Structure of PDB 4yk5 Chain A Binding Site BS01

Receptor Information
>4yk5 Chain A (length=146) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VMSSPALPAFLLCSTLLVIKMYVVAIITGQVRLRKKAFANPEDALRHGGP
QYCRSDPDVERCLRAHRNDMETIYPFLFLGFVYSFLGPNPFVAWMHFLVF
LVGRVAHTVAYLGKLRAPIRSVTYTLAQLPCASMALQILWEAARHL
Ligand information
Ligand ID4DV
InChIInChI=1S/C34H31ClFNO2/c1-21-7-5-6-8-27(21)28-15-11-25(18-30(28)36)24-12-16-31-29(17-24)22(2)32(19-34(3,4)33(38)39)37(31)20-23-9-13-26(35)14-10-23/h5-18H,19-20H2,1-4H3,(H,38,39)
InChIKeyIYCJVTFMIQICDJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccccc1c2ccc(cc2F)c3ccc4n(Cc5ccc(Cl)cc5)c(CC(C)(C)C(O)=O)c(C)c4c3
ACDLabs 12.01O=C(O)C(Cc5n(Cc1ccc(Cl)cc1)c2c(cc(cc2)c3ccc(c(c3)F)c4ccccc4C)c5C)(C)C
OpenEye OEToolkits 1.9.2Cc1ccccc1c2ccc(cc2F)c3ccc4c(c3)c(c(n4Cc5ccc(cc5)Cl)CC(C)(C)C(=O)O)C
FormulaC34 H31 Cl F N O2
Name3-[1-(4-chlorobenzyl)-5-(2-fluoro-2'-methylbiphenyl-4-yl)-3-methyl-1H-indol-2-yl]-2,2-dimethylpropanoic acid
ChEMBLCHEMBL180650
DrugBank
ZINCZINC000028135431
PDB chain4yk5 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4yk5 Crystal Structures of mPGES-1 Inhibitor Complexes Form a Basis for the Rational Design of Potent Analgesic and Anti-Inflammatory Therapeutics.
Resolution1.42 Å
Binding residue
(original residue number in PDB)		P124 S127 Y130 T131 Q134
Binding residue
(residue number reindexed from 1)		P118 S121 Y124 T125 Q128
Annotation score1
Binding affinityMOAD: ic50=0.96uM
PDBbind-CN: -logKd/Ki=7.64,IC50=0.023uM
BindingDB: IC50=3nM
Enzymatic activity
Enzyme Commision number 1.11.1.-
2.5.1.18: glutathione transferase.
5.3.99.3: prostaglandin-E synthase.
Gene Ontology
Molecular Function
GO:0004364 glutathione transferase activity
GO:0004602 glutathione peroxidase activity
GO:0004667 prostaglandin-D synthase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016740 transferase activity
GO:0016853 isomerase activity
GO:0043295 glutathione binding
GO:0050220 prostaglandin-E synthase activity
Biological Process
GO:0001516 prostaglandin biosynthetic process
GO:0006693 prostaglandin metabolic process
GO:0007165 signal transduction
GO:0008283 cell population proliferation
GO:0008285 negative regulation of cell population proliferation
GO:0019233 sensory perception of pain
GO:0031620 regulation of fever generation
GO:0032308 positive regulation of prostaglandin secretion
GO:0050727 regulation of inflammatory response
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0005641 nuclear envelope lumen
GO:0005737 cytoplasm
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4yk5, PDBe:4yk5, PDBj:4yk5
PDBsum4yk5
PubMed25961169
UniProtO14684|PTGES_HUMAN Prostaglandin E synthase (Gene Name=PTGES)

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