› 5ivs

X-ray diffraction
1.46Å resolution

Crystal Structure of HIV Protease complexed with methyl N-[(1S)-1-benzhydryl-2-[2-[2-[(2R,5S)-5-(benzylcarbamoyloxymethyl)morpholin-2-yl]ethyl]anilino]-2-oxo-ethyl]carbamate

Released:
DOI: 10.2210/pdb5ivs/pdb
PDB entry 5ivs coloured by chain, front view.
PDB entry 5ivs coloured by chain, side view.
PDB entry 5ivs coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Discovery of MK-8718, an HIV Protease Inhibitor Containing a Novel Morpholine Aspartate Binding Group.
Bungard CJ, Williams PD, Ballard JE, Bennett DJ, Beaulieu C, Bahnck-Teets C, Carroll SS, Chang RK, Dubost DC, Fay JF, Diamond TL, Greshock TJ, Hao L, Holloway MK, Felock PJ, Gesell JJ, Su HP, Manikowski JJ, McKay DJ, Miller M, Min X, Molinaro C, Moradei OM, Nantermet PG, Nadeau C, Sanchez RI, Satyanarayana T, Shipe WD, Singh SK, Truong VL, Vijayasaradhi S, Wiscount CM, Vacca JP, Crane SN, McCauley JA
ACS Med Chem Lett 7 702-7 (2016)
PMID: 27437081

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181217 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase A2 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 99 amino acids
Theoretical weight: 10.83 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q77VV3 (Residues: 1-99; Coverage: 100%)
Gene name: pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

2 bound ligands:
Ligand CL 3 x CL
Ligand 6EF 1 x 6EF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ DW
Spacegroup: P21212
Unit cell:
a: 57.79Å b: 86.14Å c: 46.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.184 0.198
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Drug Design Strategies to Avoid Resistance in Direct-Acting Antivirals and Beyond.
Matthew et al. (2021)
1 more

1 mention without citation

Accurate Binding Free Energy Method from End-State MD Simulations.
Akkus et al. (2022)