Structure of PDB 6m07 Chain B Binding Site BS01

Receptor Information
>6m07 Chain B (length=369) 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
QWDCLIEGDDENLIPGTNI
Ligand information
Ligand IDBWO
InChIInChI=1S/C30H35F6N3O5/c1-3-37(4-2)14-15-38(27(41)17-25(40)24-6-5-13-39(24)28(42)43)18-20-7-9-21(10-8-20)23-12-11-22(30(34,35)36)16-26(23)44-19-29(31,32)33/h7-12,16-17,24,40H,3-6,13-15,18-19H2,1-2H3,(H,42,43)/b25-17+/t24-/m0/s1
InChIKeyMYCHXHCCMGJMEM-IOCYEQIYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2OCC(F)(F)F)C(F)(F)F)C(=O)C=C(C3CCCN3C(=O)O)O
OpenEye OEToolkits 2.0.7CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2OCC(F)(F)F)C(F)(F)F)C(=O)/C=C(\[C@@H]3CCCN3C(=O)O)/O
CACTVS 3.385CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2OCC(F)(F)F)C(F)(F)F)C(=O)\C=C(O)/[C@@H]3CCCN3C(O)=O
CACTVS 3.385CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2OCC(F)(F)F)C(F)(F)F)C(=O)C=C(O)[CH]3CCCN3C(O)=O
FormulaC30 H35 F6 N3 O5
Name(2S)-2-[(E)-3-[2-(diethylamino)ethyl-[[4-[4-(trifluoromethyl)-2-[2,2,2-tris(fluoranyl)ethoxy]phenyl]phenyl]methyl]amino]-1-oxidanyl-3-oxidanylidene-prop-1-enyl]pyrrolidine-1-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6m07 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

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PDB6m07 Identification of Highly Selective Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Inhibitors by a Covalent Fragment-Based Approach.
Resolution2.64 Å
Binding residue
(original residue number in PDB)		F110 G152 L153 S273 F274 W298 H351 Q352 F357 K370 L371
Binding residue
(residue number reindexed from 1)		F57 G99 L100 S220 F221 W245 H298 Q299 F304 K317 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:6m07, PDBe:6m07, PDBj:6m07
PDBsum6m07
PubMed32459096
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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