2I5J

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with DHBNH, an RNASE H inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.

Himmel, D.M.Sarafianos, S.G.Dharmasena, S.Hossain, M.M.McCoy-Simandle, K.Ilina, T.Clark, A.D.Knight, J.L.Julias, J.G.Clark, P.K.Krogh-Jespersen, K.Levy, R.M.Hughes, S.H.Parniak, M.A.Arnold, E.

(2006) Acs Chem.Biol. 1: 702-712

  • DOI: 10.1021/cb600303y

  • PubMed Abstract: 
  • The rapid emergence of drug-resistant variants of human immunodeficiency virus, type 1 (HIV-1), has limited the efficacy of anti-acquired immune deficiency syndrome (AIDS) treatments, and new lead compounds that target novel binding sites are needed. ...

    The rapid emergence of drug-resistant variants of human immunodeficiency virus, type 1 (HIV-1), has limited the efficacy of anti-acquired immune deficiency syndrome (AIDS) treatments, and new lead compounds that target novel binding sites are needed. We have determined the 3.15 A resolution crystal structure of HIV-1 reverse transcriptase (RT) complexed with dihydroxy benzoyl naphthyl hydrazone (DHBNH), an HIV-1 RT RNase H (RNH) inhibitor (RNHI). DHBNH is effective against a variety of drug-resistant HIV-1 RT mutants. While DHBNH has little effect on most aspects of RT-catalyzed DNA synthesis, at relatively high concentrations it does inhibit the initiation of RNA-primed DNA synthesis. Although primarily an RNHI, DHBNH binds >50 A away from the RNH active site, at a novel site near both the polymerase active site and the non-nucleoside RT inhibitor (NNRTI) binding pocket. When DHBNH binds, both Tyr181 and Tyr188 remain in the conformations seen in unliganded HIV-1 RT. DHBNH interacts with conserved residues (Asp186, Trp229) and has substantial interactions with the backbones of several less well-conserved residues. On the basis of this structure, we designed substituted DHBNH derivatives that interact with the NNRTI-binding pocket. These compounds inhibit both the polymerase and RNH activities of RT.


    Related Citations: 
    • Crystal Structures for HIV-1 Reverse Transcriptase in Complexes with Three Pyridinone Derivatives: A New Class of Non-nucleoside Inhibitors Effective Against a Broad Range of Drug-Resistant Strains
      Himmel, D.M.,Das, K.,Clark Jr., A.D.,Hughes, S.H.,Benjahad, A.,Oumouch, S.,Guillemont, J.,Coupa, S.,Poncelet, A.,Csoka, I.,Meyer, C.,Andries, K.,Nguyen, C.H.,Grierson, D.S.,Arnold, E.
      (2005) J.Med.Chem. 48: 7582
    • Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA
      Sarafianos, S.G.,Das, K.,Tantillo, C.,Clark Jr., A.D.,Ding, J.,Whitcomb, J.M.,Boyer, P.L.,Hughes, S.H.,Arnold, E.
      (2001) EMBO J. 20: 1449
    • Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA Template-Primer and an Antibody Fab Fragment at 2.8 A Resolution.
      Ding, J.,Das, K.,Hsiou, Y.,Sarafianos, S.G.,Clark Jr., A.D.,Jacobo-Molina, A.,Tantillo, C.,Hughes, S.H.,Arnold, E.
      (1998) J.Mol.Biol. 284: 1095
    • Structure of unliganded HIV-1 reverse transcriptase t 2.7 A resolution: implications of conformational hanges for polymerization and inhibition mechanisms
      Hsiou, Y.,Ding, J.,Das, K.,Clark Jr., A.D.,Hughes, S.H.,Arnold, E.
      (1996) Structure 4: 853
    • Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent and Effective Against Wild-Type and Drug-Resistant HIV-1 Variants
      Das, K.,Clark Jr., A.D.,Lewi, P.J.,Heeres, J.,De Jonge, M.R.,Koymans, L.M.H.,Vinkers, H.M.,Daeyaert, F.,Ludovici, D.W.,Kukla, M.J.,De Corte, B.,Kavash, R.W.,Ho, C.Y.,Ye, H.,Lichtenstein, M.A.,Andries, K.,Pauwels, R.,De Bethune, M.-P.,Boyer, P.L.,Clark, P.,Hughes, S.H.,Janssen, P.A.J.,Arnold, E.
      (2004) J.Med.Chem. 47: 2550


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H P66 subunit
A
552Human 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/ribonuclease H P51 subunit
B
429Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
Find proteins for Q8UM83 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q8UM83
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
A, B
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
K05
Query on K05

Download SDF File 
Download CCD File 
A
(E)-3,4-DIHYDROXY-N'-[(2-METHOXYNAPHTHALEN-1-YL)METHYLENE]BENZOHYDRAZIDE
C19 H16 N2 O4
TVOPERZEGKBKAY-RGVLZGJSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K05IC50: 500 - >25000 nM (100) BINDINGDB
K05IC50: 500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 224.815α = 90.00
b = 68.896β = 106.48
c = 104.662γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
HKL-2000data collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description