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

Complex of human hematopoietic prostagandin D2 synthase (hH-PGDS) in complex with an active site inhibitor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

2 x M1W: 3-(1H-indol-4-yl)-N-(3-methoxypropyl)-1,2,4-oxadiazole-5-carboxamide(Non-covalent)

M1W.1: 12 residues within 4Å: Chain A: F.9, M.11, G.13, R.14, Q.36, D.96, M.99, S.100, W.104, Y.152, L.199 Ligands: GSH.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.14 Hydrogen bonds: A:D.96, A:D.96, A:Y.152 Water bridges: A:G.13 pi-Stacking: A:W.104, A:W.104 M1W.4: 12 residues within 4Å: Chain B: F.9, M.11, G.13, R.14, Q.36, D.96, M.99, W.104, Y.152, C.156, L.199 Ligands: GSH.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.9, B:R.14, B:M.99 Hydrogen bonds: B:Y.152 Water bridges: B:G.13 pi-Stacking: B:W.104, B:W.104

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.2: 12 residues within 4Å: Chain A: Y.8, R.14, W.39, K.43, G.49, K.50, I.51, P.52, Q.63, S.64 Chain B: D.97 Ligands: M1W.1 17 PLIP interactions: 1 interactions with chain B, 16 interactions with chain A Water bridges: B:D.93, A:K.43, A:Q.63, A:Q.63, A:S.64, A:L.65, A:D.96 Hydrophobic interactions: A:K.50 Hydrogen bonds: A:R.14, A:K.50, A:I.51, A:I.51, A:Q.63, A:Q.63, A:S.64 Salt bridges: A:R.14, A:K.43 GSH.5: 13 residues within 4Å: Chain A: D.97 Chain B: Y.8, F.9, R.14, W.39, K.43, G.49, K.50, I.51, P.52, Q.63, S.64 Ligands: M1W.4 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.14, B:I.51, B:I.51, B:Q.63, B:S.64, A:D.97 Water bridges: B:Q.63, B:S.64, B:L.65 Salt bridges: B:R.14, B:K.43

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.96 Chain B: D.96 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edfeldt, F. et al., Identification of Indole Inhibitors of Human Hematopoietic Prostaglandin D2 Synthase (Hh-Pgds). Bioorg.Med.Chem.Lett. (2015)

Release Date

2015-06-03

Peptides

HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE

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