3LAK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2010.01.086

  • 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 in ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV Reverse transcriptase
A, B
560Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
KR1
Query on KR1

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Download CCD File 
A
3-({3-[(2-amino-6-fluoropyridin-4-yl)methyl]-5-(1-methylethyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl}carbonyl)-5-methylbenzonitrile
C22 H20 F N5 O3
SORPAQIMHXALKW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 118.025α = 90.00
b = 154.603β = 90.00
c = 154.478γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
BOSdata collection
EPMRphasing
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance