Crystal structure of fabi from F. tularensis in complex with novel inhibitors based on the benzimidazole scaffold

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).

Ligands and binding sites

• NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
• 1JU · 1-(1,3-benzodioxol-5-ylmethyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole · ligand · 8 copies · chains A, B, C, D, E, G, F, H
• NA · Sodium ion · metal · 3 copies · chains B, F, H
• GOL · Glycerol · additive · 7 copies · chains A, D, C, B, F, H, E
• ACT · Acetate ion · additive · 2 copies · chains B, D

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

Pockets

19 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Interfaces

20 interfaces between chains.

• A–C · 1725 Ų buried · 38 hydrogen bonds · protein-protein
• E–H · 1722 Ų buried · 39 hydrogen bonds · protein-protein
• F–G · 1714 Ų buried · 38 hydrogen bonds · protein-protein
• B–D · 1706 Ų buried · 40 hydrogen bonds · protein-protein
• A–B · 1384 Ų buried · 14 hydrogen bonds · protein-protein

Compared structures

• 4J4T · Crystal Structure of FabI from F. tularensis in complex with novel inhibitors based on… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q5NGQ3
• Elsewhere: RCSB PDB 4J4T · PDBe 4J4T · UniProt Q5NGQ3