Crystal structure of HIV-1 reverse transcriptase in complex with N1-heterocycle pyrimidinedione non-nucleoside inhibitor

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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N1-Heterocyclic pyrimidinediones as non-nucleoside inhibitors of HIV-1 reverse transcriptase.

Mitchell, M.L.Son, J.C.Lee, I.Y.Lee, C.K.Kim, H.S.Guo, H.Wang, J.Hayes, J.Wang, M.Paul, A.Lansdon, E.B.Chen, J.M.Eisenberg, G.Geleziunas, R.Xu, L.Kim, C.U.

(2010) Bioorg Med Chem Lett 20: 1585-1588

  • DOI: https://doi.org/10.1016/j.bmcl.2010.01.086
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A series of N1-heterocyclic pyrimidinediones were extensively evaluated as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). Inhibitor 1 is active against NNRTI-resistant viruses including RT mutant K103N. The co-crystal structure of inhibitor 1 with HIV-1 RT revealed that H-bonds are formed with K101 and K103. Efforts to improve the suboptimal pharmacokinetic profile of 1 resulted in the discovery of compound 13, which represents the lead compound in this series with improved pharmacokinetics and similar potency as inhibitor 1.

  • Organizational Affiliation

    Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA. mmitchell@gilead.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV Reverse transcriptase
A, B
560HIV-1 M:B_HXB2RMutation(s): 0 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.025α = 90
b = 154.603β = 90
c = 154.478γ = 90
Software Package:
Software NamePurpose
BOSdata collection
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: 2010-02-23
    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