Structure of PDB 3kek Chain A Binding Site BS06

Receptor Information
>3kek Chain A (length=164) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFM
LPDDDVQGIQSLYG
Ligand information
Ligand ID3EK
InChIInChI=1S/C24H26FN5O3/c1-15-10-19(11-21(28-15)23(31)26-12-16-4-8-20(25)9-5-16)22-27-14-30(29-22)13-17-2-6-18(7-3-17)24(32)33/h4-5,8-11,14,17-18H,2-3,6-7,12-13H2,1H3,(H,26,31)(H,32,33)/t17-,18-
InChIKeyPBYUEXSDWHTFAM-IYARVYRRSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02Fc1ccc(cc1)CNC(=O)c4nc(cc(c2ncn(n2)CC3CCC(C(=O)O)CC3)c4)C
CACTVS 3.352Cc1cc(cc(n1)C(=O)NCc2ccc(F)cc2)c3ncn(C[CH]4CC[CH](CC4)C(O)=O)n3
CACTVS 3.352Cc1cc(cc(n1)C(=O)NCc2ccc(F)cc2)c3ncn(C[C@@H]4CC[C@H](CC4)C(O)=O)n3
OpenEye OEToolkits 1.7.0Cc1cc(cc(n1)C(=O)NCc2ccc(cc2)F)c3ncn(n3)CC4CCC(CC4)C(=O)O
FormulaC24 H26 F N5 O3
Nametrans-4-[(3-{2-[(4-fluorobenzyl)carbamoyl]-6-methylpyridin-4-yl}-1H-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid;
(1r,4r)-4-((3-(2((4-fluorobenzyl)carbamoyl)-6-methylpyridin-4-yl)-1h-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain3kek Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kek Discovery of (pyridin-4-yl)-2H-tetrazole as a novel scaffold to identify highly selective matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		K140 F217 L218 V219 H222 A238 L239 F241 I243 Y244 T245 Y246 T247 F252 P255
Binding residue
(residue number reindexed from 1)		K37 F114 L115 V116 H119 A135 L136 F138 I140 Y141 T142 Y143 T144 F149 P152
Annotation score1
Binding affinityMOAD: Ki=4.4nM
PDBbind-CN: -logKd/Ki=8.36,Ki=4.4nM
Enzymatic activity
Catalytic site (original residue number in PDB) H222 E223 H226 H232
Catalytic site (residue number reindexed from 1) H119 E120 H123 H129
Enzyme Commision number 3.4.24.-
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0031012 extracellular matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3kek, PDBe:3kek, PDBj:3kek
PDBsum3kek
PubMed20005097
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

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