Crystal structure of wild-type HIV-1 protease with cyclopentyltetrahydro- furanyl urethanes as P2-ligand, grl-0249A

Structure

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

Ligands and binding sites

• 0JV · methyl N-[(3S,3aR,5R,6aR)-5-[[(2S,3R)-4-[(4-methoxyphenyl)sulfonyl-(2-methylpropyl)amino]-3-oxidanyl-1-phenyl-butan-2-yl]carbamoyloxy]-3,3a,4,5,6,6a-hexahydro-2H-cyclopenta[b]furan-3-yl]carbamate · ligand · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 4 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 · 1862 Ų buried · 35 hydrogen bonds · protein-protein

Compared structures

• 4DFG · Crystal Structure of Wild-type HIV-1 Protease with Cyclopentyltetrahydro- furanyl… · the same entry in another collection · chain B against B, 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 P03367
• Elsewhere: RCSB PDB 4DFG · PDBe 4DFG · UniProt P03367