SMTL ID : 5i9i.2 (1 other biounit)

Crystal structure of LP_PLA2 in complex with Darapladib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x 5HV: N-[2-(diethylamino)ethyl]-2-{2-[(4-fluorobenzyl)sulfanyl]-4-oxo-4,5,6,7-tetrahydro-1H-cyclopenta[d]pyrimidin-1-yl}-N-{[ 4'-(trifluoromethyl)biphenyl-4-yl]methyl}acetamide(Non-covalent)

5HV.1: 20 residues within 4Å: Chain A: L.66, F.69, L.70, L.80, F.84, G.111, L.112, G.113, A.114, L.118, Y.119, S.232, F.233, W.257, H.310, Q.311, A.314, F.316, L.328, L.330 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.66, A:F.69, A:L.70, A:L.70, A:W.257, A:Q.311, A:A.314, A:F.316, A:L.330 Hydrogen bonds: A:L.112, A:S.232, A:F.233 pi-Stacking: A:W.257, A:W.257, A:H.310

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: P.58, N.59, K.60, E.61, R.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.59, A:K.60, A:E.61 Salt bridges: A:R.81 SO4.3: 1 residues within 4Å: Chain A: R.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.141 Salt bridges: A:R.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Q.F. et al., Structural and Thermodynamic Characterization of Protein-Ligand Interactions Formed between Lipoprotein-Associated Phospholipase A2 and Inhibitors. J.Med.Chem. (2016)

Release Date

2016-06-15

Peptides

Platelet-activating factor acetylhydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Platelet-activating factor acetylhydrolase

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