SMTL ID : 4uy1.2 (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: 5 residues within 4Å: Chain A: F.26, G.28, G.30, D.47 Ligands: TJM.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.26, A:G.28, A:G.30, A:D.47, H2O.1

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

1PE.2: 6 residues within 4Å: Chain A: L.29, H.46, D.47, Y.50, K.61 Ligands: TJM.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.46, A:D.47, A:K.61

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

DMS.3: 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.4: 9 residues within 4Å: Chain A: K.22, Y.23, G.24, C.25, F.26, C.27, G.28, L.29, G.30 No protein-ligand interaction detected (PLIP) DMS.5: 2 residues within 4Å: Chain A: G.7, W.67 No protein-ligand interaction detected (PLIP)

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

TJM.6: 17 residues within 4Å: Chain A: I.2, L.5, A.6, V.9, P.17, Y.20, M.21, F.26, C.27, G.28, C.43, H.46, D.47, I.94, L.98 Ligands: CA.1, 1PE.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.2, 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

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

PEG.7: 5 residues within 4Å: Chain A: E.54, S.59, P.60, K.61, T.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.59, A:K.61, A:T.62 PEG.8: 6 residues within 4Å: Chain A: L.3, E.4, G.7, R.64, Y.65, W.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.4, A:G.7 Water bridges: A:W.67 PEG.9: 5 residues within 4Å: Chain A: A.38, W.41, C.42, C.97, Q.100 No protein-ligand interaction detected (PLIP)

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
B

GROUP 10 SECRETORY PHOSPHOLIPASE A2

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