PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z1367324110

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.

Douangamath, A.Fearon, D.Gehrtz, P.Krojer, T.Lukacik, P.Owen, C.D.Resnick, E.Strain-Damerell, C.Aimon, A.Abranyi-Balogh, P.Brandao-Neto, J.Carbery, A.Davison, G.Dias, A.Downes, T.D.Dunnett, L.Fairhead, M.Firth, J.D.Jones, S.P.Keeley, A.Keseru, G.M.Klein, H.F.Martin, M.P.Noble, M.E.M.O'Brien, P.Powell, A.Reddi, R.N.Skyner, R.Snee, M.Waring, M.J.Wild, C.London, N.von Delft, F.Walsh, M.A.

(2020) Nat Commun 11: 5047-5047

  • DOI: https://doi.org/10.1038/s41467-020-18709-w
  • Primary Citation of Related Structures:  
    5R7Y, 5R7Z, 5R80, 5R81, 5R82, 5R83, 5R84, 5RE4, 5RE5, 5RE6, 5RE7, 5RE8, 5RE9, 5REA, 5REB, 5REC, 5RED, 5REE, 5REF, 5REG, 5REH, 5REI, 5REJ, 5REK, 5REL, 5REM, 5REN, 5REO, 5REP, 5RER, 5RES, 5RET, 5REU, 5REV, 5REW, 5REX, 5REY, 5REZ, 5RF0, 5RF1, 5RF2, 5RF3, 5RF4, 5RF5, 5RF6, 5RF7, 5RF8, 5RF9, 5RFA, 5RFB

  • PubMed Abstract: 

    COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.

  • Organizational Affiliation

    Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.78α = 90
b = 53.49β = 101.7
c = 44.45γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Structure summary
  • Version 1.2: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2021-01-27
    Changes: Structure summary
  • Version 1.4: 2021-02-24
    Changes: Database references
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references