SMTL ID : 5jal.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.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.6, H2O.12

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

CL.2: 4 residues within 4Å: Chain A: Y.276, F.277, V.305, H.306 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: Y.279, P.280, A.281 Ligand excluded by PLIP

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

DMS.4: 5 residues within 4Å: Chain A: L.108, S.228, W.253, F.277, H.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.228 pi-Cation interactions: A:W.253, A:W.253

1 x 6HO: (2,5-dihydro-1H-pyrrol-1-yl)(3-fluorophenyl)methanone(Non-covalent)

6HO.5: 10 residues within 4Å: Chain A: L.62, F.65, L.66, L.108, G.109, A.110, Q.307, F.312, L.324, L.326 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.62, A:F.65, A:L.66, A:L.326 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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