SMTL ID : 6ztc.1

CRYSTAL STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE IN COMPLEX WITH FRAGMENT 1A AT 1.84A RESOLUTION.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 12 residues within 4Å: Chain A: Y.9, R.15, W.40, K.44, G.50, K.51, I.52, P.53, Q.64, S.65 Chain B: D.98 Ligands: QPN.3 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.51 Hydrogen bonds: A:R.15, A:G.50, A:I.52, A:I.52, A:Q.64, A:S.65, B:D.98 Water bridges: A:K.44, A:Q.64, A:Q.64, A:S.65, A:L.66, A:D.97, A:D.97, B:D.98 Salt bridges: A:R.15, A:K.44 GSH.6: 13 residues within 4Å: Chain A: D.98 Chain B: Y.9, F.10, R.15, W.40, K.44, G.50, K.51, I.52, P.53, Q.64, S.65 Ligands: QPN.7 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.51 Hydrogen bonds: B:R.15, B:I.52, B:I.52, B:Q.64, B:S.65, A:D.98 Water bridges: B:R.15, B:K.51, B:I.52, B:Q.64, B:S.65, B:S.65, B:L.66, A:D.94 Salt bridges: B:R.15, B:K.44

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.97 Chain B: D.97 No protein-ligand interaction detected (PLIP)

2 x QPN: 1-[1-(3-fluorophenyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-5-yl]propan-1-one(Non-covalent)

QPN.3: 12 residues within 4Å: Chain A: Y.9, M.12, G.14, R.15, D.97, M.100, S.101, W.105, Y.153, T.160, L.200 Ligands: GSH.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.15, A:W.105, A:W.105, A:W.105 Water bridges: A:L.200 pi-Stacking: A:W.105 Halogen bonds: A:S.101 QPN.7: 12 residues within 4Å: Chain B: Y.9, M.12, G.14, R.15, D.97, M.100, S.101, W.105, Y.153, T.160, L.200 Ligands: GSH.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.15, B:M.100, B:W.105, B:W.105, B:W.105 Hydrogen bonds: B:T.160 Water bridges: B:K.113 pi-Stacking: B:W.105 Halogen bonds: B:S.101

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: E.83 Chain B: Y.5, Y.71, K.74 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.71, B:K.74, A:E.83 Water bridges: B:Y.71, B:L.72, B:N.75 GOL.5: 7 residues within 4Å: Chain A: K.6, I.43, T.46, L.47, I.54, E.56, T.61 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.6, A:K.6, A:T.46, A:T.61 GOL.8: 3 residues within 4Å: Chain B: Q.110, K.113, F.117 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.110, B:K.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulte, C.A. et al., A knowledge-based, structural-aided discovery of a novel class of 2-phenylimidazo[1,2-a]pyridine-6-carboxamide H-PGDS inhibitors. Bioorg.Med.Chem.Lett. (2021)

Release Date

2021-07-28

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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