Experimental Data Snapshot

  • Resolution: 3.2 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.274 

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant.

Das, K.Ding, J.Hsiou, Y.Clark Jr., A.D.Moereels, H.Koymans, L.Andries, K.Pauwels, R.Janssen, P.A.Boyer, P.L.Clark, P.Smith Jr., R.H.Kroeger Smith, M.B.Michejda, C.J.Hughes, S.H.Arnold, E.

(1996) J.Mol.Biol. 264: 1085-1100

  • Primary Citation of Related Structures:  
  • Also Cited By: 3BGR, 2ZE2, 2ZD1, 2IC3, 2IAJ, 1SV5, 1SUQ

  • PubMed Abstract: 
  • Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is an important target for chemotherapeutic agents used in the treatment of AIDS; the TIBO compounds are potent non-nucleoside inhibitors of HIV-1 RT (NNRTIs). Crystal structures ...

    Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is an important target for chemotherapeutic agents used in the treatment of AIDS; the TIBO compounds are potent non-nucleoside inhibitors of HIV-1 RT (NNRTIs). Crystal structures of HIV-1 RT complexed with 8-Cl TIBO (R86183, IC50 = 4.6 nM) and 9-Cl TIBO (R82913, IC50 = 33 nM) have been determined at 3.0 A resolution. Mutant HIV-1 RT, containing Cys in place of Tyr at position 181 (Tyrl81Cys), is highly resistant to many NNRTIs and HIV-1 variants containing this mutation have been selected in both cell culture and clinical trials. We also report the crystal structure of Tyrl81Cys HIV-1 RT in complex with 8-Cl TIBO (IC50 = 130 nM) determined at 3.2 A resolution. Averaging of the electron density maps computed for different HIV-1 RT/NNRTI complexes and from diffraction datasets obtained using a synchrotron source from frozen (-165 degrees C) and cooled (-10 degrees C) crystals of the same complex was employed to improve the quality of electron density maps and to reduce model bias. The overall locations and conformations of the bound inhibitors in the complexes containing wild-type HIV-1 RT and the two TIBO inhibitors are very similar, as are the overall shapes and volumes of the non-nucleoside inhibitor-binding pocket (NNIBP). The major differences between the two wild-type HIV-1 RT/TIBO complexes occur in the vicinity of the TIBO chlorine substituents and involve the polypeptide segments around the beta5-beta6 connecting loop (residues 95 to 105) and the beta13-beta14 hairpin (residues 235 and 236). In all known structures of HIV-1 RT/NNRTI complexes, including these two, the position of the beta12-beta13 hairpin or the "primer grip" is significantly displaced relative to the position in the structure of HIV-1 RT complexed with a double-stranded DNA and in unliganded HIV-1 RT structures. Since the primer grip helps to position the template-primer, this displacement suggests that binding of NNRTIs would affect the relative positions of the primer terminus and the polymerase active site. This could explain biochemical data showing that NNRTI binding to HIV-1 RT reduces efficiency of the chemical step of DNA polymerization, but does not prevent binding of either dNTPs or DNA. When the structure of the Tyr181Cys mutant HIV-1 RT in complex with 8-Cl TIBO is compared with the corresponding structure containing wild-type HIV-1 RT, the overall conformations of Tyr181Cys and wild-type HIV-1 RT and of the 8-Cl TIBO inhibitors are very similar. Some positional changes in the polypeptide backbone of the beta6-beta10-beta9 sheet containing residue 181 are observed when the Tyr181Cys and wild-type complexes are compared, particularlty near residue Val179 of beta9. In the p51 subunit, the Cys181 side-chain is oriented in a similar direction to the Tyr181 side-chain in the wild-type complex. However, the electron density corresponding to the sulfur of the Cys181 side-chain in the p66 subunit is very weak, indicating that the thiol group is disordered, presumably because there is no significant interaction with either 8-Cl TIBO or nearby amino acid residues. In the mutant complex, there are slight rearrangements of the side-chains of other amino acid residues in the NNIBP and of the flexible dimethylallyl group of 8-Cl TIBO; these conformational changes could potentially compensate for the interactions that were lost when the relatively large tyrosine at position 181 was replaced by a less bulky cysteine residue. In the corresponding wild-type complex, Tyr181 iin the p66 subunit has significant interactions with the bound inhibitor and the position of the Tyr181 side-chain is well defined in both subunits. Apparently the Tyr181 --> Cys mutation eliminates favorable contacts of the aromatic ring of the tyrosine and the bou

    Related Citations: 
    • 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.,Arnold, E.
      (1994) J.Mol.Biol. 243: 369
    • Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms
      Hsiou, Y.,Ding, J.,Das, K.,Clark Junior, A.D.,Hughes, S.H.,Arnold, E.
      (1996) Structure 4: 853
    • Insights Into DNA Polymerization Mechanisms from Structure and Function Analysis of HIV-1 Reverse Transcriptase
      Patel, P.H.,Jacobo-Molina, A.,Ding, J.,Tantillo, C.,Clark Junior, A.D.,Raag, R.,Nanni, R.G.,Hughes, S.H.,Arnold, E.
      (1995) Biochemistry 34: 5351
    • 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
    • Targeting HIV Reverse Transcriptase for Anti-Aids Drug Design: Structural and Biological Considerations for Chemotherapeutic Strategies
      Arnold, E.,Das, K.,Ding, J.,Yadav, P.N.,Hsiou, Y.,Boyer, P.L.,Hughes, S.H.
      (1996) Drug Des.Discovery 13: 29
    • Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution
      Ding, J.,Das, K.,Tantillo, C.,Zhang, W.,Clark Junior, A.D.,Jessen, S.,Lu, X.,Hsiou, Y.,Jacobo-Molina, A.,Andries, K.,al., et
      (1995) Structure 3: 365
    • Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 A 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.,al., et
      (1993) Proc.Natl.Acad.Sci.USA 90: 6320

    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine and Department of Chemistry, Rutgers University, Piscataway, NJ 08854-5638, USA.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
558Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 2 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
427Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 2 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on TBO

Download SDF File 
Download CCD File 
TBO 8; TIBO R86183
C16 H20 Cl N3 S
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TBOIC50: 5 - 4300 nM (98) BINDINGDB
TBOEC50: 5.1 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Resolution: 3.2 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.274 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 225.700α = 90.00
b = 69.200β = 106.60
c = 104.900γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-05-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance