SMTL ID : 5jao.1

Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA₂) Discovered Through X-Ray Fragment Screening

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: E.240, D.241 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.240, H2O.8, H2O.16

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: Y.276, F.277, V.305, H.306, K.325 Ligand excluded by PLIP

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: L.108, S.228, W.253, F.277 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.253, A:W.253

1 x 6HX: 2'-chloro-6-methyl[1,1'-biphenyl]-3-amine(Non-covalent)

6HX.4: 12 residues within 4Å: Chain A: W.52, I.53, F.59, L.62, L.66, L.76, F.80, Q.307, F.312, A.315, L.324, L.326 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.52, A:W.52, A:L.62, A:L.66, A:L.66, A:F.80, A:F.312, A:L.326 Water bridges: A:Q.307 pi-Stacking: A:F.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woolford, A.J. et al., Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening. J.Med.Chem. (2016)

Release Date

2016-05-25

Peptides

Platelet-activating factor acetylhydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Platelet-activating factor acetylhydrolase

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