1HNV

STRUCTURE OF HIV-1 RT(SLASH)TIBO R 86183 COMPLEX REVEALS SIMILARITY IN THE BINDING OF DIVERSE NONNUCLEOSIDE INHIBITORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of HIV-1 RT/TIBO R 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors.

Ding, J.Das, K.Moereels, H.Koymans, L.Andries, K.Janssen, P.A.Hughes, S.H.Arnold, E.

(1995) Nat.Struct.Mol.Biol. 2: 407-415

  • Also Cited By: 1SV5, 1SUQ

  • PubMed Abstract: 
  • We report the structure of HIV-1 reverse transcriptase (RT) complexed with the nonnucleoside inhibitor TIBO R 86183 at 3.0 A resolution. Comparing this structure with those of complexes of HIV-1 RT/alpha-APA R 95845 and HIV-1 RT/nevirapine provides a ...

    We report the structure of HIV-1 reverse transcriptase (RT) complexed with the nonnucleoside inhibitor TIBO R 86183 at 3.0 A resolution. Comparing this structure with those of complexes of HIV-1 RT/alpha-APA R 95845 and HIV-1 RT/nevirapine provides a basis for understanding the nature of nonnucleoside inhibitor binding, the structure of the binding site and the interactions between the bound inhibitors and surrounding amino acid residues as well as for understanding mechanisms of inhibition by and resistance to nonnucleoside inhibitors. All three inhibitors considered assume a similar butterfly-like shape and bind to HIV-1 RT in a very similar way. Important differences occur in the conformation of amino acid residues that form the binding pocket.


    Related Citations: 
    • Structure of HIV-1 Reverse Transcriptase(Slash)DNA Complex at 7 Angstroms Resolution Showing Active Site Locations
      Arnold, E.,Jacobo-Molina, A.,Nanni, R.G.,Williams, R.L.,Lu, X.,Ding, J.,Clark Junior, A.D.,Zhang, A.,Ferris, A.L.,Clark, P.,Hizi, A.,Hughes, S.H.
      (1992) Nature 357: 85
    • Crystals of a Ternary Complex of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with a Monoclonal Antibody Fab Fragment and Double-Stranded DNA Diffract X-Rays to 3.5 Angstroms Resolution
      Jacobo-Molina, A.,Clark Junior, A.D.,Williams, R.L.,Nanni, R.G.,Clark, P.,Ferris, A.L.,Hughes, S.H.,Arnold, E.
      (1991) Proc.Natl.Acad.Sci.USA 88: 10895
    • Structure of HIV-1 Reverse Transcriptase in a Complex with the Nonnucleoside Inhibitor Alpha-Apa R95845 at 2.8 Angstroms Resolution
      Ding, J.,Das, K.,Tantillo, C.,Zhang, W.,Clark Junior, A.D.,Jessen, S.,Lu, X.,Hsiou, Y.,Jacobo-Molina, A.,Andries, K.,Pauwels, R.,Moereels, H.,Koymans, L.,Janssen, P.A.J.,Smith Junior, R.H.,Koepke, M.K.,Michejda, C.J.,Hughes, S.H.,Arnold, E.
      (1995) Structure 3: 365
    • Review of HIV-1 Reverse Transcriptase Three-Dimensional Structure: Implications for Drug Design
      Nanni, R.G.,Ding, J.,Jacobo-Molina, A.,Hughes, S.H.,Arnold, E.
      (1993) Perspect.Drug Discovery Des. 1: 129
    • Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 Angstroms Resolution Shows Bent DNA
      Jacobo-Molina, A.,Ding, J.,Nanni, R.G.,Clark Junior, A.D.,Lu, X.,Tantillo, C.,Williams, R.L.,Kamer, G.,Ferris, A.L.,Clark, P.,Hizi, A.,Hughes, S.H.,Arnold, E.
      (1993) Proc.Natl.Acad.Sci.USA 90: 6320
    • Buried Surface Analysis of HIV-1 Reverse Transcriptase P66(Slash)P51 Heterodimer and its Interaction with DsDNA Template(Slash)Primer
      Ding, J.,Jacobo-Molina, A.,Tantillo, C.,Lu, X.,Nanni, R.G.,Arnold, E.
      (1994) J.Mol.Recog. 7: 157
    • Locations of Anti-Aids Drug Binding Sites and Resistance Mutations in the Three-Dimensional Structure of HIV-1 Reverse Transcriptase: Implications for Mechanisms of Drug Inhibition and Resistance
      Tantillo, C.,Ding, J.,Jacobo-Molina, A.,Nanni, R.G.,Boyer, P.L.,Hughes, S.H.,Pauwels, R.,Andries, K.,Janssen, P.A.J.,Arnold, E.
      (1994) J.Mol.Biol. 243: 369


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine (CABM), Piscataway, New Jersey 08854-5638, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
A
558Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
B
427Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TBO
Query on TBO

Download SDF File 
Download CCD File 
A
5-CHLORO-8-METHYL-7-(3-METHYL-BUT-2-ENYL)-6,7,8,9-TETRAHYDRO-2H-2,7,9A-TRIAZA-BENZO[CD]AZULENE-1-THIONE
TBO 8; TIBO R86183
C16 H20 Cl N3 S
ZNFFMCYSMBXZQU-NSHDSACASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TBOEC50: 5.1 nM (98) BINDINGDB
TBOIC50: 4300 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 227.200α = 90.00
b = 70.200β = 105.60
c = 105.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-10
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance