SMTL ID : 4uy1.1 (1 other biounit)

Novel pyrazole series of group X Secretory Phospholipase A2 (sPLA2-X) inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: F.26, G.28, G.30, D.47 Ligands: 1PE.3, TJM.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.26, A:G.28, A:G.30, A:D.47, A:D.47

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 5 residues within 4Å: Chain A: R.15, T.16, I.18, A.19, Y.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.15 Water bridges: A:T.16, A:Y.103 1PE.3: 10 residues within 4Å: Chain A: I.2, G.28, L.29, G.30, D.47, Y.50, K.61 Ligands: CA.1, DMS.7, TJM.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.30, A:K.61 Water bridges: A:D.47

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

DMS.4: 3 residues within 4Å: Chain A: L.75, C.76, Q.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.76, A:Q.92 DMS.5: 9 residues within 4Å: Chain A: Y.23, G.24, C.25, F.26, C.27, G.28, L.29, G.30, G.31 No protein-ligand interaction detected (PLIP) DMS.6: 4 residues within 4Å: Chain A: E.54, S.59, P.60, K.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.61 Salt bridges: A:E.54 DMS.7: 6 residues within 4Å: Chain A: D.47, Y.50, T.51, E.54, K.61 Ligands: 1PE.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.54

1 x TJM: 5-(2,5-DIMETHYL-3-THIENYL)-1H-PYRAZOLE-3-CARBOXAMIDE(Non-covalent)

TJM.8: 15 residues within 4Å: Chain A: L.5, A.6, V.9, P.17, Y.20, F.26, C.27, G.28, C.43, H.46, D.47, I.94, L.98 Ligands: CA.1, 1PE.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.5, A:A.6, A:V.9, A:P.17, A:Y.20, A:I.94, A:L.98 Hydrogen bonds: A:G.28, A:C.43, A:H.46, A:D.47

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 5 residues within 4Å: Chain A: S.66, W.67, Q.68, C.69 Ligands: PEG.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.67, A:C.69, A:C.69 PEG.10: 6 residues within 4Å: Chain A: A.6, G.7, G.10, C.11, W.67 Ligands: PEG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.10 PEG.11: 5 residues within 4Å: Chain A: R.64, Y.65, S.66, P.78, E.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.66 Water bridges: A:S.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, H. et al., Discovery of a Novel Pyrazole Series of Group X Secreted Phospholipase A2 Inhibitor (Spla2X) Via Fragment Based Virtual Screening. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-10-15

Peptides

GROUP 10 SECRETORY PHOSPHOLIPASE A2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GROUP 10 SECRETORY PHOSPHOLIPASE A2

Related Entries With Identical Sequence