Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 21% strand (DSSP).

Ligands and binding sites

• AVX · 3-(7-bromo-1,3-benzodioxol-5-yl)-1-methyl-1H-pyrazol-5-amine · ligand · 2 copies · chains A, B
• DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · chains A
• CD · Cadmium ion · metal · 4 copies · chains A, B
• MG · Magnesium ion · metal · chains A
• SO4 · Sulfate ion · ion · 4 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1505 Ų buried · 18 hydrogen bonds · protein-protein

Compared structures

• 3AO2 · Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase · 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 Q72498
• Elsewhere: RCSB PDB 3AO2 · PDBe 3AO2 · UniProt Q72498