3QO9

Crystal structure of HIV-1 Reverse Transcriptase (RT) in complex with TSAO-T, a non-nucleoside RT inhibitor (NNRTI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of tert-Butyldimethylsilyl-spiroaminooxathioledioxide-thymine (TSAO-T) in Complex with HIV-1 Reverse Transcriptase (RT) Redefines the Elastic Limits of the Non-nucleoside Inhibitor-Binding Pocket.

Das, K.Bauman, J.D.Rim, A.S.Dharia, C.Clark, A.D.Camarasa, M.J.Balzarini, J.Arnold, E.

(2011) J Med Chem 54: 2727-2737

  • DOI: 10.1021/jm101536x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • tert-Butyldimethylsilyl-spiroaminooxathioledioxide (TSAO) compounds have an embedded thymidine-analogue backbone; however, TSAO compounds invoke non-nucleoside RT inhibitor (NNRTI) resistance mutations. Our crystal structure of RT:7 (TSAO-T) complex ...

    tert-Butyldimethylsilyl-spiroaminooxathioledioxide (TSAO) compounds have an embedded thymidine-analogue backbone; however, TSAO compounds invoke non-nucleoside RT inhibitor (NNRTI) resistance mutations. Our crystal structure of RT:7 (TSAO-T) complex shows that 7 binds inside the NNRTI-binding pocket, assuming a "dragon" shape, and interacts extensively with almost all the pocket residues. The structure also explains the structure-activity relationships and resistance data for TSAO compounds. The binding of 7 causes hyper-expansion of the pocket and significant rearrangement of RT subdomains. This nonoptimal complex formation is apparently responsible (1) for the lower stability of a RT (p66/p51) dimer and (2) for the lower potency of 7 despite of its extensive interactions with RT. However, the HIV-1 RT:7 structure reveals novel design features such as (1) interactions with the conserved Tyr183 from the YMDD-motif and (2) a possible way for an NNRTI to reach the polymerase active site that may be exploited in designing new NNRTIs.


    Related Citations: 
    • High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations
      (2008) Proc Natl Acad Sci U S A 105: 1466
    • 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.
      (2004) J Med Chem 47: 2550

    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, New Jersey 08854, United States. kalyan@cabm.rutgers.edu



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ ribonuclease H
A
557Human immunodeficiency virus type 1 BH10Mutation(s): 2 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.4.23.16 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
p51 RT
B
428Human immunodeficiency virus type 1 BH10Mutation(s): 1 
Gene Names: gag-pol
EC: 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
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
QO9
Query on QO9

Download CCD File 
A
1-[(5R,6R,8R,9R)-4-amino-9-{[tert-butyl(dimethyl)silyl]oxy}-6-({[tert-butyl(dimethyl)silyl]oxy}methyl)-2,2-dioxido-1,7-dioxa-2-thiaspiro[4.4]non-3-en-8-yl]-5-methylpyrimidine-2,4(1H,3H)-dione
C24 H43 N3 O8 S Si2
YMSLYTIPSGCZRM-DSPLJNTKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QO9IC50:  1200   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.76α = 90
b = 72.59β = 98.75
c = 108.97γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-02-09 
  • Released Date: 2011-05-04 
  • Deposition Author(s): Das, K., Arnold, E.

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-19
    Changes: Database references