HIV-1 wild type protease with grl-0518A , an isophthalamide-derived P2-P3 ligand with the para-hydoxymethyl sulfonamide isostere as the P2' group

Structure

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

Ligands and binding sites

• 8HD · N~3~-{(2S,3R)-3-hydroxy-4-[{[4-(hydroxymethyl) phenyl]sulfonyl}(2-methylpropyl)amino]-1-phenylbutan-2-yl}-N~1~-methyl-N~1~-[(4-methyl-1,3-oxazol-2-yl) methyl]benzene-1,3-dicarboxamide · ligand · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 3 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, 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 · 1876 Ų buried · 39 hydrogen bonds · protein-protein

Compared structures

• 5UPZ · HIV-1 wild Type protease with GRL-0518A , an isophthalamide-derived P2-P3 ligand with the… · 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 C8B467
• Elsewhere: RCSB PDB 5UPZ · PDBe 5UPZ · UniProt C8B467