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2YIG
Asym. Unit
Info
Asym.Unit (123 KB)
Biol.Unit 1 (115 KB)
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(1)
Title
:
MMP13 IN COMPLEX WITH A NOVEL SELECTIVE NON ZINC BINDING INHIBITOR
Authors
:
S. Gerhardt, D. Hargreaves
Date
:
13 May 11 (Deposition) - 29 Jun 11 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrolase, Collagenase 3, Mmp-13, Matrixmetalloprotease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. D. Savi, A. D. Morley, A. Ting, I. Nash, K. Karabelas, C. M. Wood, M. James, S. J. Norris, G. Karoutchi, N. Rankine, G. Hamlin, P. A. Macfaul, D. Ryan, S. V. Baker, D. Hargreaves, S. Gerhardt
Selective Non Zinc Binding Inhibitors Of Mmp13.
Bioorg. Med. Chem. Lett. V. 21 4215 2011
[
close entry info
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Hetero Components
(4, 13)
Info
All Hetero Components
1a: 4-(4-{[(3S)-3-HYDROXY-1-AZABICYCLO... (5ELa)
1b: 4-(4-{[(3S)-3-HYDROXY-1-AZABICYCLO... (5ELb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5EL
2
Ligand/Ion
4-(4-{[(3S)-3-HYDROXY-1-AZABICYCLO[2.2.2]OCT-3-YL]ETHYNYL}PHENOXY)-N-(PYRIDIN-4-YLMETHYL)BENZAMIDE
2
CA
4
Ligand/Ion
CALCIUM ION
3
NA
3
Ligand/Ion
SODIUM ION
4
ZN
4
Ligand/Ion
ZINC ION
[
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:183 , LEU A:185 , LEU A:218 , HIS A:222 , GLU A:223 , GLY A:237 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , TYR A:244 , THR A:245 , THR A:247 , HOH A:418 , HOH A:427
BINDING SITE FOR RESIDUE 5EL A 1273
02
AC2
SOFTWARE
GLY B:183 , LEU B:184 , LEU B:185 , HIS B:222 , GLU B:223 , GLY B:237 , LEU B:239 , PHE B:241 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , THR B:247 , PHE B:252 , HOH B:406 , HOH B:434
BINDING SITE FOR RESIDUE 5EL B 1270
03
AC3
SOFTWARE
HIS B:222 , HIS B:226 , HIS B:232 , HOH B:500
BINDING SITE FOR RESIDUE ZN B 1271
04
AC4
SOFTWARE
HIS B:172 , ASP B:174 , HIS B:187 , HIS B:200
BINDING SITE FOR RESIDUE ZN B 1272
05
AC5
SOFTWARE
ASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:416 , HOH B:414
BINDING SITE FOR RESIDUE CA B 1273
06
AC6
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 1274
07
AC7
SOFTWARE
HIS A:222 , HIS A:226 , HIS A:232 , HOH A:480
BINDING SITE FOR RESIDUE ZN A 1274
08
AC8
SOFTWARE
ASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:431 , HOH A:464
BINDING SITE FOR RESIDUE CA A 1275
09
AC9
SOFTWARE
HIS A:172 , ASP A:174 , HIS A:187 , HIS A:200
BINDING SITE FOR RESIDUE ZN A 1276
10
BC1
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 1277
11
BC2
SOFTWARE
ASP A:128 , ASP A:203 , GLU A:205
BINDING SITE FOR RESIDUE NA A 1278
12
BC3
SOFTWARE
THR B:126 , ASP B:128 , ASP B:203 , GLU B:205 , HOH A:533
BINDING SITE FOR RESIDUE NA B 1275
13
BC4
SOFTWARE
ALA A:188 , HOH A:504 , HOH A:481 , HOH A:543 , HOH A:551
BINDING SITE FOR RESIDUE NA M 811
[
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
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)
;
View:
Select:
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
(5, 10)
Info
All Exons
Exon 1.2 (A:104-121 | B:104-121)
Exon 1.3 (A:121-171 | B:121-171)
Exon 1.4 (A:171-213 | B:171-213)
Exon 1.5 (A:213-267 (gaps) | B:213-267)
Exon 1.6 (A:267-272 | B:267-269)
View:
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All Exon Boundaries
1: Boundary 1.1a/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
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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
1.1a
ENST00000260302
1a
ENSE00001105391
chr11:
102826463-102826315
149
MMP13_HUMAN
1-40
40
0
-
-
1.2
ENST00000260302
2
ENSE00001105386
chr11:
102826222-102825981
242
MMP13_HUMAN
41-121
81
2
A:104-121
B:104-121
18
18
1.3
ENST00000260302
3
ENSE00001105401
chr11:
102825335-102825187
149
MMP13_HUMAN
121-171
51
2
A:121-171
B:121-171
51
51
1.4
ENST00000260302
4
ENSE00001105398
chr11:
102825010-102824885
126
MMP13_HUMAN
171-213
43
2
A:171-213
B:171-213
43
43
1.5
ENST00000260302
5
ENSE00001139473
chr11:
102822902-102822741
162
MMP13_HUMAN
213-267
55
2
A:213-267 (gaps)
B:213-267
55
55
1.6
ENST00000260302
6
ENSE00000930343
chr11:
102820956-102820839
118
MMP13_HUMAN
267-306
40
2
A:267-272
B:267-269
6
3
1.7
ENST00000260302
7
ENSE00000930342
chr11:
102819887-102819754
134
MMP13_HUMAN
306-351
46
0
-
-
1.8
ENST00000260302
8
ENSE00000930341
chr11:
102818779-102818620
160
MMP13_HUMAN
351-404
54
0
-
-
1.9
ENST00000260302
9
ENSE00000930340
chr11:
102816478-102816375
104
MMP13_HUMAN
404-439
36
0
-
-
1.11b
ENST00000260302
11b
ENSE00002188786
chr11:
102815095-102813724
1372
MMP13_HUMAN
439-471
33
0
-
-
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2yiga_ (A:)
1b: SCOP_d2yigb_ (B:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d2yiga_
A:
1b
d2yigb_
B:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_2yigB01 (B:112-267)
1b: PFAM_Peptidase_M10_2yigB02 (B:112-267)
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Clans
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-2yigB01
B:112-267
1b
Peptidase_M10-2yigB02
B:112-267
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