SMTL ID : 2cvd.2 (1 other biounit)

Crystal structure analysis of human hematopoietic prostaglandin D synthase complexed with HQL-79

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.95 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: HQL.3 15 PLIP interactions: 14 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:R.13, A:K.42, A:I.50, A:Q.62, A:L.64 Salt bridges: A:R.13, A:K.42, A:K.49 GSH.6: 10 residues within 4Å: Chain A: D.96 Chain B: Y.7, R.13, W.38, K.42, K.49, I.50, P.51, Q.62, S.63 15 PLIP interactions: 13 interactions with chain B, 2 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:K.42, B:I.50, B:Q.62, B:L.64, A:D.92 Salt bridges: B:R.13, B:K.42, B:K.49

2 x HQL: 4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZOL-5-YL)PROPYL]PIPERIDINE(Non-covalent)

HQL.3: 12 residues within 4Å: Chain A: Y.7, M.10, G.12, R.13, M.98, F.101, W.103, Y.151, T.158, F.162, L.198 Ligands: GSH.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.13, A:M.98, A:F.101, A:W.103, A:T.158, A:F.162, A:L.198 pi-Stacking: A:F.101, A:W.103, A:W.103 HQL.7: 13 residues within 4Å: Chain B: Y.7, M.10, G.12, R.13, D.95, M.98, F.101, W.103, Y.151, T.158, L.159, F.162, L.198 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.13, B:M.98, B:F.101, B:F.101, B:T.158, B:L.159, B:F.162, B:L.198 Water bridges: B:Y.7 pi-Stacking: B:W.103, B:W.103

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Q.27, Y.28, D.30, W.189, R.192 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.27, A:Y.28, A:D.30, A:R.192, A:R.192 Water bridges: A:Y.28 GOL.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.8: 4 residues within 4Å: Chain B: Q.27, Y.28, E.29 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.27 GOL.9: 4 residues within 4Å: Chain B: Q.27, Y.28, W.189 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.27, B:Y.28, B:Y.28 Water bridges: B:Q.27 GOL.10: 5 residues within 4Å: Chain B: R.11, Q.195, T.196, K.197 Ligands: GOL.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.11, B:T.196, B:T.196 Water bridges: B:R.193, B:R.193, B:Q.195 GOL.11: 2 residues within 4Å: Chain B: K.197 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.197, B:K.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aritake, K. et al., Structural and Functional Characterization of HQL-79, an Orally Selective Inhibitor of Human Hematopoietic Prostaglandin D Synthase. J.Biol.Chem. (2006)

Release Date

2006-04-18

Peptides

Glutathione-requiring prostaglandin D synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Glutathione-requiring prostaglandin D synthase

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