3DCK image
Deposition Date 2008-06-03
Release Date 2008-08-19
Last Version Date 2024-03-20
Entry Detail
PDB ID:
3DCK
Keywords:
HYDROLASE/HYDROLASE INHIBITOR
Title:
X-ray structure of D25N chemical analogue of HIV-1 protease complexed with ketomethylene isostere inhibitor
Biological Source:
Source Organism:
(Taxon ID: )
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.80 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
3DCK validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Chemical analogue HIV-1 protease
Mutations:D25N
Chain IDs:A, B
Chain Length:99
Number of Molecules:2
Biological Source:
UniProt ID:O38732 Pfam ID:PF00077
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ABA A ALA ALPHA-AMINOBUTYRIC ACID
NLE A LEU NORLEUCINE
YCM A CYS S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE
Ligand Molecules
KVI
Peptide-like Molecules
PRD_001174
Primary Citation
Crystal structure of chemically synthesized HIV-1 protease and a ketomethylene isostere inhibitor based on the p2/NC cleavage site
Bioorg.Med.Chem.Lett. 18 4554 4557 (2008)
PMID: 18657969 DOI: 10.1016/j.bmcl.2008.07.039

Abstact

Here we report the X-ray structures of chemically synthesized HIV-1 protease and the inactive [D25N]HIV-1 protease complexed with the ketomethylene isostere inhibitor Ac-Thr-Ile-Nle psi[CO-CH(2)]Nle-Gln-Arg.amide at 1.4 and 1.8A resolution, respectively. In complex with the active enzyme, the keto-group was found to be converted into the hydrated gem-diol, while the structure of the complex with the inactive D25N enzyme revealed an intact keto-group. These data support the general acid-general base mechanism for HIV-1 protease catalysis.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
3DCR