9CYB | pdb_00009cyb

SARS-CoV-2 PLpro in complex with inhibitor WEHI-P1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.208 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID.

M Bader, S.Calleja, D.J.Devine, S.M.Kuchel, N.W.Lu, B.G.C.Wu, X.Birkinshaw, R.W.Bhandari, R.Loi, K.Volpe, R.Khakham, Y.Au, A.E.Blackmore, T.R.Mackiewicz, L.Dayton, M.Schaefer, J.Scherer, L.Stock, A.T.Cooney, J.P.Schoffer, K.Maluenda, A.Kleeman, E.A.Davidson, K.C.Allison, C.C.Ebert, G.Chen, G.Katneni, K.Klemm, T.A.Nachbur, U.Georgy, S.R.Czabotar, P.E.Hannan, A.J.Putoczki, T.L.Tanzer, M.Pellegrini, M.Lechtenberg, B.C.Charman, S.A.Call, M.J.Mitchell, J.P.Lowes, K.N.Lessene, G.Doerflinger, M.Komander, D.

(2025) Nat Commun 16: 2900-2900

  • DOI: https://doi.org/10.1038/s41467-025-57905-4
  • Primary Citation of Related Structures:  
    9CYB, 9CYC, 9CYD, 9CYK

  • PubMed Abstract: 

    The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has highlighted the vulnerability of a globally connected population to zoonotic viruses. The FDA-approved coronavirus antiviral Paxlovid targets the essential SARS-CoV-2 main protease, Mpro. Whilst effective in the acute phase of a COVID infection, Paxlovid cannot be used by all patients, can lead to viral recurrence, and does not protect against post-acute sequelae of COVID-19 (PASC), commonly known as long COVID, an emerging significant health burden that remains poorly understood and untreated. Alternative antivirals that are addressing broader patient needs are urgently required. We here report our drug discovery efforts to target PLpro, a further essential coronaviral protease, for which we report a novel chemical scaffold that targets SARS-CoV-2 PLpro with low nanomolar activity, and which exhibits activity against PLpro of other pathogenic coronaviruses. Our lead compound shows excellent in vivo efficacy in a mouse model of severe acute disease. Importantly, our mouse model recapitulates long-term pathologies matching closely those seen in PASC patients. Our lead compound offers protection against a range of PASC symptoms in this model, prevents lung pathology and reduces brain dysfunction. This provides proof-of-principle that PLpro inhibition may have clinical relevance for PASC prevention and treatment going forward.


  • Organizational Affiliation

    Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease
A, B
318Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
EC: 3.4.19.12
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.455α = 90
b = 71.073β = 90
c = 176.118γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT117812
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT2016461
Wellcome TrustUnited Kingdom222698/Z/21/Z
National Health and Medical Research Council (NHMRC, Australia)AustraliaMRF2002119
National Health and Medical Research Council (NHMRC, Australia)AustraliaMRF2016781

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references