SMTL ID : 6n4e.1

hPGDS complexed with a quinoline-3-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 11 residues within 4Å: Chain A: Y.9, F.10, R.15, W.40, K.44, K.51, I.52, P.53, Q.64, S.65 Chain B: D.98 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.51 Hydrogen bonds: A:W.40, A:I.52, A:I.52, A:Q.64, A:S.65, B:D.98 Water bridges: A:Q.64, A:L.66, A:D.97, B:D.94 Salt bridges: A:R.15, A:K.44, A:K.51 GSH.3: 11 residues within 4Å: Chain A: D.98 Chain B: Y.9, F.10, R.15, W.40, K.44, K.51, I.52, P.53, Q.64, S.65 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.51 Hydrogen bonds: B:W.40, B:I.52, B:I.52, B:Q.64, B:S.65, A:D.98 Water bridges: B:R.15, B:Q.64, B:L.66, B:D.97 Salt bridges: B:R.15, B:K.44, B:K.51

2 x KCD: 7-(difluoromethoxy)-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]quinoline-3-carboxamide(Non-covalent)

KCD.2: 13 residues within 4Å: Chain A: F.10, M.12, G.14, R.15, Q.37, W.40, M.100, W.105, A.106, Y.153, I.156, C.157, L.200 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.10, A:F.10, A:R.15, A:W.105, A:W.105, A:A.106 Hydrogen bonds: A:Q.37 Water bridges: A:G.14 pi-Stacking: A:W.105, A:W.105, A:W.105 KCD.4: 13 residues within 4Å: Chain B: F.10, M.12, G.14, R.15, Q.37, W.40, M.100, W.105, A.106, Y.153, I.156, C.157, L.200 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.10, B:F.10, B:R.15, B:W.105, B:W.105, B:A.106 Hydrogen bonds: B:Q.37, B:Y.153 Water bridges: B:G.14 pi-Stacking: B:W.105, B:W.105, B:W.105

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
A

Hematopoietic prostaglandin D synthase

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