5CUQ

Identification and characterization of novel broad spectrum inhibitors of the flavivirus methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Identification and Characterization of Novel Broad-Spectrum Inhibitors of the Flavivirus Methyltransferase.

Brecher, M.Chen, H.Li, Z.Banavali, N.K.Jones, S.A.Zhang, J.Kramer, L.D.Li, H.

(2015) ACS Infect Dis 1: 340-349

  • DOI: https://doi.org/10.1021/acsinfecdis.5b00070
  • Primary Citation of Related Structures:  
    5CUQ

  • PubMed Abstract: 

    Flavivirus methyltransferase (MTase) is essential for viral replication. Here we report the identification of small molecules through virtual screening that putatively bind to the SAM-binding site of flavivirus MTase and inhibit its function. Six of these computationally predicted binders were identified to show significant MTase inhibition with low micromolar inhibitory activity. The most active compounds showed broad-spectrum activity against the MTase proteins of other flaviviruses. Two of these compounds also showed low cytotoxicity and high antiviral efficacy in cell-based assays. Competitive binding analyses indicated that the inhibitors performed their inhibitory function through competitive binding to the SAM cofactor binding site of the MTase. The crystal structure of the MTase-inhibitor complex further supports the mode of action and provides routes for their further optimization as flavivirus MTase inhibitors.


  • Organizational Affiliation

    Wadsworth Center, New York State Department of Health , 120 New Scotland Avenue, Albany, New York 12208, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nonstructural protein NS5
A, B
267dengue virus type 3Mutation(s): 0 
UniProt
Find proteins for C0LMU0 (dengue virus type 3)
Explore C0LMU0 
Go to UniProtKB:  C0LMU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0LMU0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NSC
Query on NSC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N,N'-BIS(4-AMINO-2-METHYLQUINOLIN-6-YL)UREA
C21 H20 N6 O
HOUSDILKOJMENG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NSC Binding MOAD:  5CUQ IC50: 7700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.337α = 90
b = 99.299β = 99.2
c = 57.849γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI09433501

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description