5EIW

DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-ADENOSYL METHIONINE AND FRAGMENT NB3C2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.611 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of novel dengue virus NS5 methyltransferase non-nucleoside inhibitors by fragment-based drug design.

Benmansour, F.Trist, I.Coutard, B.Decroly, E.Querat, G.Brancale, A.Barral, K.

(2016) Eur.J.Med.Chem. 125: 865-880

  • DOI: 10.1016/j.ejmech.2016.10.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • With the aim to help drug discovery against dengue virus (DENV), a fragment-based drug design approach was applied to identify ligands targeting a main component of DENV replication complex: the NS5 AdoMet-dependent mRNA methyltransferase (MTase) dom ...

    With the aim to help drug discovery against dengue virus (DENV), a fragment-based drug design approach was applied to identify ligands targeting a main component of DENV replication complex: the NS5 AdoMet-dependent mRNA methyltransferase (MTase) domain, playing an essential role in the RNA capping process. Herein, we describe the identification of new inhibitors developed using fragment-based, structure-guided linking and optimization techniques. Thermal-shift assay followed by a fragment-based X-ray crystallographic screening lead to the identification of three fragment hits binding DENV MTase. We considered linking two of them, which bind to proximal sites of the AdoMet binding pocket, in order to improve their potency. X-ray crystallographic structures and computational docking were used to guide the fragment linking, ultimately leading to novel series of non-nucleoside inhibitors of flavivirus MTase, respectively N-phenyl-[(phenylcarbamoyl)amino]benzene-1-sulfonamide and phenyl [(phenylcarbamoyl)amino]benzene-1-sulfonate derivatives, that show a 10-100-fold stronger inhibition of 2'-O-MTase activity compared to the initial fragments.


    Organizational Affiliation

    Aix-Marseille Université, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille cedex 09, France; CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille cedex 09, France; Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS5 methyltransferase
A, C
276Dengue virus type 3 (strain Sri Lanka/1266/2000)Mutation(s): 0 
Gene Names: pol
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000))
Go to UniProtKB:  Q6YMS4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X0V
Query on X0V

Download SDF File 
Download CCD File 
A
4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE
C7 H7 F3 N2
RQWJHUJJBYMJMN-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, C
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.611 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.260α = 90.00
b = 184.370β = 90.00
c = 51.980γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
AutoPROCdata collection
PDB_EXTRACTdata extraction
SCALAdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-13-JS07-0006-01

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Advisory, Author supporting evidence, Data collection, Refinement description