4L1A

Crystallographic study of multi-drug resistant HIV-1 protease Lopinavir complex: mechanism of drug recognition and resistance


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


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Literature

Crystallographic study of multi-drug resistant HIV-1 protease lopinavir complex: mechanism of drug recognition and resistance.

Liu, Z.Yedidi, R.S.Wang, Y.Dewdney, T.G.Reiter, S.J.Brunzelle, J.S.Kovari, I.A.Kovari, L.C.

(2013) Biochem.Biophys.Res.Commun. 437: 199-204

  • DOI: 10.1016/j.bbrc.2013.06.027

  • PubMed Abstract: 
  • Lopinavir (LPV) is a second generation HIV-1 protease inhibitor. Drug resistance has rapidly emerged against LPV since its US FDA approval on September 15, 2000. Mutations at residues 32I, L33F, 46I, 47A, I54V, V82A, I84V, and L90M render the proteas ...

    Lopinavir (LPV) is a second generation HIV-1 protease inhibitor. Drug resistance has rapidly emerged against LPV since its US FDA approval on September 15, 2000. Mutations at residues 32I, L33F, 46I, 47A, I54V, V82A, I84V, and L90M render the protease drug resistant against LPV. We report the crystal structure of a clinical isolate multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, and 90) complexed with LPV and the in vitro enzymatic IC50 of LPV against MDR 769. The structural and functional studies demonstrate significant drug resistance of MDR 769 against LPV, arising from reduced interactions between LPV and the protease target.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MDR769 HIV-1 protease
A
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
Find proteins for Q000H7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q000H7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MDR769 HIV-1 protease
B
99Human immunodeficiency virus 1Mutation(s): 0 
Gene 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
AB1
Query on AB1

Download SDF File 
Download CCD File 
A
N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE
ABT-378, LOPINAVIR
C37 H48 N4 O5
KJHKTHWMRKYKJE-SUGCFTRWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AB1IC50: 5.39 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 43.828α = 90.00
b = 43.828β = 90.00
c = 101.805γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
HKL-2000data collection
d*TREKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release