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: 3.00 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

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Ligand Structure Quality Assessment 


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 Biol 2: 407-415

  • DOI: 10.1038/nsb0595-407
  • Primary Citation of Related Structures:  
    1HNV

  • 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 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 ...

    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 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
    • 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 Recognit 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
    • 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 U S A 90: 6320
    • 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 Discov Des 1: 129
    • 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 U S A 88: 10895

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)A558Human immunodeficiency virus 1Mutation(s): 0 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)B427Human immunodeficiency virus 1Mutation(s): 0 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TBO
Query on TBO

Download Ideal Coordinates CCD File 
C [auth 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
C16 H20 Cl N3 S
ZNFFMCYSMBXZQU-NSHDSACASA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TBO BindingDB:  1HNV IC50: min: 5, max: 4300 (nM) from 2 assay(s)
EC50: 5.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 227.2α = 90
b = 70.2β = 105.6
c = 105.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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