchi, O. Uchikawa, M. Kori
Thieno[2, 3-D]Pyrimidine-2-Carboxamides Bearing A Carboxybenzene Group At 5-Position: Highly Potent, Selective, And Orally Available Mmp-13 Inhibitors Interacting With The S1 Binding Site
Bioorg. Med. Chem. 2014
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: FORMIC ACID (FMTa)
3b: FORMIC ACID (FMTb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: N-(3-METHOXYBENZYL)-4-OXO-3,4-DIHY... (WLLa)
5b: N-(3-METHOXYBENZYL)-4-OXO-3,4-DIHY... (WLLb)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
FMT
2
Ligand/Ion
FORMIC ACID
4
NA
-1
Ligand/Ion
SODIUM ION
5
WLL
2
Ligand/Ion
N-(3-METHOXYBENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE
6
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(16, 16)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:222 , HIS A:226 , HIS A:232 , FMT A:306
BINDING SITE FOR RESIDUE ZN A 301
02
AC2
SOFTWARE
HIS A:172 , ASP A:174 , HIS A:187 , HIS A:200
BINDING SITE FOR RESIDUE ZN A 302
03
AC3
SOFTWARE
ASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205
BINDING SITE FOR RESIDUE CA A 303
04
AC4
SOFTWARE
ASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:409 , HOH A:416
BINDING SITE FOR RESIDUE CA A 304
05
AC5
SOFTWARE
ASP A:128 , ASP A:203 , GLU A:205 , HOH A:501
BINDING SITE FOR RESIDUE NA A 305
06
AC6
SOFTWARE
HIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , ZN A:301 , HOH A:433 , HOH A:600
BINDING SITE FOR RESIDUE FMT A 306
07
AC7
SOFTWARE
TYR A:176 , HIS A:187 , ALA A:188 , PHE A:189 , PRO A:190 , HOH A:611 , HOH A:613
BINDING SITE FOR RESIDUE EDO A 307
08
AC8
SOFTWARE
LEU A:218 , HIS A:222 , ALA A:238 , LEU A:239 , PHE A:241 , ILE A:243 , TYR A:244 , THR A:245 , TYR A:246 , PHE A:252 , MET A:253 , PRO A:255 , HOH A:476 , HOH A:636
BINDING SITE FOR RESIDUE WLL A 308
09
AC9
SOFTWARE
HIS B:222 , HIS B:226 , HIS B:232 , FMT B:306
BINDING SITE FOR RESIDUE ZN B 301
10
BC1
SOFTWARE
HIS B:172 , ASP B:174 , HIS B:187 , HIS B:200
BINDING SITE FOR RESIDUE ZN B 302
11
BC2
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 303
12
BC3
SOFTWARE
ASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:423 , HOH B:449
BINDING SITE FOR RESIDUE CA B 304
13
BC4
SOFTWARE
ASP B:128 , ASP B:203 , GLU B:205 , HOH B:533
BINDING SITE FOR RESIDUE NA B 305
14
BC5
SOFTWARE
HIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , ZN B:301 , HOH B:464
BINDING SITE FOR RESIDUE FMT B 306
15
BC6
SOFTWARE
TYR B:176 , ALA B:188 , PHE B:189 , HOH B:566
BINDING SITE FOR RESIDUE EDO B 307
16
BC7
SOFTWARE
LEU B:218 , HIS B:222 , GLU B:223 , ALA B:238 , LEU B:239 , PHE B:241 , ILE B:243 , TYR B:244 , THR B:245 , THR B:247 , PHE B:252 , MET B:253 , PRO B:255 , HOH B:587
BINDING SITE FOR RESIDUE WLL B 308
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_073418 (W207G, chain A/B, )
2: VAR_063434 (H232N, chain A/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)
---
A/B
W
207
G
2
UniProt
VAR_063434
H
232
N
MMP13_HUMAN
Disease (MANDP1)
---
A/B
H
232
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:219-228,B:219-228)
;
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Label:
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
2
A:219-228
B:219-228
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Exons
(0, 0)
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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
(0, 0)
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CATH Domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (126 KB)
Header - Asym.Unit
Biol.Unit 1 (62 KB)
Header - Biol.Unit 1
Biol.Unit 2 (60 KB)
Header - Biol.Unit 2
Biol.Unit 3 (119 KB)
Header - Biol.Unit 3
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