7T7H

Crystal structure of Vaccinia Virus decapping enzyme D9 in complex with inhibitor CP100356


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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This is version 1.2 of the entry. See complete history


Literature

Fluorescence-Based Activity Screening Assay Reveals Small Molecule Inhibitors of Vaccinia Virus mRNA Decapping Enzyme D9.

Bednarczyk, M.Peters, J.K.Kasprzyk, R.Starek, J.Warminski, M.Spiewla, T.Mugridge, J.S.Gross, J.D.Jemielity, J.Kowalska, J.

(2022) ACS Chem Biol 17: 1460-1471

  • DOI: https://doi.org/10.1021/acschembio.2c00049
  • Primary Citation of Related Structures:  
    7T7H

  • PubMed Abstract: 

    Vaccinia virus (VACV) represents a family of poxviruses, which possess their own decapping machinery as a part of their strategy to eliminate host mRNAs and evade the innate immune response. D9 is one of the two encoded VACV decapping enzymes that is responsible for cap removal from the 5' end of both host mRNA transcripts and viral double-stranded RNAs. Little is known about the structural requirements for D9 inhibition by small molecules. Here, we identified a minimal D9 substrate and used it to develop a real-time fluorescence assay for inhibitor discovery and characterization. We screened a panel of nucleotide-derived substrate analogues and pharmacologically active candidates to identify several compounds with nano- and low micromolar IC 50 values. m 7 GpppCH 2 p was the most potent nucleotide inhibitor (IC 50 ∼ 0.08 μM), and seliciclib and CP-100356 were the most potent drug-like compounds (IC 50 0.57 and 2.7 μM, respectively). The hits identified through screening inhibited D9-catalyzed decapping of 26 nt RNA substrates but were not active toward VACV D10 or human decapping enzyme, Dcp1/2. The inhibition mode for one of the compounds (CP-100356) was elucidated based on the X-ray cocrystal structure, opening the possibility for structure-based design of novel D9 inhibitors and binding probes.


  • Organizational Affiliation

    Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair NTP-phosphohydrolase
A, B
221Vaccinia virus Western ReserveMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P04311 (Vaccinia virus (strain Western Reserve))
Explore P04311 
Go to UniProtKB:  P04311
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04311
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.77α = 90
b = 82.77β = 90
c = 96.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5F32GM133084

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description