4H4O

Crystal Structure of HIV-1 Reverse Transcriptase (RT) in Complex with (E)-3-(3-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)- 4-fluorophenoxy)-5-fluorophenyl)acrylonitrile (JLJ506), A Non-nucleoside inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of HIV-1 Reverse Transcriptase with Picomolar Inhibitors Reveal Key Interactions for Drug Design.

Frey, K.M.Bollini, M.Mislak, A.C.Cisneros, J.A.Gallardo-Macias, R.Jorgensen, W.L.Anderson, K.S.

(2012) J.Am.Chem.Soc. 134: 19501-19503

  • DOI: 10.1021/ja3092642
  • Primary Citation of Related Structures:  4H4M

  • PubMed Abstract: 
  • X-ray crystal structures at 2.9 Å resolution are reported for two complexes of catechol diethers with HIV-1 reverse transcriptase. The results help elucidate the structural origins of the extreme antiviral activity of the compounds. The possibility o ...

    X-ray crystal structures at 2.9 Å resolution are reported for two complexes of catechol diethers with HIV-1 reverse transcriptase. The results help elucidate the structural origins of the extreme antiviral activity of the compounds. The possibility of halogen bonding between the inhibitors and Pro95 is addressed. Structural analysis reveals key interactions with conserved residues P95 and W229 of importance for design of inhibitors with high potency and favorable resistance profiles.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H, Exoribonuclease H, p66 RT
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
Reverse transcriptase/ribonuclease H, Exoribonuclease H, p51 RT
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
506
Query on 506

Download SDF File 
Download CCD File 
A
(2E)-3-(3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-5-fluorophenyl)prop-2-enenitrile
C21 H15 F2 N3 O4
USRHSVZSPKDGMT-OWOJBTEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 225.451α = 90.00
b = 69.575β = 106.21
c = 104.401γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
PHASERphasing
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description