5C25

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 6-((4-((4-cyanophenyl)amino)-1,3,5-triazin-2-yl)amino)-5,7-dimethyl-2-naphthonitrile (JLJ639), a Non-nucleoside Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.841 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase.

Lee, W.G.Frey, K.M.Gallardo-Macias, R.Spasov, K.A.Chan, A.H.Anderson, K.S.Jorgensen, W.L.

(2015) Bioorg.Med.Chem.Lett. 25: 4824-4827

  • DOI: 10.1016/j.bmcl.2015.06.074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Non-nucleoside inhibitors of HIV-1 reverse transcriptase (HIV-RT) are reported that incorporate a 7-indolizinylamino or 2-naphthylamino substituent on a pyrimidine or 1,3,5-triazine core. The most potent compounds show below 10 nanomolar activity tow ...

    Non-nucleoside inhibitors of HIV-1 reverse transcriptase (HIV-RT) are reported that incorporate a 7-indolizinylamino or 2-naphthylamino substituent on a pyrimidine or 1,3,5-triazine core. The most potent compounds show below 10 nanomolar activity towards wild-type HIV-1 and variants bearing Tyr181Cys and Lys103Asn/Tyr181Cys resistance mutations. The compounds also feature good aqueous solubility. Crystal structures for two complexes enhance the analysis of the structure-activity data.


    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 B (isolate BH10)Mutation(s): 3 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT
B
428Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
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
639
Query on 639

Download SDF File 
Download CCD File 
A
6-({4-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}amino)-5,7- dimethyl-2-naphthonitrile
C23 H17 N7
KPKGAKOSWKZAAI-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.841 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/168 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 162.554α = 90.00
b = 72.969β = 100.66
c = 109.479γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI27690
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI44616
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM32136
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM49551
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI104334

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-11
    Type: Author supporting evidence