1N49

Viability of a Drug-Resistant HIV-1 Protease Variant: Structural Insights for Better Anti-Viral Therapy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Viability of a Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variant: Structural Insights for Better Antiviral Therapy

Prabu-Jeyabalan, M.Nalivaika, E.A.King, N.M.Schiffer, C.A.

(2003) J.VIROL. 77: 1306-1315

  • Primary Citation of Related Structures:  1MT7, 1MT8, 1MT9, 1MTB

  • PubMed Abstract: 
  • Under the selective pressure of protease inhibitor therapy, patients infected with human immunodeficiency virus (HIV) often develop drug-resistant HIV strains. One of the first drug-resistant mutations to arise in the protease, particularly in patien ...

    Under the selective pressure of protease inhibitor therapy, patients infected with human immunodeficiency virus (HIV) often develop drug-resistant HIV strains. One of the first drug-resistant mutations to arise in the protease, particularly in patients receiving indinavir or ritonavir treatment, is V82A, which compromises the binding of these and other inhibitors but allows the virus to remain viable. To probe this drug resistance, we solved the crystal structures of three natural substrates and two commercial drugs in complex with an inactive drug-resistant mutant (D25N/V82A) HIV-1 protease. Through structural analysis and comparison of the protein-ligand interactions, we found that Val82 interacts more closely with the drugs than with the natural substrate peptides. The V82A mutation compromises these interactions with the drugs while not greatly affecting the substrate interactions, which is consistent with previously published kinetic data. Coupled with our earlier observations, these findings suggest that future inhibitor design may reduce the probability of the appearance of drug-resistant mutations by targeting residues that are essential for substrate recognition.


    Related Citations: 
    • Lack of synergy for inhibitors targeting a multi-drug resistant HIV-1 protease
      King, N.M.,Melnick, L.,Prabu-Jeyabalan, M.,Nalivaika, E.A.,Yang, S.S.,Gao, Y.,Nie, X.,Zepp, C.,Heefner, D.L.,Schiffer, C.A.
      (2002) Protein Sci. 11: 418
    • How does a symmetric dimer recognize an asymmetric substrate? a substrate complex of HIV-1 protease
      Prabu-Jeyabalan, M.,Nalivaika, E.,Schiffer, C.A.
      (2000) J.Mol.Biol. 301: 1207
    • Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes
      Prabu-Jeyabalan, M.,Nalivaika, E.,Schiffer, C.A.
      (2002) Structure 10: 369
    • ABT-538 Is a Potent Inhibitor of Human Immunodeficiency Virus Protease and has High Oral Bioavailability in Humans
      Kempf, D.J.,Marsh, K.C.,Denissen, J.F.,McDonald, E.,Vasavanonda, S.,Flentge, C.A.,Green, B.E.,Fino, L.,Park, C.H.,Kong, X.,Wideburg, N.E.,Saldivar, A.,Ruiz, L.,Kati, W.M.,Sham, H.L.,Robins, T.,Stewart, K.D.,Hsu, A.,Plattner, J.J.,Leonard, J.M.,Norbeck, D.W.
      (1995) Proc.Natl.Acad.Sci.USA 92: 2484


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B, C, D
99Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03369
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RIT
Query on RIT

Download SDF File 
Download CCD File 
B, D
RITONAVIR
A-84538
C37 H48 N6 O5 S2
NCDNCNXCDXHOMX-XGKFQTDJSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001001 (RIT)
Query on PRD_001001
B,DRITONAVIRPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.620α = 90.00
b = 61.350β = 81.20
c = 59.040γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Type: Other
  • Version 1.4: 2017-10-11
    Type: Refinement description