SMTL ID : 4b1f.1

Design of Inhibitors of Helicobacter pylori Glutamate Racemase as Selective Antibacterial Agents: Incorporation of Imidazoles onto a Core Pyrazolopyrimidinedione Scaffold to Improve Bioavailabilty

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x KRH: 5-methyl-3-(1-methyl-1H-imidazol-5-yl)-7-(2-methylpropyl)-2-(naphthalen-1-ylmethyl)-2H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione(Non-covalent)

KRH.1: 14 residues within 4Å: Chain A: V.10, G.11, F.13, K.17, I.149, E.150, S.152, L.154, T.182, H.183, L.186, Q.248, W.252, L.253 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.10, A:K.17, A:E.150, A:L.186, A:L.253 pi-Stacking: A:H.183, A:W.252, A:W.252, A:W.252 KRH.4: 12 residues within 4Å: Chain B: V.10, G.11, F.13, K.17, I.149, E.150, S.152, L.154, H.183, L.186, Q.248, W.252 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.10, B:K.17, B:L.186, B:L.186 pi-Stacking: B:H.183, B:W.252, B:W.252, B:W.252

2 x DGL: D-GLUTAMIC ACID(Non-covalent)

DGL.2: 13 residues within 4Å: Chain A: D.7, S.8, V.37, P.38, Y.39, G.40, C.70, N.71, T.72, T.116, C.181, T.182, H.183 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.8, A:Y.39, A:G.40, A:N.71, A:T.72, A:T.72, A:T.72, A:T.182, A:T.182 Water bridges: A:T.119 DGL.3: 13 residues within 4Å: Chain B: D.7, S.8, V.37, P.38, Y.39, G.40, C.70, N.71, T.72, T.116, C.181, T.182, H.183 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.8, B:S.8, B:Y.39, B:G.40, B:N.71, B:T.72, B:T.72, B:T.72, B:T.182, B:T.182 Water bridges: B:T.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basarab, G.S. et al., Design of Inhibitors of Helicobacter Pylori Glutamate Racemase as Selective Antibacterial Agents: Incorporation of Imidazoles Onto a Core Pyrazolopyrimidinedione Scaffold to Improve Bioavailabilty. Bioorg.Med.Chem.Lett. (2012)

Release Date

2012-07-18

Peptides

GLUTAMATE RACEMASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GLUTAMATE RACEMASE

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