1BQM

HIV-1 RT/HBY 097


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.362 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance.

Hsiou, Y.Das, K.Ding, J.Clark Jr., A.D.Kleim, J.P.Rosner, M.Winkler, I.Riess, G.Hughes, S.H.Arnold, E.

(1998) J.Mol.Biol. 284: 313-323

  • DOI: 10.1006/jmbi.1998.2171
  • Primary Citation of Related Structures:  
  • Also Cited By: 2IC3, 2IAJ

  • PubMed Abstract: 
  • The second generation Hoechst-Bayer non-nucleoside inhibitor, HBY 097 (S-4-isopropoxycarbonyl-6-methoxy-3-(methylthiomethyl)-3, 4-dihydroqui noxalin-2(1H)-thione), is an extremely potent inhibitor of HIV-1 reverse transcriptase (RT) and of HIV-1 infe ...

    The second generation Hoechst-Bayer non-nucleoside inhibitor, HBY 097 (S-4-isopropoxycarbonyl-6-methoxy-3-(methylthiomethyl)-3, 4-dihydroqui noxalin-2(1H)-thione), is an extremely potent inhibitor of HIV-1 reverse transcriptase (RT) and of HIV-1 infection in cell culture. HBY 097 selects for unusual drug-resistance mutations in HIV-1 RT (e.g. Gly190Glu) when compared with other non-nucleoside RT inhibitors (NNRTIs), such as nevirapine, alpha-APA and TIBO. We have determined the structure of HBY 097 complexed with wild-type HIV-1 RT at 3.1 A resolution. The HIV-1 RT/HBY 097 structure reveals an overall inhibitor geometry and binding mode differing significantly from RT/NNRTI structures reported earlier, in that HBY 097 does not adopt the usual butterfly-like shape. We have determined the structure of the Tyr188Leu HIV-1 RT drug-resistant mutant in complex with HBY 097 at 3.3 A resolution. HBY 097 binds to the mutant RT in a manner similar to that seen in the wild-type RT/HBY 097 complex, although there are some repositioning and conformational alterations of the inhibitor. Conformational changes of the structural elements forming the inhibitor-binding pocket, including the orientation of some side-chains, are observed. Reduction in the size of the 188 side-chain and repositioning of the Phe227 side-chain increases the volume of the binding cavity in the Tyr188Leu HIV-1 RT/HBY 097 complex. Loss of important protein-inhibitor interactions may account for the reduced potency of HBY 097 against the Tyr188Leu HIV-1 RT mutant. The loss of binding energy may be partially offset by additional contacts resulting from conformational changes of the inhibitor and nearby amino acid residues. This would suggest that inhibitor flexibility can help to minimize drug resistance.


    Related Citations: 
    • 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
    • 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.,Pauwels, R.,Moereels, H.,Koymans, L.,Janssen, P.A.J.,Smith Junior, R.H.,Kroeger Koepke, M.,Michejda, C.J.,Hughes, S.H.,Arnold, E.
      (1995) Structure 3: 365
    • 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 Junior, A.D.,Moereels, H.,Koymans, L.,Andries, K.,Pauwels, R.,Janssen, P.A.,Boyer, P.L.,Clark, P.,Smith Junior, R.H.,Kroeger Smith, M.B.,Michejda, C.J.,Hughes, S.H.,Arnold, E.
      (1996) J.Mol.Biol. 264: 1085
    • 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
    • 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.,Hizi, A.,Hughes, S.H.,Arnold, E.
      (1993) Proc.Natl.Acad.Sci.USA 90: 6320
    • 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


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine (CABM) and Rutgers University Chemistry Department, 679 Hoes Lane, Piscataway, NJ, 08854-5638, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REVERSE TRANSCRIPTASE
A
556Human immunodeficiency virus type 1 group M subtype BMutation(s): 1 
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
REVERSE TRANSCRIPTASE
B
430Human immunodeficiency virus type 1 group M subtype BMutation(s): 1 
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
HBY
Query on HBY

Download SDF File 
Download CCD File 
A
(S)-4-ISOPROPOXYCARBONYL-6-METHOXY-3-METHYLTHIOMETHYL-3,4-DIHYDROQUINOXALIN-2(1H)-THIONE
HBY 097
C15 H20 N2 O3 S2
GWKIPRVERALPRD-ZDUSSCGKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HBYIC50: 8 - 56 nM (98) BINDINGDB
HBYIC50: 45 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.362 
  • R-Value Work: 0.258 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 225.200α = 90.00
b = 69.400β = 106.40
c = 104.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
X-PLORphasing
CCP4data scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-06
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance