6Y2E

Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.

Zhang, L.Lin, D.Sun, X.Curth, U.Drosten, C.Sauerhering, L.Becker, S.Rox, K.Hilgenfeld, R.

(2020) Science --: --

  • DOI: 10.1126/science.abb3405
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The COVID-19 pandemic caused by SARS-CoV-2 is a global health emergency. An attractive drug target among coronaviruses is the main protease (M <sup>pro </sup>, 3CL <sup>pro </sup>), due to its essential role in processing the polyproteins that are tr ...

    The COVID-19 pandemic caused by SARS-CoV-2 is a global health emergency. An attractive drug target among coronaviruses is the main protease (M pro , 3CL pro ), due to its essential role in processing the polyproteins that are translated from the viral RNA. We report the X-ray structures of the unliganded SARS-CoV-2 M pro and its complex with an α-ketoamide inhibitor. This was derived from a previously designed inhibitor but with the P3-P2 amide bond incorporated into a pyridone ring to enhance the half-life of the compound in plasma. Based on the structure, we developed the lead compound into a potent inhibitor of the SARS-CoV-2 M pro The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route.


    Organizational Affiliation

    German Center for Infection Research (DZIF), Marburg-Gießen-Langen Site, University of Marburg, 35043 Marburg, Germany.,Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23562 Lübeck, Germany. rolf.hilgenfeld@uni-luebeck.de.,Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23562 Lübeck, Germany.,Institute for Biophysical Chemistry, Hannover Medical School, 30625 Hannover, Germany.,Institute of Virology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany.,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany.,Institute of Virology, University of Marburg, 35043 Marburg, Germany.,Changchun Discovery Sciences Ltd., 789 Shunda Road, Changchun, Jilin 130012, China.,Department of Chemical Biology, Helmholtz Center for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SARS-CoV-2 (2019-nCoV) main protease
AAA
306N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.983α = 90.00
b = 53.763β = 101.24
c = 44.774γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermanyDZIF-TTU01 grant 8011801806

Revision History 

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-25
    Type: Database references
  • Version 1.2: 2020-04-01
    Type: Database references