6XHO

Covalent complex of SARS-CoV main protease with ethyl (4R)-4-({N-[(4-methoxy-1H-indol-2-yl)carbonyl]-L-leucyl}amino)-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 

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

  • 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 ...

    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

    Southern Research Institute, 2000 9th Avenue South, Birmingham, Alabama 35205 United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseAB307Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: 1a
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt)
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus)
Explore P0C6U8 
Go to UniProtKB:  P0C6U8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V34
Query on V34

Download CCD File 
A, B
ethyl (2E,4S)-4-{[N-(4-methoxy-1H-indole-2-carbonyl)-L-leucyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate
C27 H36 N4 O6
LBYBJSLPFZFADD-BNMFZAHFSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.946α = 90
b = 99.454β = 108.77
c = 60.037γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata scaling
BUSTERphasing
autoPROCdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references, Refinement description