4QAG

Structure of a dihydroxycoumarin active-site inhibitor in complex with the RNASE H domain of HIV-1 reverse transcriptase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.712 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Dihydroxycoumarin Active-Site Inhibitor in Complex with the RNase H Domain of HIV-1 Reverse Transcriptase and Structure-Activity Analysis of Inhibitor Analogs.

Himmel, D.M.Myshakina, N.S.Ilina, T.Van Ry, A.Ho, W.C.Parniak, M.A.Arnold, E.

(2014) J.Mol.Biol. 426: 2617-2631

  • DOI: 10.1016/j.jmb.2014.05.006

  • PubMed Abstract: 
  • Human immunodeficiency virus (HIV) encodes four essential enzymes: protease, integrase, reverse transcriptase (RT)-associated DNA polymerase, and RT-associated ribonuclease H (RNase H). Current clinically approved anti-AIDS drugs target all HIV enzym ...

    Human immunodeficiency virus (HIV) encodes four essential enzymes: protease, integrase, reverse transcriptase (RT)-associated DNA polymerase, and RT-associated ribonuclease H (RNase H). Current clinically approved anti-AIDS drugs target all HIV enzymatic activities except RNase H, which has proven to be a very difficult target for HIV drug discovery. Our high-throughput screening activities identified the dihydroxycoumarin compound F3284-8495 as a specific inhibitor of RT RNase H, with low micromolar potency in vitro. Optimization of inhibitory potency can be facilitated by structural information about inhibitor-target binding. Here, we report the crystal structure of F3284-8495 bound to the active site of an isolated RNase H domain of HIV-1 RT at a resolution limit of 1.71Å. From predictions based on this structure, compounds were obtained that showed improved inhibitory activity. Computational analysis suggested structural alterations that could provide additional interactions with RT and thus improve inhibitory potency. These studies established proof of concept that F3284-8495 could be used as a favorable chemical scaffold for development of HIV RNase H inhibitors.


    Related Citations: 
    • HIGH-RESOLUTION STRUCTURES OF HIV-1 REVERSE TRANSCRIPTASE/TMC278 COMPLEXES: STRATEGIC FLEXIBILITY EXPLAINS POTENCY AGAINST RESISTANCE MUTATIONS
      Das, K.,Bauman, J.D.,Clark Jr., A.D.,Frenkel, Y.V.,Lewi, P.J.,Shatkin, A.J.,Hughes, S.H.,Arnold, E.
      (2008) Proc.Natl.Acad.Sci.USA 105: 1466
    • Structure of HIV-1 Reverse Transcriptase with the Inhibitor beta-Thujaplicinol Bound at the RNase H Active Site
      Himmel, D.M.,Maegley, K.A.,Pauly, T.A.,Bauman, J.D.,Das, K.,Dharia, C.,Clark Jr., A.D.,Ryan, K.,Hickey, M.J.,Love, R.A.,Hughes, S.H.,Bergqvist, S.,Arnold, E.
      (2009) Structure 17: 1625
    • 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 Jr., 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
    • Synthesis, Activity, and Structural Analysis of Novel ALPHA-HYDROXYTROPOLONE INHIBITORS OF HUMAN IMMUNODEFICIENCY VIRUS REVERSE TRANSCRIPTASE-ASSOCIATED RIBONUCLEASE H
      Chung, S.,Himmel, D.M.,Jiang, J.,Wojtak, K.,Bauman, J.D.,Rausch, J.W.,Wilson, J.A.,Beutler, J.A.,Thomas, C.J.,Arnold, E.,Le Grice, S.F.J.
      (2011) J.Med.Chem. 54: 4462


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-5627, USA. Electronic address: himmel@cabm.rutgers.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
A, B
133Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 0 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
F95
Query on F95

Download SDF File 
Download CCD File 
A, B
(7,8-dihydroxy-2-oxo-2H-chromen-4-yl)acetic acid
C11 H8 O6
LNRFNPKOQGRTFS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F95IC50: 4800 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.712 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.182 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 51.164α = 90.00
b = 51.164β = 90.00
c = 112.100γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-06-25
    Type: Database references
  • Version 1.2: 2014-07-09
    Type: Database references