› 6m07

X-ray diffraction
2.64Å resolution

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

Released:
DOI: 10.2210/pdb6m07/pdb
PDB entry 6m07 coloured by chain, front view.
PDB entry 6m07 coloured by chain, side view.
PDB entry 6m07 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: 369 amino acids
Theoretical weight: 42.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13093 (Residues: 54-422; Coverage: 88%)
Gene names: PAFAH, PLA2G7
Sequence domains: Platelet-activating factor acetylhydrolase, isoform II

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: C2
Unit cell:
a: 112.687Å b: 77.857Å c: 94.698Å
α: 90° β: 115.32° γ: 90°
R-values:
R R work R free
0.203 0.2 0.249
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

2 mentions without citation

Stapled ACE2 peptidomimetics designed to target the SARS-CoV-2 spike protein do not prevent virus internalization.
Morgan et al. (2021)
1 more