6XHL

Covalent complex of SARS-CoV main protease with N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted V2MClick on this verticalbar to view details

This is version 2.2 of the entry. See complete history


Literature

Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19.

Hoffman, R.L.Kania, R.S.Brothers, M.A.Davies, J.F.Ferre, R.A.Gajiwala, K.S.He, M.Hogan, R.J.Kozminski, K.Li, L.Y.Lockner, J.W.Lou, J.Marra, M.T.Mitchell Jr., L.J.Murray, B.W.Nieman, J.A.Noell, S.Planken, S.P.Rowe, T.Ryan, K.Smith 3rd, G.J.Solowiej, J.E.Steppan, C.M.Taggart, B.

(2020) J Med Chem 63: 12725-12747

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01063
  • Primary Citation of Related Structures:  
    6XHL, 6XHM, 6XHN, 6XHO

  • PubMed Abstract: 

    The novel coronavirus disease COVID-19 that emerged in 2019 is caused by the virus SARS CoV-2 and named for its close genetic similarity to SARS CoV-1 that caused severe acute respiratory syndrome (SARS) in 2002. Both SARS coronavirus genomes encode two overlapping large polyproteins, which are cleaved at specific sites by a 3C-like cysteine protease (3CL pro ) in a post-translational processing step that is critical for coronavirus replication. The 3CL pro sequences for CoV-1 and CoV-2 viruses are 100% identical in the catalytic domain that carries out protein cleavage. A research effort that focused on the discovery of reversible and irreversible ketone-based inhibitors of SARS CoV-1 3CL pro employing ligand-protease structures solved by X-ray crystallography led to the identification of 3 and 4 . Preclinical experiments reveal 4 ( PF-00835231 ) as a potent inhibitor of CoV-2 3CL pro with suitable pharmaceutical properties to warrant further development as an intravenous treatment for COVID-19.


  • Organizational Affiliation

    Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121 United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
307Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: 1a
EC: 3.4.22.69
UniProt
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus)
Explore P0C6U8 
Go to UniProtKB:  P0C6U8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6U8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V2M (Subject of Investigation/LOI)
Query on V2M

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
C24 H34 N4 O6
FDQSUXUTXIGUIA-PRIDNEQBSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
V2M BindingDB:  6XHL Ki: 4.9 (nM) from 1 assay(s)
IC50: min: 4, max: 2000 (nM) from 3 assay(s)
EC50: 5100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.77α = 90
b = 98.49β = 108.31
c = 59.63γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata scaling
BUSTERphasing
autoPROCdata reduction

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 V2MClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references, Refinement description
  • Version 1.2: 2020-11-25
    Changes: Database references
  • Version 2.0: 2022-08-03
    Changes: Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary