SMTL ID : 4ec0.1

Crystal structure of hH-PGDS with water displacing inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 13 residues within 4Å: Chain A: Y.9, F.10, R.15, W.40, K.44, G.50, K.51, I.52, P.53, Q.64, S.65 Chain B: D.98 Ligands: 7PQ.3 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.51 Hydrogen bonds: A:R.15, A:W.40, A:I.52, A:I.52, A:Q.64, A:S.65, B:D.98 Water bridges: A:K.51, A:I.52, A:Q.64, A:S.65, A:S.65, A:L.66 Salt bridges: A:K.44 GSH.4: 11 residues within 4Å: Chain A: D.98 Chain B: Y.9, R.15, W.40, K.44, G.50, K.51, I.52, P.53, Q.64, S.65 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.51 Hydrogen bonds: B:R.15, B:I.52, B:I.52, B:Q.64, B:Q.64, B:S.65, A:D.98 Water bridges: B:K.44, B:S.65, B:S.65, B:L.66, B:D.97 Salt bridges: B:K.44

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.97 No protein-ligand interaction detected (PLIP)

1 x 7PQ: 4-[2-(aminomethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide(Non-covalent)

7PQ.3: 12 residues within 4Å: Chain A: Y.9, M.12, R.13, G.14, R.15, D.97, M.100, W.105, Y.153, T.160, L.200 Ligands: GSH.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.15, A:M.100, A:W.105, A:T.160, A:L.200 Hydrogen bonds: A:R.13, A:G.14, A:W.105, A:T.160, A:L.200

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

2012-05-16

Peptides

Hematopoietic prostaglandin D synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hematopoietic prostaglandin D synthase