Structure of PDB 6esm Chain A Binding Site BS06

Receptor Information
>6esm Chain A (length=158) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYS
RDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWS
LGKGVGYSLFLVAAHQFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDV
NGIRHLYG
Ligand information
Ligand IDB9Z
InChIInChI=1S/C24H22O5S/c1-29-18-10-6-16(7-11-18)17-8-12-19(13-9-17)30-22-5-3-2-4-20(22)21(24(27)28)14-15-23(25)26/h2-13,21H,14-15H2,1H3,(H,25,26)(H,27,28)/t21-/m0/s1
InChIKeyKSEPBMMZVPGILK-NRFANRHFSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(cc1)c2ccc(Sc3ccccc3[CH](CCC(O)=O)C(O)=O)cc2
OpenEye OEToolkits 2.0.6COc1ccc(cc1)c2ccc(cc2)Sc3ccccc3C(CCC(=O)O)C(=O)O
OpenEye OEToolkits 2.0.6COc1ccc(cc1)c2ccc(cc2)Sc3ccccc3[C@H](CCC(=O)O)C(=O)O
CACTVS 3.385COc1ccc(cc1)c2ccc(Sc3ccccc3[C@H](CCC(O)=O)C(O)=O)cc2
FormulaC24 H22 O5 S
Name(2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfanylphenyl]pentanedioic acid
ChEMBL
DrugBank
ZINC
PDB chain6esm 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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PDB6esm Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, NMR, and Crystallographic Studies.
Resolution1.104 Å
Binding residue
(original residue number in PDB)		G186 L187 A189 H226 Q227 H230 H236 L243 P246 M247 Y248 R249
Binding residue
(residue number reindexed from 1)		G75 L76 A78 H115 Q116 H119 H125 L132 P135 M136 Y137 R138
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.53,IC50=2960nM
BindingDB: IC50=2960nM
Enzymatic activity
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:6esm, PDBe:6esm, PDBj:6esm
PDBsum6esm
PubMed29727184
UniProtP14780|MMP9_HUMAN Matrix metalloproteinase-9 (Gene Name=MMP9)

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