6W0T

Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design.

Zhang, S.Garzan, A.Haese, N.Bostwick, R.Martinez-Gzegozewska, Y.Rasmussen, L.Streblow, D.N.Haise, M.T.Pathak, A.K.Augelli-Szafran, C.E.Wu, M.

(2021) PLoS One 16: e0245013-e0245013

  • DOI: 10.1371/journal.pone.0245013
  • Primary Citation of Related Structures:  
    6W0T, 6VUQ, 6W7H, 6W91, 6W8Q, 6W8K, 6W8M, 6W8Z, 6W8Y

  • PubMed Abstract: 
  • The macrodomain of nsP3 (nsP3MD) is highly conserved among the alphaviruses and ADP-ribosylhydrolase activity of Chikungunya Virus (CHIKV) nsP3MD is critical for CHIKV viral replication and virulence. No small molecule drugs targeting CHIKV nsP3 have been identified to date ...

    The macrodomain of nsP3 (nsP3MD) is highly conserved among the alphaviruses and ADP-ribosylhydrolase activity of Chikungunya Virus (CHIKV) nsP3MD is critical for CHIKV viral replication and virulence. No small molecule drugs targeting CHIKV nsP3 have been identified to date. Here we report small fragments that bind to nsP3MD which were discovered by virtually screening a fragment library and X-ray crystallography. These identified fragments share a similar scaffold, 2-pyrimidone-4-carboxylic acid, and are specifically bound to the ADP-ribose binding site of nsP3MD. Among the fragments, 2-oxo-5,6-benzopyrimidine-4-carboxylic acid showed anti-CHIKV activity with an IC50 of 23 μM. Our fragment-based drug discovery approach provides valuable information to further develop a specific and potent nsP3 inhibitor of CHIKV viral replication based on the 2-pyrimidone-4-carboxylic acid scaffold. In silico studies suggest this pyrimidone scaffold could also bind to the macrodomains of other alphaviruses and coronaviruses and thus, have potential pan-antiviral activity.


    Organizational Affiliation

    Drug Discovery Division, Chemistry Department, Southern Research, Birmingham, Alabama, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 3A, B, C, D168Chikungunya virus strain Senegal 37997Mutation(s): 0 
EC: 3.1.3.84 (PDB Primary Data), 2.1.1 (UniProt), 2.7.7 (UniProt), 3.1.3.33 (UniProt), 3.4.22 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.19 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q5XXP4 (Chikungunya virus (strain 37997))
Explore Q5XXP4 
Go to UniProtKB:  Q5XXP4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S6Y
Query on S6Y

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]6-(2-methylpropyl)-2-oxidanylidene-5~{H}-pyrimidine-4-carboxylic acid
C9 H12 N2 O3
WDIFSCKLWBVBLR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.774α = 90
b = 87.774β = 90
c = 83.105γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-03-02 
  • Released Date: 2021-01-13 
  • Deposition Author(s): Wu, M., Zhang, S.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1U19AI142759-01

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references