Structure of PDB 6m06 Chain A Binding Site BS01

Receptor Information

>6m06 Chain A (length=371) Species: 9606 (Homo sapiens)

TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEY
FWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGL
GAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSW
LYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKF
DMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLG
DEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQN
FADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFD
QWDCLIEGDDENLIPGTNINT

Ligand information

• Ligand ID: BWF
• InChI: InChI=1S/C8H11NO5/c10-6(4-7(11)12)5-2-1-3-9(5)8(13)14/h4-5,10H,1-3H2,(H,11,12)(H,13,14)/b6-4-/t5-/m0/s1
• InChIKey: ROSCYVZNGZEOEY-YIWIKUPCSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: C1CC(N(C1)C(=O)O)C(=CC(=O)O)O
  CACTVS 3.385: OC(=O)C=C(O)[CH]1CCCN1C(O)=O
  OpenEye OEToolkits 2.0.7: C1C[C@H](N(C1)C(=O)O)/C(=C/C(=O)O)/O
  CACTVS 3.385: OC(=O)\C=C(O)\[C@@H]1CCCN1C(O)=O
• Formula: C8 H11 N O5
• Name: (2S)-2-[(Z)-1,3-bis(oxidanyl)-3-oxidanylidene-prop-1-enyl]pyrrolidine-1-carboxylic acid
• PDB chain: 6m06 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6m06 Identification of Highly Selective Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Inhibitors by a Covalent Fragment-Based Approach.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): L153 S273 F274 W298 F322 H351
• Binding residue (residue number reindexed from 1): L100 S220 F221 W245 F269 H298
• Annotation score: 1

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

External links

• PDB: RCSB:6m06, PDBe:6m06, PDBj:6m06
• PDBsum: 6m06
• PubMed: 32459096
• UniProt: Q13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)