3R0Y

Crystal Structures of Multidrug-resistant HIV-1 Protease in Complex with Mechanism-Based Aspartyl Protease Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of multidrug-resistant HIV-1 protease in complex with two potent anti-malarial compounds.

Yedidi, R.S.Liu, Z.Wang, Y.Brunzelle, J.S.Kovari, I.A.Woster, P.M.Kovari, L.C.Gupta, D.

(2012) Biochem.Biophys.Res.Commun. 421: 413-417

  • DOI: 10.1016/j.bbrc.2012.03.096
  • Primary Citation of Related Structures:  3R0W

  • PubMed Abstract: 
  • Two potent inhibitors (compounds 1 and 2) of malarial aspartyl protease, plasmepsin-II, were evaluated against wild type (NL4-3) and multidrug-resistant clinical isolate 769 (MDR) variants of human immunodeficiency virus type-1 (HIV-1) aspartyl prote ...

    Two potent inhibitors (compounds 1 and 2) of malarial aspartyl protease, plasmepsin-II, were evaluated against wild type (NL4-3) and multidrug-resistant clinical isolate 769 (MDR) variants of human immunodeficiency virus type-1 (HIV-1) aspartyl protease. Enzyme inhibition assays showed that both 1 and 2 have better potency against NL4-3 than against MDR protease. Crystal structures of MDR protease in complex with 1 and 2 were solved and analyzed. Crystallographic analysis revealed that the MDR protease exhibits a typical wide-open conformation of the flaps (Gly48 to Gly52) causing an overall expansion in the active site cavity, which, in turn caused unstable binding of the inhibitors. Due to the expansion of the active site cavity, both compounds showed loss of direct contacts with the MDR protease compared to the docking models of NL4-3. Multiple water molecules showed a rich network of hydrogen bonds contributing to the stability of the ligand binding in the distorted binding pockets of the MDR protease in both crystal structures. Docking analysis of 1 and 2 showed a decrease in the binding affinity for both compounds against MDR supporting our structure-function studies. Thus, compounds 1 and 2 show promising inhibitory activity against HIV-1 protease variants and hence are good candidates for further development to enhance their potency against NL4-3 as well as MDR HIV-1 protease variants.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, 540 E. Canfield Avenue, Detroit, MI 48201, USA. yedidirs@mail.nih.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Multidrug-resistant clinical isolate 769 HIV-1 Protease
A, B
99Human immunodeficiency virus 1Gene Names: pol
Find proteins for Q000H7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q000H7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RSZ
Query on RSZ

Download SDF File 
Download CCD File 
A
N-[(2S)-1-{[(2S,3S)-3-hydroxy-5-oxo-5-{[(2R)-1-oxo-3-phenyl-1-(prop-2-yn-1-ylamino)propan-2-yl]amino}-1-phenylpentan-2-yl]amino}-3-methyl-1-oxobutan-2-yl]pyridine-2-carboxamide
C34 H39 N5 O5
RAZZBARIWRCYLK-MOWYSQRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RSZIC50: 14530 nM BINDINGMOAD
RSZKd: 14530 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 45.637α = 90.00
b = 45.637β = 90.00
c = 102.005γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Database references
  • Version 1.2: 2012-05-23
    Type: Database references
  • Version 1.3: 2012-12-12
    Type: Other