› 4b1f

X-ray diffraction
2.05Å resolution

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

Released:
DOI: 10.2210/pdb4b1f/pdb
PDB entry 4b1f coloured by chain, front view.
PDB entry 4b1f coloured by chain, side view.
PDB entry 4b1f coloured by chain, top view.
Source organism: Helicobacter pylori
Primary publication:
Design of inhibitors of Helicobacter pylori glutamate racemase as selective antibacterial agents: incorporation of imidazoles onto a core pyrazolopyrimidinedione scaffold to improve bioavailabilty.
Basarab GS, Hill P, Eyermann CJ, Gowravaram M, Käck H, Osimoni E
Bioorg Med Chem Lett 22 5600-7 (2012)
PMID: 22877632

Function and Biology Details

Reaction catalysed: 
L-glutamate = D-glutamate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195675 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glutamate racemase Chains: A, B
Molecule details ›
Chains: A, B
Length: 255 amino acids
Theoretical weight: 28.53 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9ZLT0 (Residues: 1-255; Coverage: 100%)
Gene names: glr, jhp_0496, murI
Sequence domains: Asp/Glu/Hydantoin racemase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand KRH 2 x KRH
Ligand DGL 2 x DGL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF
Spacegroup: P212121
Unit cell:
a: 61.933Å b: 75.974Å c: 108.935Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.185 0.239
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Comprehensive review in current developments of imidazole-based medicinal chemistry.
Zhang et al. (2014)
9 other articles

3 mentions without citation

Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations.
Whalen et al. (2013)
2 more