SMTL ID : 4edy.1

Crystal structure of hH-PGDS with water displacing inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 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 GSH: GLUTATHIONE(Non-covalent)

GSH.2: 12 residues within 4Å: Chain A: Y.8, F.9, R.14, W.39, K.43, K.50, I.51, P.52, Q.63, S.64 Chain B: D.97 Ligands: 9PQ.3 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.50 Hydrogen bonds: A:R.14, A:W.39, A:I.51, A:I.51, A:Q.63, A:S.64, B:D.97 Water bridges: A:K.50, A:I.51, A:Q.63, A:S.64, A:S.64, A:L.65 Salt bridges: A:K.43, A:K.50 GSH.5: 10 residues within 4Å: Chain A: D.97 Chain B: Y.8, R.14, W.39, K.43, K.50, I.51, P.52, Q.63, S.64 15 PLIP interactions: 14 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:Q.63, B:Q.63, B:S.64, B:S.64, B:L.65, B:D.96 Salt bridges: B:R.14, B:K.43, B:K.50

1 x 9PQ: 4-[2-(hydroxymethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide(Non-covalent)

9PQ.3: 14 residues within 4Å: Chain A: Y.8, F.9, M.11, R.12, G.13, R.14, Q.36, D.96, M.99, W.104, Y.152, T.159, L.199 Ligands: GSH.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.14, A:M.99, A:W.104, A:L.199 Hydrogen bonds: A:R.12, A:G.13, A:T.159, A:L.199

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 4 residues within 4Å: Chain B: G.13, M.99, Y.152, T.159 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.159

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

2012-10-03

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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