HIV-1 wild type protease with grl-026-18A, a crown-like tetrahydropyranotetrahydrofuran with a bridged methylene group as a P2 ligand

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 56% strand (DSSP).

Ligands and binding sites

• G6R · N-[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]-2-[(3s,3ar,5s, 7as,8s)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl]acetamide · ligand · chains A, B
• NA · Sodium ion · metal · chains A
• CL · Chloride ion · ion · 6 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · 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 · 1875 Ų buried · 37 hydrogen bonds · protein-protein

Compared structures

• 6VCE · HIV-1 wild type protease with GRL-026-18A, a crown-like tetrahydropyranotetrahydrofuran… · 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 6VCE · PDBe 6VCE · UniProt Q5RZ08