Structure of PDB 6m08 Chain B Binding Site BS01

Receptor Information
>6m08 Chain B (length=371) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEY
FWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGL
GAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSW
LYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKF
DMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLG
DEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQN
FADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFD
QWDCLIEGDDENLIPGTNINT
Ligand information
Ligand IDBWL
InChIInChI=1S/C28H34F3N3O4/c1-3-32(4-2)16-17-33(26(36)18-25(35)24-6-5-15-34(24)27(37)38)19-20-7-9-21(10-8-20)22-11-13-23(14-12-22)28(29,30)31/h7-14,18,24,35H,3-6,15-17,19H2,1-2H3,(H,37,38)/b25-18-/t24-/m0/s1
InChIKeyGTFYUFYLBSPPRI-BUFPPZMGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2)C(F)(F)F)C(=O)C=C(C3CCCN3C(=O)O)O
OpenEye OEToolkits 2.0.7CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2)C(F)(F)F)C(=O)/C=C(/[C@@H]3CCCN3C(=O)O)\O
CACTVS 3.385CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2)C(F)(F)F)C(=O)C=C(O)[CH]3CCCN3C(O)=O
CACTVS 3.385CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2)C(F)(F)F)C(=O)\C=C(/O)[C@@H]3CCCN3C(O)=O
FormulaC28 H34 F3 N3 O4
Name(2S)-2-[(Z)-3-[2-(diethylamino)ethyl-[[4-[4-(trifluoromethyl)phenyl]phenyl]methyl]amino]-1-oxidanyl-3-oxidanylidene-prop-1-enyl]pyrrolidine-1-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6m08 Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6m08 Identification of Highly Selective Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Inhibitors by a Covalent Fragment-Based Approach.
Resolution2.19 Å
Binding residue
(original residue number in PDB)		F110 L153 S273 F274 W298 F322 H351 Q352 F357 L371
Binding residue
(residue number reindexed from 1)		F57 L100 S220 F221 W245 F269 H298 Q299 F304 L318
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.1.47: 1-alkyl-2-acetylglycerophosphocholine esterase.
Gene Ontology
Molecular Function
GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity

View graph for
Molecular Function
External links
PDB RCSB:6m08, PDBe:6m08, PDBj:6m08
PDBsum6m08
PubMed32459096
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

[Back to BioLiP]