Structure of PDB 3wv3 Chain A Binding Site BS05

Receptor Information
>3wv3 Chain A (length=168) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYKSHFMLP
DDDVQGIQSLYGPGDEDP
Ligand information
Ligand IDWLL
InChIInChI=1S/C15H13N3O3S/c1-21-10-4-2-3-9(7-10)8-16-14(20)12-17-13(19)11-5-6-22-15(11)18-12/h2-7H,8H2,1H3,(H,16,20)(H,17,18,19)
InChIKeyJBLVGKQIAQNLEM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370COc1cccc(CNC(=O)C2=Nc3sccc3C(=O)N2)c1
ACDLabs 12.01O=C(C2=Nc1sccc1C(=O)N2)NCc3cccc(OC)c3
OpenEye OEToolkits 1.7.6COc1cccc(c1)CNC(=O)C2=Nc3c(ccs3)C(=O)N2
FormulaC15 H13 N3 O3 S
NameN-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide
ChEMBLCHEMBL3337881
DrugBank
ZINCZINC000098209577
PDB chain3wv3 Chain A Residue 308 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3wv3 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.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		L218 H222 L239 F241 I243 Y244 T245 F252 P255
Binding residue
(residue number reindexed from 1)		L115 H119 L136 F138 I140 Y141 T142 F147 P150
Annotation score1
Binding affinityMOAD: ic50=24nM
PDBbind-CN: -logKd/Ki=7.62,IC50=24nM
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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Biological Process
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Cellular Component
External links
PDB RCSB:3wv3, PDBe:3wv3, PDBj:3wv3
PDBsum3wv3
PubMed25192810
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

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