Structure of PDB 6g5j Chain A Binding Site BS03

Receptor Information
>6g5j Chain A (length=122) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCY
TRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQ
TEYNLKYLFYPQFLCEPDSPKC
Ligand information
Ligand IDEM8
InChIInChI=1S/C20H17F3N2O4/c1-11(7-18(26)27)12-3-2-4-14(8-12)25-16-10-15(29-20(21,22)23)6-5-13(16)9-17(25)19(24)28/h2-6,8-11H,7H2,1H3,(H2,24,28)(H,26,27)/t11-/m1/s1
InChIKeyOSJXLDOVNXZNHD-LLVKDONJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@H](CC(=O)O)c1cccc(c1)n2c3cc(ccc3cc2C(=O)N)OC(F)(F)F
CACTVS 3.385C[C@H](CC(O)=O)c1cccc(c1)n2c(cc3ccc(OC(F)(F)F)cc23)C(N)=O
CACTVS 3.385C[CH](CC(O)=O)c1cccc(c1)n2c(cc3ccc(OC(F)(F)F)cc23)C(N)=O
OpenEye OEToolkits 2.0.6CC(CC(=O)O)c1cccc(c1)n2c3cc(ccc3cc2C(=O)N)OC(F)(F)F
FormulaC20 H17 F3 N2 O4
Name(3~{R})-3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]butanoic acid
ChEMBLCHEMBL4207266
DrugBank
ZINC
PDB chain6g5j Chain A Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6g5j Design of Selective sPLA2-X Inhibitor (-)-2-{2-[Carbamoyl-6-(trifluoromethoxy)-1H-indol-1-yl]pyridine-2-yl}propanoic Acid.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		R15 T16 I18 Y103 F109
Binding residue
(residue number reindexed from 1)		R15 T16 I18 Y103 F109
Annotation score1
Binding affinityMOAD: ic50=0.2uM
PDBbind-CN: -logKd/Ki=6.70,IC50=0.2uM
BindingDB: IC50=200nM
Enzymatic activity
Catalytic site (original residue number in PDB) F26 G28 G30 H46 D47 Y50 Y65 D91
Catalytic site (residue number reindexed from 1) F26 G28 G30 H46 D47 Y50 Y65 D91
Enzyme Commision number 3.1.1.4: phospholipase A2.
Gene Ontology
Molecular Function
GO:0004623 phospholipase A2 activity
GO:0005509 calcium ion binding
Biological Process
GO:0006644 phospholipid metabolic process
GO:0016042 lipid catabolic process
GO:0050482 arachidonate secretion

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6g5j, PDBe:6g5j, PDBj:6g5j
PDBsum6g5j
PubMed30034586
UniProtO15496|PA2GX_HUMAN Group 10 secretory phospholipase A2 (Gene Name=PLA2G10)

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