HIV protease (pr) with inhibitor tl-3 and fragment hit 4D9 by soaking

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).

Ligands and binding sites

• 3TL · benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate · ligand · chains A, B
• 4DX · (1S,2S)-2-methylcyclohexanol · ligand · chains A
• K · Potassium ion · metal · 2 copies · chains A, B
• DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B
• BME · Beta-mercaptoethanol · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1788 Ų buried · 35 hydrogen bonds · protein-protein

Compared structures

• 3KFN · HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking · 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 Q903N5
• Elsewhere: RCSB PDB 3KFN · PDBe 3KFN · UniProt Q903N5