SMTL ID : 5owc.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: AYZ.2 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

1 x AYZ: 3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]propanoic acid(Non-covalent)

AYZ.2: 17 residues within 4Å: Chain A: L.5, A.6, P.17, I.18, Y.20, M.21, F.26, C.27, G.28, L.29, G.30, C.43, H.46, D.47, Y.50, I.94 Ligands: CA.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.20, A:Y.50, A:I.94 Hydrogen bonds: A:G.28, A:G.30, A:H.46, A:D.47, A:D.47

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

DMS.3: 7 residues within 4Å: Chain A: Y.23, G.24, C.25, C.27, G.28, L.29, G.30 No protein-ligand interaction detected (PLIP) DMS.4: 4 residues within 4Å: Chain A: V.74, L.75, C.76, Q.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.76, A:Q.92

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

PEG.5: 3 residues within 4Å: Chain A: A.19, Y.103 Ligands: PEG.8 No protein-ligand interaction detected (PLIP) PEG.6: 4 residues within 4Å: Chain A: R.64, Y.65, S.66, E.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.66, A:Q.84 PEG.7: 2 residues within 4Å: Chain A: N.71, Q.72 No protein-ligand interaction detected (PLIP) PEG.8: 3 residues within 4Å: Chain A: R.15, T.16 Ligands: PEG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.16

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
A

Group 10 secretory phospholipase A2

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