Exploitation of a novel binding pocket in human lipoprotein-associated phospholipase A2 (lp-PLA<SUB>2</SUB>) discovered through X-ray fragment screening

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).

Ligands and binding sites

• 6HZ · (2,5-dihydro-1H-pyrrol-1-yl)(2',6-dimethyl[1,1'-biphenyl]-3-yl)methanone · ligand · chains A
• CA · Calcium ion · metal · chains A
• CL · Chloride ion · ion · chains A
• DMS · Dimethyl sulfoxide · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Compared structures

• 5JAP · Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2… · the same entry in another collection · chain A against A, TM-score 1.00
• Q13093 · AlphaFold monomer V2.0 prediction for platelet-activating factor acetylhydrolase (Q13093) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q13093
• Elsewhere: RCSB PDB 5JAP · PDBe 5JAP · UniProt Q13093