Structure of PDB 4jpa Chain A Binding Site BS05

Receptor Information
>4jpa Chain A (length=165) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNF
TRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDD
DETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYHFMLPDD
DVQGIQSLYGPGDED
Ligand information
Ligand IDAZ6
InChIInChI=1S/C21H23N7O5S/c1-21(18(29)25-20(30)26-21)14-34(31,32)28-7-5-27(6-8-28)19-23-11-17(12-24-19)33-13-16-4-2-3-15(9-16)10-22/h2-4,9,11-12H,5-8,13-14H2,1H3,(H2,25,26,29,30)/t21-/m1/s1
InChIKeyPKCWEIUDUFDFAG-OAQYLSRUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@]1(C[S](=O)(=O)N2CCN(CC2)c3ncc(OCc4cccc(c4)C#N)cn3)NC(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1(C(=O)NC(=O)N1)CS(=O)(=O)N2CCN(CC2)c3ncc(cn3)OCc4cccc(c4)C#N
OpenEye OEToolkits 1.7.6C[C@]1(C(=O)NC(=O)N1)CS(=O)(=O)N2CCN(CC2)c3ncc(cn3)OCc4cccc(c4)C#N
CACTVS 3.385C[C]1(C[S](=O)(=O)N2CCN(CC2)c3ncc(OCc4cccc(c4)C#N)cn3)NC(=O)NC1=O
ACDLabs 12.01O=S(=O)(N3CCN(c2ncc(OCc1cccc(C#N)c1)cn2)CC3)CC4(C(=O)NC(=O)N4)C
FormulaC21 H23 N7 O5 S
Name3-[({2-[4-({[(4S)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl}sulfonyl)piperazin-1-yl]pyrimidin-5-yl}oxy)methyl]benzonitrile
ChEMBLCHEMBL2409696
DrugBank
ZINCZINC000096273612
PDB chain4jpa Chain A Residue 306 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jpa Hydantoin based inhibitors of MMP13--discovery of AZD6605.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L185 A186 L218 H222 E223 H232 A238 L239 F241 P242 I243 T245 Y246
Binding residue
(residue number reindexed from 1)		L82 A83 L115 H119 E120 H129 A135 L136 F138 P139 I140 T142 Y143
Annotation score1
Binding affinityMOAD: ic50=3.3nM
PDBbind-CN: -logKd/Ki=8.48,IC50=3.3nM
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:4jpa, PDBe:4jpa, PDBj:4jpa
PDBsum4jpa
PubMed23810497
UniProtP45452|MMP13_HUMAN Collagenase 3 (Gene Name=MMP13)

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