Design of inhibitors of helicobacter pylori glutamate racemase as selective antibacterial agents: incorporation of imidazoles onto a core pyrazolopyrimidinedione scaffold to improve bioavailabilty

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).

Ligands and binding sites

• 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 · ligand · 2 copies · chains A, B
• DGL · D-glutamic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 974 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 4B1F · Design of Inhibitors of Helicobacter pylori Glutamate Racemase as Selective Antibacterial… · the same entry in another collection · chain B against B, TM-score 1.00
• Q9ZLT0 · AlphaFold monomer V2.0 prediction for glutamate racemase (Q9ZLT0) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9ZLT0
• Elsewhere: RCSB PDB 4B1F · PDBe 4B1F · UniProt Q9ZLT0