8C19

SARS-CoV-2 NSP3 macrodomain in complex with 1-methyl-4-[5-(morpholin-4-ylcarbonyl)-2-furyl]-1H-pyrrolo[2,3-b]pyridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Development Strategies for SARS-CoV-2 NSP3 Macrodomain Inhibitors.

Schuller, M.Zarganes-Tzitzikas, T.Bennett, J.De Cesco, S.Fearon, D.von Delft, F.Fedorov, O.Brennan, P.E.Ahel, I.

(2023) Pathogens 12

  • DOI: https://doi.org/10.3390/pathogens12020324
  • Primary Citation of Related Structures:  
    8C19, 8C1A

  • PubMed Abstract: 

    The worldwide public health and socioeconomic consequences caused by the COVID-19 pandemic highlight the importance of increasing preparedness for viral disease outbreaks by providing rapid disease prevention and treatment strategies. The NSP3 macrodomain of coronaviruses including SARS-CoV-2 is among the viral protein repertoire that was identified as a potential target for the development of antiviral agents, due to its critical role in viral replication and consequent pathogenicity in the host. By combining virtual and biophysical screening efforts, we discovered several experimental small molecules and FDA-approved drugs as inhibitors of the NSP3 macrodomain. Analogue characterisation of the hit matter and crystallographic studies confirming binding modes, including that of the antibiotic compound aztreonam, to the active site of the macrodomain provide valuable structure-activity relationship information that support current approaches and open up new avenues for NSP3 macrodomain inhibitor development.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 3
A, B
169Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.604α = 90
b = 88.604β = 90
c = 39.826γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210634

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection