6W8K

Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report



Literature

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

Zhang, S.Garzan, A.Augelli-Szafran, C.E.Pathak, A.K.Wu, M.

(2020) PLoS One 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nonstructural polyproteinABCD168Chikungunya virusMutation(s): 0 
EC: 2.7.7.19 (UniProt), 3.1.3.33 (UniProt), 3.1.3.84 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
Find proteins for A0A4D6GPC4 (Chikungunya virus)
Explore A0A4D6GPC4 
Go to UniProtKB:  A0A4D6GPC4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TJ4
Query on TJ4

Download Ideal Coordinates CCD File 
A, B, C, D
5,6-dimethyl-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid
C7 H8 N2 O3
ZXECTTZQEACQGR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.013α = 90
b = 88.013β = 90
c = 83.552γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2021-01-13
    Type: Initial release