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

Crystal structure of hematopoietic prostaglandin D synthase in complex with F092

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 11 residues within 4Å: Chain A: Y.7, F.8, R.13, W.38, K.49, I.50, P.51, Q.62, S.63 Chain B: D.96 Ligands: 93C.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.49 Hydrogen bonds: A:I.50, A:I.50, A:Q.62, A:S.63, B:D.96 Water bridges: A:R.13, A:Q.62, A:L.64, A:D.95 Salt bridges: A:R.13 GSH.6: 13 residues within 4Å: Chain A: D.96 Chain B: Y.7, F.8, R.13, W.38, K.42, G.48, K.49, I.50, P.51, Q.62, S.63 Ligands: 93C.7 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.49 Hydrogen bonds: B:I.50, B:I.50, B:Q.62, B:S.63, A:D.96 Water bridges: B:R.13, B:R.13, B:I.50, B:Q.62, B:L.64 Salt bridges: B:R.13, B:K.42, B:K.49

2 x 93C: N-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl)pyrimidine-5-carboxamide(Non-covalent)

93C.2: 12 residues within 4Å: Chain A: F.8, M.10, G.12, R.13, Q.35, M.98, W.103, A.104, Y.151, C.155, L.198 Ligands: GSH.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.8, A:R.13, A:M.98, A:W.103 Water bridges: A:G.12, A:R.13, A:T.158, A:T.158 pi-Stacking: A:W.103, A:W.103 93C.7: 11 residues within 4Å: Chain B: M.10, G.12, R.13, Q.35, M.98, W.103, A.104, Y.151, C.155, L.198 Ligands: GSH.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.13, B:M.98, B:W.103 Water bridges: B:G.12, B:T.158, B:L.198 pi-Stacking: B:W.103

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.11, Q.195, T.196, K.197 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.11, A:Q.195, A:T.196, A:T.196 Water bridges: A:R.193, A:R.193, A:R.193 GOL.4: 3 residues within 4Å: Chain A: Q.27, Y.28, E.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.27 Water bridges: A:Y.28, A:Y.28

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain B: D.95 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takaya, D. et al., Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies. Bioorg. Med. Chem. (2018)

Release Date

2018-09-05

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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