5RE4

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1129283193


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 

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This is version 1.5 of the entry. See complete history


Literature

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.


Macromolecules
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
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

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.643α = 90
b = 52.352β = 103.08
c = 44.369γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SZYClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references, 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