HIV-1 wild type protease with grl-04315A, a tetrahydronaphthalene carboxamide with (R)-boc-amine and (S)-hydroxyl functionalities as the P2 ligand

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 56% strand (DSSP).

Ligands and binding sites

• GA5 · tert-butyl [(1R,4S)-4-hydroxy-7-{[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamoyl}-1,2,3,4-tetrahydronaphthalen-1-yl]carbamate · ligand · chains A, B
• NA · Sodium ion · metal · chains A
• CL · Chloride ion · ion · 2 copies · chains A, B
• ACT · Acetate ion · additive · chains B
• GOL · Glycerol · 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 · 1874 Ų buried · 38 hydrogen bonds · protein-protein

Compared structures

• 6DV4 · HIV-1 wild type protease with GRL-04315A, a tetrahydronaphthalene carboxamide with… · 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 Q5RZ08
• Elsewhere: RCSB PDB 6DV4 · PDBe 6DV4 · UniProt Q5RZ08