3IG1

HIV-1 Reverse Transcriptase with the Inhibitor beta-Thujaplicinol Bound at the RNase H Active Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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, A.D.Ryan, K.Hickey, M.J.Love, R.A.Hughes, S.H.Bergqvist, S.Arnold, E.

(2009) Structure 17: 1625-1635

  • DOI: 10.1016/j.str.2009.09.016
  • Primary Citation of Related Structures:  
  • Also Cited By: 3QLH

  • PubMed Abstract: 
  • Novel inhibitors are needed to counteract the rapid emergence of drug-resistant HIV variants. HIV-1 reverse transcriptase (RT) has both DNA polymerase and RNase H (RNH) enzymatic activities, but approved drugs that inhibit RT target the polymerase. I ...

    Novel inhibitors are needed to counteract the rapid emergence of drug-resistant HIV variants. HIV-1 reverse transcriptase (RT) has both DNA polymerase and RNase H (RNH) enzymatic activities, but approved drugs that inhibit RT target the polymerase. Inhibitors that act against new targets, such as RNH, should be effective against all of the current drug-resistant variants. Here, we present 2.80 A and 2.04 A resolution crystal structures of an RNH inhibitor, beta-thujaplicinol, bound at the RNH active site of both HIV-1 RT and an isolated RNH domain. beta-thujaplicinol chelates two divalent metal ions at the RNH active site. We provide biochemical evidence that beta-thujaplicinol is a slow-binding RNH inhibitor with noncompetitive kinetics and suggest that it forms a tropylium ion that interacts favorably with RT and the RNA:DNA substrate.


    Related Citations: 
    • Crystal Engineering of HIV-1 Reverse Transcriptase for Structure-based Drug Design
      Bauman, J.D.,Das, K.,Ho, W.C.,Baweja, M.,Himmel, D.M.,Clark Jr., A.D.,Oren, D.A.,Boyer, P.L.,Hughes, S.H.,Shatkin, A.J.,Arnold, E.
      (2008) Nucleic Acids Res. 36: 5083


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Reverse Transcriptase p66 subunit
A
555Human immunodeficiency virus type 1 group M subtype BMutation(s): 2 
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
HIV-1 Reverse Transcriptase p51 subunit
B
428Human 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A
2,7-dihydroxy-4-(propan-2-yl)cyclohepta-2,4,6-trien-1-one
beta-thujaplicinol
C10 H12 O3
HVGNSPLLPQWYGC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JTHIC50: 660 - 3800 nM (98) BINDINGDB
JTHKd: 730 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.238 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 164.057α = 90.00
b = 71.300β = 105.13
c = 108.541γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data collection
PDB_EXTRACTdata extraction
CNSrefinement
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description