HIV-1 wild type protease with grl-034-17A, (3AS, 5R, 6AR)-2-oxohexahyd CYCLOPENTA[D]-5-oxazolyl urethane with a bicyclic oxazolidinone scaff as the P2 ligand

Structure

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

Ligands and binding sites

• J0S · (3as,5r,6ar)-2-oxohexahydro-2H-cyclopenta[d][1, 3]oxazol-5-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate · ligand · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• FMT · Formic acid · 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 · 1871 Ų buried · 37 hydrogen bonds · protein-protein

Compared structures

• 6E9A · HIV-1 WILD TYPE PROTEASE WITH GRL-034-17A, (3aS, 5R, 6aR)-2-OXOHEXAHYD… · 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 6E9A · PDBe 6E9A · UniProt Q5RZ08