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 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QO9Click on this verticalbar to view details

This is version 1.3 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: https://doi.org/10.1021/jm101536x
  • Primary Citation of Related Structures:  
    3QO9

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse transcriptase/ ribonuclease H557Human 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)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
p51 RT428Human 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)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QO9
Query on QO9

Download Ideal Coordinates CCD File 
C [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
QO9 BindingDB:  3QO9 IC50: min: 1000, max: 5.00e+5 (nM) from 6 assay(s)
EC50: min: 50, max: 60 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.286 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
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



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QO9Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description