› 5lp1

X-ray diffraction
1.91Å resolution

CRYSTAL STRUCTURE OF HUMAN LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2 IN COMPLEX WITH A [1.1.1]BICYCLOPENTANE-CONTAINING INHIBITOR AT 1.91A RESOLUTION.

Released:
DOI: 10.2210/pdb5lp1/pdb
PDB entry 5lp1 coloured by chain, front view.
PDB entry 5lp1 coloured by chain, side view.
PDB entry 5lp1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Investigation of a Bicyclo[1.1.1]pentane as a Phenyl Replacement within an LpPLA2 Inhibitor.
Measom ND, Down KD, Hirst DJ, Jamieson C, Manas ES, Patel VK, Somers DO
ACS Med Chem Lett 8 43-48 (2017)
PMID: 28105273

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:
Cellular component:
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 Chain: A
Molecule details ›
Chain: A
Length: 388 amino acids
Theoretical weight: 44.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13093 (Residues: 46-428; Coverage: 91%)
Gene names: PAFAH, PLA2G7
Sequence domains: Platelet-activating factor acetylhydrolase, isoform II
Structure domains: alpha/beta hydrolase

Ligands and Environments

2 bound ligands:
Ligand CL 2 x CL
Ligand 71H 1 x 71H
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2
Unit cell:
a: 100.28Å b: 91.56Å c: 51.65Å
α: 90° β: 111.88° γ: 90°
R-values:
R R work R free
0.164 0.162 0.192
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Put a ring on it: application of small aliphatic rings in medicinal chemistry.
Bauer et al. (2021)
6 more

2 mentions without citation

Lipoprotein-associated phospholipase A2: The story continues.
Huang et al. (2020)
1 more