Structure of PDB 2ovx Chain A Binding Site BS08

Receptor Information
>2ovx Chain A (length=159) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRV
YSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDEL
WSLGKGQGYSLFLVAAHQFGHALGLDHSSVPEALMYPMYRFTEGPPLHKD
DVNGIRHLY
Ligand information
Ligand ID4MR
InChIInChI=1S/C24H22N6O4/c31-20-24(21(32)28-23(33)27-20,30-15-13-29(14-16-30)22-25-11-4-12-26-22)17-7-9-19(10-8-17)34-18-5-2-1-3-6-18/h1-12H,13-16H2,(H2,27,28,31,32,33)
InChIKeyFMKQJGOROFNCGM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O=C1NC(=O)C(N2CCN(CC2)c3ncccn3)(C(=O)N1)c4ccc(Oc5ccccc5)cc4
ACDLabs 10.04O=C3NC(=O)NC(=O)C3(c2ccc(Oc1ccccc1)cc2)N5CCN(c4ncccn4)CC5
OpenEye OEToolkits 1.5.0c1ccc(cc1)Oc2ccc(cc2)C3(C(=O)NC(=O)NC3=O)N4CCN(CC4)c5ncccn5
FormulaC24 H22 N6 O4
Name5-(4-PHENOXYPHENYL)-5-(4-PYRIMIDIN-2-YLPIPERAZIN-1-YL)PYRIMIDINE-2,4,6(2H,3H)-TRIONE
ChEMBL
DrugBankDB07117
ZINCZINC000016052323
PDB chain2ovx Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ovx Crystal Structures of MMP-9 Complexes with Five Inhibitors: Contribution of the Flexible Arg424 Side-chain to Selectivity.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L188 A189 H401 Q402 H405 H411 L418 Y420 P421 M422 Y423
Binding residue
(residue number reindexed from 1)		L79 A80 H117 Q118 H121 H127 L134 Y136 P137 M138 Y139
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.70,IC50=2nM
Enzymatic activity
Catalytic site (original residue number in PDB) H401 Q402 H405 H411
Catalytic site (residue number reindexed from 1) H117 Q118 H121 H127
Enzyme Commision number 3.4.24.35: gelatinase B.
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:2ovx, PDBe:2ovx, PDBj:2ovx
PDBsum2ovx
PubMed17599356
UniProtP14780|MMP9_HUMAN Matrix metalloproteinase-9 (Gene Name=MMP9)

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