SMTL ID : 6w8h.1

H-PGDS complexed with inhibitor 1Y

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 12 residues within 4Å: Chain A: Y.22, F.23, R.28, W.53, K.57, K.64, I.65, P.66, Q.77, S.78 Chain B: D.111 Ligands: TJG.3 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.53, A:I.65, A:I.65, A:Q.77, A:S.78, B:D.111 Water bridges: A:I.65, A:Q.77, A:L.79 Salt bridges: A:R.28, A:K.57, A:K.64 GSH.4: 11 residues within 4Å: Chain A: D.111 Chain B: Y.22, R.28, W.53, K.57, K.64, I.65, P.66, Q.77, S.78 Ligands: TJG.5 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.65, B:I.65, B:Q.77, B:S.78, A:D.111 Water bridges: B:Q.77, B:L.79 Salt bridges: B:R.28, B:K.57, B:K.64

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: Q.42, Y.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.43 Water bridges: A:I.41

2 x TJG: 7-cyclopropyl-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-1,8-naphthyridine-3-carboxamide(Non-covalent)

TJG.3: 13 residues within 4Å: Chain A: F.23, M.25, G.27, R.28, Q.50, W.53, M.113, W.118, A.119, Y.166, C.170, L.213 Ligands: GSH.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.23, A:F.23, A:M.113, A:W.118, A:A.119 Water bridges: A:G.27, A:G.27, A:T.173 pi-Stacking: A:W.118, A:W.118, A:W.118 TJG.5: 12 residues within 4Å: Chain B: F.23, M.25, G.27, R.28, Q.50, W.53, M.113, W.118, A.119, Y.166, L.213 Ligands: GSH.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.23, B:F.23, B:R.28, B:M.113, B:W.118, B:A.119 Water bridges: B:G.27, B:G.27 pi-Stacking: B:W.118, B:W.118, B:W.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cadilla, R. et al., The exploration of aza-quinolines as hematopoietic prostaglandin D synthase (H-PGDS) inhibitors with low brain exposure. Bioorg.Med.Chem. (2020)

Release Date

2020-11-04

Peptides

Hematopoietic prostaglandin D synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Hematopoietic prostaglandin D synthase