SMTL ID : 5ow8.2 (1 other biounit)

Indole-2 carboxamides as selective secreted phospholipase A2 type X (sPLA2-X) inhibitors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: DMS.2, AYN.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:F.26, A:G.28, A:G.30, A:D.47, DMS.2

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

DMS.2: 7 residues within 4Å: Chain A: G.28, L.29, G.30, D.47, Y.50 Ligands: CA.1, AYN.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.30 Salt bridges: A:D.47 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, G.24, C.25, C.27, G.28, L.29, G.30, G.31, Q.112 No protein-ligand interaction detected (PLIP) DMS.5: 3 residues within 4Å: Chain A: I.2, L.29 Ligands: AYN.6 No protein-ligand interaction detected (PLIP)

1 x AYN: 1-[3-(trifluoromethyl)phenyl]indole-2-carboxamide(Non-covalent)

AYN.6: 17 residues within 4Å: Chain A: L.5, V.9, P.17, Y.20, F.26, C.27, G.28, L.29, C.43, H.46, D.47, Y.50, K.61, I.94 Ligands: CA.1, DMS.2, DMS.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.9, A:P.17, A:Y.20, A:Y.20, A:I.94 Hydrogen bonds: A:G.28, A:D.47

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

PEG.7: 4 residues within 4Å: Chain A: R.64, S.66, E.80, Q.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.66 Water bridges: A:S.66

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

CL.8: 1 residues within 4Å: Chain A: K.61 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: L.3, E.4, W.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knerr, L. et al., Discovery of a Series of Indole-2 Carboxamides as Selective Secreted Phospholipase A2Type X (sPLA2-X) Inhibitors. Acs Med.Chem.Lett. (2018)

Release Date

2018-08-01

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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