7AEH

SARS-CoV-2 main protease in a covalent complex with a pyridine derivative of ABT-957, compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19.

Redhead, M.A.Owen, C.D.Brewitz, L.Collette, A.H.Lukacik, P.Strain-Damerell, C.Robinson, S.W.Collins, P.M.Schafer, P.Swindells, M.Radoux, C.J.Hopkins, I.N.Fearon, D.Douangamath, A.von Delft, F.Malla, T.R.Vangeel, L.Vercruysse, T.Thibaut, J.Leyssen, P.Nguyen, T.T.Hull, M.Tumber, A.Hallett, D.J.Schofield, C.J.Stuart, D.I.Hopkins, A.L.Walsh, M.A.

(2021) Sci Rep 11: 13208-13208

  • DOI: https://doi.org/10.1038/s41598-021-92416-4
  • Primary Citation of Related Structures:  
    7AEG, 7AEH

  • PubMed Abstract: 

    Effective agents to treat coronavirus infection are urgently required, not only to treat COVID-19, but to prepare for future outbreaks. Repurposed anti-virals such as remdesivir and human anti-inflammatories such as barcitinib have received emergency approval but their overall benefits remain unclear. Vaccines are the most promising prospect for COVID-19, but will need to be redeveloped for any future coronavirus outbreak. Protecting against future outbreaks requires the identification of targets that are conserved between coronavirus strains and amenable to drug discovery. Two such targets are the main protease (M pro ) and the papain-like protease (PL pro ) which are essential for the coronavirus replication cycle. We describe the discovery of two non-antiviral therapeutic agents, the caspase-1 inhibitor SDZ 224015 and Tarloxotinib that target M pro and PL pro , respectively. These were identified through extensive experimental screens of the drug repurposing ReFRAME library of 12,000 therapeutic agents. The caspase-1 inhibitor SDZ 224015, was found to be a potent irreversible inhibitor of M pro (IC 50 30 nM) while Tarloxotinib, a clinical stage epidermal growth factor receptor inhibitor, is a sub micromolar inhibitor of PL pro (IC 50 300 nM, K i 200 nM) and is the first reported PL pro inhibitor with drug-like properties. SDZ 224015 and Tarloxotinib have both undergone safety evaluation in humans and hence are candidates for COVID-19 clinical evaluation.


  • Organizational Affiliation

    Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK. mredhead@exscientia.co.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5305Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69
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: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.954α = 90
b = 53.08β = 103.02
c = 44.546γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 2.0: 2021-08-11
    Type: Coordinate replacement
    Reason: Chirality error
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2021-12-22
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 2.2: 2024-01-31
    Changes: Data collection, Refinement description