› 6m06

X-ray diffraction
2.1Å resolution

Crystal structure of Lp-PLA2 in complex with a novel covalent inhibitor

Released:
DOI: 10.2210/pdb6m06/pdb
PDB entry 6m06 coloured by chain, front view.
PDB entry 6m06 coloured by chain, side view.
PDB entry 6m06 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of Highly Selective Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Inhibitors by a Covalent Fragment-Based Approach.
Huang F, Hu H, Wang K, Peng C, Xu W, Zhang Y, Gao J, Liu Y, Zhou H, Huang R, Li M, Shen J, Xu Y
J Med Chem 63 7052-7065 (2020)
PMID: 32459096

Function and Biology Details

Reaction catalysed: 
1-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H(2)O = 1-alkyl-sn-glycero-3-phosphocholine + acetate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171527 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Platelet-activating factor acetylhydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 371 amino acids
Theoretical weight: 42.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13093 (Residues: 54-424; Coverage: 88%)
Gene names: PAFAH, PLA2G7
Sequence domains: Platelet-activating factor acetylhydrolase, isoform II

Ligands and Environments

1 bound ligand:
Ligand BWF 2 x BWF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 116.014Å b: 83.22Å c: 96.581Å
α: 90° β: 115.04° γ: 90°
R-values:
R R work R free
0.188 0.186 0.22
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Fragment-to-Lead Medicinal Chemistry Publications in 2020.
de Esch et al. (2022)
2 more

3 mentions without citation

Discovery of a first-in-class inhibitor of sulfide:quinone oxidoreductase that protects against adverse cardiac remodelling and heart failure.
Jackson et al. (2022)
2 more