4KKO

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 4-((4-methoxy-6-(2-morpholinoethoxy)-1,3,5-triazin-2-yl)amino)-2-((3-methylbut-2-en-1-yl)oxy)benzonitrile (JLJ513), a non-nucleoside inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Extension into the entrance channel of HIV-1 reverse transcriptase-Crystallography and enhanced solubility.

Bollini, M.Frey, K.M.Cisneros, J.A.Spasov, K.A.Das, K.Bauman, J.D.Arnold, E.Anderson, K.S.Jorgensen, W.L.

(2013) Bioorg.Med.Chem.Lett. 23: 5209-5212

  • DOI: 10.1016/j.bmcl.2013.06.093
  • Primary Citation of Related Structures:  4KO0

  • PubMed Abstract: 
  • Non-nucleoside inhibitors of HIV-1 reverse transcriptase (HIV-RT) are reported that feature extension into the entrance channel near Glu138. Complexes of the parent anilinylpyrimidine 1 and the morpholinoethoxy analog 2j with HIV-RT have received cry ...

    Non-nucleoside inhibitors of HIV-1 reverse transcriptase (HIV-RT) are reported that feature extension into the entrance channel near Glu138. Complexes of the parent anilinylpyrimidine 1 and the morpholinoethoxy analog 2j with HIV-RT have received crystallographic characterization confirming the designs. Measurement of aqueous solubilities of 2j, 2k, the parent triazene 2a, and other NNRTIs demonstrate profound benefits for addition of the morpholinyl substituent.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 reverse transcriptase, p66 subunit
A
557Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 reverse transcriptase, p51 subunit
B
428Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1RE
Query on 1RE

Download SDF File 
Download CCD File 
A
4-({4-methoxy-6-[2-(morpholin-4-yl)ethoxy]-1,3,5-triazin-2-yl}amino)-2-(3-methylbutoxy)benzonitrile
C22 H30 N6 O4
VZBHPTCAQDOYJZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 162.584α = 90.00
b = 73.886β = 100.16
c = 109.416γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
CBASSdata collection
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description