Structure of PDB 3dpe Chain A Binding Site BS05

Receptor Information
>3dpe Chain A (length=163) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFT
RISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAE
ETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSL
PQDDIDGIQAIYG
Ligand information
Ligand IDAXB
InChIInChI=1S/C24H21N5O6S2/c25-17-18(20(31)19(17)30)29-5-3-12-2-1-11(7-13(12)9-29)8-26-23(33)21-27-22(32)16-14-4-6-37(34,35)10-15(14)36-24(16)28-21/h1-2,7H,3-6,8-10,25H2,(H,26,33)(H,27,28,32)
InChIKeyQHDIXGPUTSAIJX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc2c(cc1CNC(=O)C3=Nc4c(c5c(s4)CS(=O)(=O)CC5)C(=O)N3)C[N@@](CC2)C6=C(C(=O)C6=O)N
CACTVS 3.341NC1=C(N2CCc3ccc(CNC(=O)C4=Nc5sc6C[S](=O)(=O)CCc6c5C(=O)N4)cc3C2)C(=O)C1=O
ACDLabs 10.04O=C1C(N)=C(C1=O)N3CCc2ccc(cc2C3)CNC(=O)C5=Nc4sc6c(c4C(=O)N5)CCS(=O)(=O)C6
OpenEye OEToolkits 1.5.0c1cc2c(cc1CNC(=O)C3=Nc4c(c5c(s4)CS(=O)(=O)CC5)C(=O)N3)CN(CC2)C6=C(C(=O)C6=O)N
FormulaC24 H21 N5 O6 S2
NameN-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-4-oxo-3,5,6,8-tetrahydro-4H-thiopyrano[4',3':4,5]thieno[2,3-d]pyrimidine-2-carboxamide 7,7-dioxide
ChEMBLCHEMBL460725
DrugBank
ZINCZINC000100416718
PDB chain3dpe Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dpe Extra Binding Region Induced by Non-Zinc Chelating Inhibitors into the S(1)' Subsite of Matrix Metalloproteinase 8 (MMP-8)
Resolution1.6 Å
Binding residue
(original residue number in PDB)		I159 L160 A161 L193 H197 L214 Y216 P217 N218 Y219 A220 R222 Y227 S228 P230
Binding residue
(residue number reindexed from 1)		I80 L81 A82 L114 H118 L135 Y137 P138 N139 Y140 A141 R143 Y148 S149 P151
Annotation score1
Binding affinityMOAD: ic50=57nM
PDBbind-CN: -logKd/Ki=7.24,IC50=57nM
BindingDB: IC50=57nM
Enzymatic activity
Catalytic site (original residue number in PDB) H197 E198 H201 H207
Catalytic site (residue number reindexed from 1) H118 E119 H122 H128
Enzyme Commision number 3.4.24.34: neutrophil collagenase.
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:3dpe, PDBe:3dpe, PDBj:3dpe
PDBsum3dpe
PubMed19173605
UniProtP22894|MMP8_HUMAN Neutrophil collagenase (Gene Name=MMP8)

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