5FIU

Binding and structural studies of a 5,5-difluoromethyl adenosine nucleoside with the fluorinase enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Exploration of a Potential Difluoromethyl-Nucleoside Substrate with the Fluorinase Enzyme.

Thompson, S.Mcmahon, S.A.Naismith, J.H.O'Hagan, D.

(2015) Bioorg.Chem. 64: 37

  • DOI: 10.1016/j.bioorg.2015.11.003

  • PubMed Abstract: 
  • The investigation of a difluoromethyl-bearing nucleoside with the fluorinase enzyme is described. 5',5'-Difluoro-5'-deoxyadenosine 7 (F2DA) was synthesised from adenosine, and found to bind to the fluorinase enzyme by isothermal titration calorimetry ...

    The investigation of a difluoromethyl-bearing nucleoside with the fluorinase enzyme is described. 5',5'-Difluoro-5'-deoxyadenosine 7 (F2DA) was synthesised from adenosine, and found to bind to the fluorinase enzyme by isothermal titration calorimetry with similar affinity compared to 5'-fluoro-5'-deoxyadenosine 2 (FDA), the natural product of the enzymatic reaction. F2DA7 was found, however, not to undergo the enzyme catalysed reaction with L-selenomethionine, unlike FDA 2, which undergoes reaction with L-selenomethionine to generate Se-adenosylselenomethionine. A co-crystal structure of the fluorinase and F2DA7 and tartrate was solved to 1.8Å, and revealed that the difluoromethyl group bridges interactions known to be essential for activation of the single fluorine in FDA 2. An unusual hydrogen bonding interaction between the hydrogen of the difluoromethyl group and one of the hydroxyl oxygens of the tartrate ligand was also observed. The bridging interactions, coupled with the inherently stronger C-F bond in the difluoromethyl group, offers an explanation for why no reaction is observed.


    Organizational Affiliation

    School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, St Andrews KY16 9ST, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-FLUORO-5'-DEOXY-ADENOSINE SYNTHASE
A, B, C
299Streptomyces cattleyaMutation(s): 0 
Gene Names: flA
EC: 2.5.1.63
Find proteins for Q70GK9 (Streptomyces cattleya)
Go to UniProtKB:  Q70GK9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download SDF File 
Download CCD File 
A, B, C
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Y3J
Query on Y3J

Download SDF File 
Download CCD File 
A, B, C
5,5-DIFLUOROMETHYL ADENOSINE
C10 H11 F2 N5 O3
YQLJSFYLQCBEKY-AVGUDYQDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 76.260α = 90.00
b = 129.160β = 90.00
c = 182.330γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release