Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 A resolution

Structure. 1995 Apr 15;3(4):365-79. doi: 10.1016/s0969-2126(01)00168-x.


Background: HIV-1 reverse transcriptase (RT) is a multifunctional enzyme that copies the RNA genome of HIV-1 into DNA. It is a heterodimer composed of a 66 kDa (p66) and a 51 kDa (p51) subunit. HIV-1 RT is a crucial target for structure-based drug design, and potent inhibitors have been identified, whose efficacy, however, is limited by drug resistance.

Results: The crystal structure of HIV-1 RT in complex with the non-nucleoside inhibitor alpha-anilinophenyl-acetamide (alpha-APA) R95845 has been determined at 2.8 A resolution. The inhibitor binds in a hydrophobic pocket near the polymerase active site. The pocket contains five aromatic amino acid residues and the interactions of the side chains of these residues with the aromatic rings of non-nucleoside inhibitors appear to be important for inhibitor binding. Most of the amino acid residues where mutations have been correlated with high levels of resistance to non-nucleoside inhibitors of HIV-1 RT are located close to alpha-APA. The overall fold of HIV-1 RT in complex with alpha-APA is similar to that found when in complex with nevirapine, another non-nucleoside inhibitor, but there are significant conformational changes relative to an HIV-1 RT/DNA/Fab complex.

Conclusions: The non-nucleoside inhibitor-binding pocket has a flexible structure whose mobility may be required for effective polymerization, and may be part of a hinge that permits relative movements of two subdomains of the p66 subunit denoted the 'palm' and 'thumb'. An understanding of the structure of the inhibitor-binding pocket, of the interactions between HIV-1 RT and alpha-APA, and of the locations of mutations that confer resistance to inhibitors provides a basis for structure-based design of chemotherapeutic agents for the treatment of AIDS.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Acetamides / chemistry
  • Acetamides / metabolism*
  • Acetamides / pharmacology
  • Acetophenones / chemistry
  • Acetophenones / metabolism*
  • Acetophenones / pharmacology
  • Amino Acid Sequence
  • Antiviral Agents / chemistry
  • Antiviral Agents / metabolism*
  • Antiviral Agents / pharmacology
  • Binding Sites
  • Crystallography, X-Ray
  • Deoxyuracil Nucleotides / metabolism
  • Drug Resistance, Microbial
  • Fourier Analysis
  • HIV Antibodies / metabolism
  • HIV Reverse Transcriptase
  • Immunoglobulin Fab Fragments / metabolism
  • Methylmercury Compounds / metabolism
  • Models, Molecular*
  • Molecular Sequence Data
  • Organomercury Compounds / metabolism
  • Protein Binding
  • Protein Conformation*
  • RNA-Directed DNA Polymerase / chemistry
  • RNA-Directed DNA Polymerase / immunology
  • RNA-Directed DNA Polymerase / metabolism*
  • Reverse Transcriptase Inhibitors
  • Sequence Alignment
  • Sequence Homology, Amino Acid


  • Acetamides
  • Acetophenones
  • Antiviral Agents
  • Deoxyuracil Nucleotides
  • HIV Antibodies
  • Immunoglobulin Fab Fragments
  • Methylmercury Compounds
  • Organomercury Compounds
  • Reverse Transcriptase Inhibitors
  • tetrakis(acetoxymercuri)methane
  • loviride
  • 5-mercurideoxyuridine triphosphate
  • reverse transcriptase, Human immunodeficiency virus 2
  • HIV Reverse Transcriptase
  • RNA-Directed DNA Polymerase
  • R 95845