Crystal structure of a complex of HIV-1 protease with a dihydroethylene-containing inhibitor: comparisons with molecular modeling

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 57% strand (DSSP).

Ligands and binding sites

• 1ZK · 4-[(2R)-3-{[(1S,2S,3R,4S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methyl-4-({(1S,2R)-2-methyl-1-[(pyridin-2-ylmethyl)carba moyl]butyl}carbamoyl)hexyl]amino}-2-{[(naphthalen-1-yloxy)acetyl]amino}-3-oxopropyl]-1H-imidazol-3-ium · ligand · 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 · 1834 Ų buried · 34 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (oxidation).

Compared structures

• 1HIV · Crystal structure of a complex of HIV-1 protease with a dihydroethylene-containing… · 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 P04585
• Elsewhere: RCSB PDB 1HIV · PDBe 1HIV · UniProt P04585