SMTL ID : 4ee0.1

Crystal structure of hH-PGDS with water displacing inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.96 Chain B: D.96 No protein-ligand interaction detected (PLIP)

2 x 0O4: 4-(isoquinolin-1-yl)-N-[2-(morpholin-4-yl)ethyl]benzamide(Non-covalent)

0O4.2: 11 residues within 4Å: Chain A: F.9, M.11, G.13, R.14, D.96, M.99, S.100, W.104, Y.152, L.199 Ligands: GSF.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.14, A:M.99, A:W.104 Water bridges: A:G.13, A:T.159 pi-Stacking: A:W.104, A:W.104 0O4.4: 11 residues within 4Å: Chain B: F.9, M.11, G.13, R.14, D.96, M.99, S.100, W.104, Y.152, L.199 Ligands: GSF.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.14, B:M.99, B:L.199 Water bridges: B:G.13, B:T.159 pi-Stacking: B:W.104, B:W.104

2 x GSF: L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE(Non-covalent)

GSF.3: 12 residues within 4Å: Chain A: Y.8, F.9, R.14, K.43, G.49, K.50, I.51, P.52, Q.63, S.64 Chain B: D.97 Ligands: 0O4.2 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.14, A:G.49, A:I.51, A:I.51, A:I.51, A:Q.63, A:Q.63, A:S.64, B:D.97 Water bridges: A:R.14, A:R.14, A:I.51, A:S.64, A:L.65 Salt bridges: A:R.14 GSF.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: 0O4.4 13 PLIP interactions: 12 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:R.14, B:Q.63, B:S.64, B:S.64, B:L.65 Salt bridges: B:R.14, B:K.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trujillo, J.I. et al., Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): a tale of two waters. Bioorg.Med.Chem.Lett. (2012)

Release Date

2012-07-18

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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