3I0R

crystal structure of HIV reverse transcriptase in complex with inhibitor 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Substituted tetrahydroquinolines as potent allosteric inhibitors of reverse transcriptase and its key mutants.

Su, D.S.Lim, J.J.Tinney, E.Wan, B.L.Young, M.B.Anderson, K.D.Rudd, D.Munshi, V.Bahnck, C.Felock, P.J.Lu, M.Lai, M.T.Touch, S.Moyer, G.Distefano, D.J.Flynn, J.A.Liang, Y.Sanchez, R.Prasad, S.Yan, Y.Perlow-Poehnelt, R.Torrent, M.Miller, M.Vacca, J.P.Williams, T.M.Anthony, N.J.

(2009) Bioorg Med Chem Lett 19: 5119-5123

  • DOI: https://doi.org/10.1016/j.bmcl.2009.07.031
  • Primary Citation of Related Structures:  
    3I0R, 3I0S

  • PubMed Abstract: 

    Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are key elements of multidrug regimens, called HAART (Highly Active Antiretroviral Therapy), that are used to treat HIV-1 infections. Elucidation of the structure-activity relationships of the thiocarbamate moiety of the previous published lead compound 2 provided a series of novel tetrahydroquinoline derivatives as potent inhibitors of HIV-1 RT with nanomolar intrinsic activity on the WT and key mutant enzymes and potent antiviral activity in infected cells. The SAR optimization, mutation profiles, preparation of compounds, and pharmacokinetic profile of compounds are described.


  • Organizational Affiliation

    Department of Medicinal Chemistry and Structural Biology, Merck Research Laboratory, West Point, PA 19486, USA. Dai-Shi.X.Su@gsk.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse transcriptase/ribonuclease H563HIV-1 M:B_HXB2RMutation(s): 0 
Gene Names: gag-polHIV-1 pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
p51 RT443HIV-1 M:B_HXB2RMutation(s): 0 
Gene Names: gag-polHIV-1 pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RT3
Query on RT3

Download Ideal Coordinates CCD File 
C [auth A]S-{2-[(2-chloro-4-sulfamoylphenyl)amino]-2-oxoethyl} 6-methyl-3,4-dihydroquinoline-1(2H)-carbothioate
C19 H20 Cl N3 O4 S2
AWAKIULNKVOBKE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RT3 BindingDB:  3I0R IC50: min: 3, max: 1300 (nM) from 2 assay(s)
PDBBind:  3I0R IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.327α = 90
b = 155.308β = 90
c = 154.59γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description