3DCR

X-ray structure of HIV-1 protease and hydrated form of ketomethylene isostere inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of chemically synthesized HIV-1 protease and a ketomethylene isostere inhibitor based on the p2/NC cleavage site

Torbeev, V.Y.Mandal, K.Terechko, V.A.Kent, S.B.H.

(2008) Bioorg.Med.Chem.Lett. 18: 4554-4557

  • DOI: 10.1016/j.bmcl.2008.07.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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, respectiv ...

    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.


    Organizational Affiliation

    Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA. torbeev@uchicago.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chemical analogue HIV-1 protease
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
Find proteins for O38732 (Human immunodeficiency virus 1)
Go to UniProtKB:  O38732
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KVS
Query on KVS

Download SDF File 
Download CCD File 
B
N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide
C36 H66 N10 O10
UUSXLKOKWOAAGR-WZGNFWQUSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
YCM
Query on YCM
A, B
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
NLE
Query on NLE
A, B
L-PEPTIDE LINKINGC6 H13 N O2LEU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KVSIC50: 6.3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.200α = 90.00
b = 58.077β = 90.00
c = 61.658γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement
Locallydata collection
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2013-10-16
    Type: Non-polymer description
  • Version 1.3: 2017-10-25
    Type: Refinement description