› 5g3m

X-ray diffraction
1.85Å resolution

Discovery of a novel secreted phospholipase A2 (sPLA2) inhibitor.

Released:
DOI: 10.2210/pdb5g3m/pdb
PDB entry 5g3m coloured by chain, front view.
PDB entry 5g3m coloured by chain, side view.
PDB entry 5g3m coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of AZD2716: A Novel Secreted Phospholipase A2 (sPLA2) Inhibitor for the Treatment of Coronary Artery Disease.
Giordanetto F, Pettersen D, Starke I, Nordberg P, Dahlström M, Knerr L, Selmi N, Rosengren B, Larsson LO, Sandmark J, Castaldo M, Dekker N, Karlsson U, Hurt-Camejo E
ACS Med Chem Lett 7 884-889 (2016)
PMID: 27774123

Function and Biology Details

Reaction catalysed: 
Phosphatidylcholine + H(2)O = 1-acylglycerophosphocholine + a carboxylate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127495 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Group 10 secretory phospholipase A2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 123 amino acids
Theoretical weight: 13.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O15496 (Residues: 43-165; Coverage: 92%)
Gene name: PLA2G10
Sequence domains: Phospholipase A2
Structure domains: Phospholipase A2 domain

Ligands and Environments

4 bound ligands:
Ligand CA 2 x CA
Ligand DMS 10 x DMS
Ligand PEG 11 x PEG
Ligand 9JH 2 x 9JH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+
Spacegroup: P212121
Unit cell:
a: 27.57Å b: 85.122Å c: 103.316Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.232
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Small-molecule inhibitors as potential therapeutics and as tools to understand the role of phospholipases A2.
Nikolaou et al. (2019)
1 more

2 mentions without citation

Wen-Luo-Tong Decoction Attenuates Paclitaxel-Induced Peripheral Neuropathy by Regulating Linoleic Acid and Glycerophospholipid Metabolism Pathways.
Wu et al. (2018)
1 more