SMTL ID : 6n69.1

rat hPGDS complexed with a quinoline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 13 residues within 4Å: Chain A: Y.11, F.12, R.17, W.42, K.46, G.52, K.53, I.54, P.55, Q.66, S.67 Chain B: D.100 Ligands: KDV.2 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:D.100, A:R.17, A:I.54, A:I.54, A:Q.66, A:Q.66, A:S.67 Hydrophobic interactions: A:K.53 Water bridges: A:S.67, A:L.68 Salt bridges: A:R.17, A:K.46, A:K.53 GSH.3: 12 residues within 4Å: Chain A: D.100 Chain B: Y.11, R.17, W.42, K.46, G.52, K.53, I.54, P.55, Q.66, S.67 Ligands: KDV.4 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.42, B:I.54, B:I.54, B:Q.66, B:Q.66, B:S.67, A:D.100 Water bridges: B:R.17, B:L.68, A:D.100 Salt bridges: B:R.17, B:K.46, B:K.53

2 x KDV: quinoline-3-carbonitrile(Non-covalent)

KDV.2: 10 residues within 4Å: Chain A: M.14, G.16, R.17, D.99, M.102, W.107, Y.155, C.159, T.162 Ligands: GSH.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.17, A:M.102 pi-Stacking: A:W.107, A:W.107 KDV.4: 10 residues within 4Å: Chain B: M.14, G.16, R.17, D.99, M.102, S.103, W.107, Y.155, L.202 Ligands: GSH.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.17, B:M.102 Water bridges: B:G.16 pi-Stacking: B:W.107, B:W.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deaton, D.N. et al., The discovery of quinoline-3-carboxamides as hematopoietic prostaglandin D synthase (H-PGDS) inhibitors. Bioorg. Med. Chem. (2019)

Release Date

2019-03-27

Peptides

Hematopoietic prostaglandin D synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hematopoietic prostaglandin D synthase