SMTL ID : 5ywx.2 (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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.95, D.96 Chain B: D.95 No protein-ligand interaction detected (PLIP)

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.2: 12 residues within 4Å: Chain A: Y.7, F.8, R.13, W.38, K.42, K.49, I.50, P.51, Q.62, S.63 Chain B: D.96 Ligands: 93C.3 13 PLIP interactions: 12 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:Q.62, A:S.63, B:D.96 Water bridges: A:R.13, A:L.64, A:D.95 Salt bridges: A:R.13, A:K.42, A:K.49 GSH.4: 11 residues within 4Å: Chain A: D.96 Chain B: Y.7, F.8, R.13, W.38, K.49, I.50, P.51, Q.62, S.63 Ligands: 93C.5 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.49 Hydrogen bonds: B:K.49, B:I.50, B:I.50, B:Q.62, B:S.63, A:D.96 Water bridges: B:R.13, B:R.13, B:Q.62, B:L.64, B:D.95 Salt bridges: B:R.13

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

93C.3: 11 residues within 4Å: Chain A: M.10, G.12, R.13, Q.35, M.98, W.103, A.104, Y.151, C.155, L.198 Ligands: GSH.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.13, A:M.98, A:W.103 Water bridges: A:G.12, A:G.12, A:T.158 pi-Stacking: A:W.103, A:W.103 93C.5: 12 residues within 4Å: Chain B: F.8, M.10, G.12, R.13, Q.35, M.98, W.103, A.104, Y.151, C.155, L.198 Ligands: GSH.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.8, B:R.13, B:M.98, B:W.103 Water bridges: B:G.12, B:L.198 pi-Stacking: B:W.103, B:W.103

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain B: Q.27, Y.28, W.189 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.27, B:Y.28, B:Y.28

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
C

B
D

Hematopoietic prostaglandin D synthase

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