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: 1.90 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 

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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
  • Primary Citation of Related Structures:  
    4L1A

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MDR769 HIV-1 proteaseA99Human immunodeficiency virus 1Mutation(s): 4 
Gene Names: pol
EC: 2.7.7.49 (UniProt), 3.1.26.13 (UniProt)
Find proteins for Q000H7 (Human immunodeficiency virus 1)
Explore Q000H7 
Go to UniProtKB:  Q000H7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MDR769 HIV-1 proteaseB99Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
EC: 2.7.7.49 (UniProt), 3.1.26.13 (UniProt)
Find proteins for Q000H7 (Human immunodeficiency virus 1)
Explore Q000H7 
Go to UniProtKB:  Q000H7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AB1
Query on AB1

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
C37 H48 N4 O5
KJHKTHWMRKYKJE-SUGCFTRWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AB1IC50:  5.389999866485596   nM  Binding MOAD
AB1IC50:  2.5   nM  BindingDB
AB1EC50:  1160   nM  BindingDB
AB1Kd:  0   nM  BindingDB
AB1Ki:  0.019999999552965164   nM  BindingDB
AB1Ki:  0   nM  BindingDB
AB1Ki:  1.399999976158142   nM  BindingDB
AB1Ki:  16   nM  BindingDB
AB1IC50:  25   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.828α = 90
b = 43.828β = 90
c = 101.805γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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