7JU7

The crystal structure of SARS-CoV-2 Main Protease in complex with masitinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2.

Drayman, N.DeMarco, J.K.Jones, K.A.Azizi, S.A.Froggatt, H.M.Tan, K.Maltseva, N.I.Chen, S.Nicolaescu, V.Dvorkin, S.Furlong, K.Kathayat, R.S.Firpo, M.R.Mastrodomenico, V.Bruce, E.A.Schmidt, M.M.Jedrzejczak, R.Munoz-Alia, M.A.Schuster, B.Nair, V.Han, K.Y.O'Brien, A.Tomatsidou, A.Meyer, B.Vignuzzi, M.Missiakas, D.Botten, J.W.Brooke, C.B.Lee, H.Baker, S.C.Mounce, B.C.Heaton, N.S.Severson, W.E.Palmer, K.E.Dickinson, B.C.Joachimiak, A.Randall, G.Tay, S.

(2021) Science 373: 931-936

  • DOI: 10.1126/science.abg5827
  • Primary Citation of Related Structures:  
    7JU7, 7L5D

  • PubMed Abstract: 
  • There is an urgent need for antiviral agents that treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We screened a library of 1900 clinically safe drugs against OC43, a human beta coronavirus that causes the common cold, and evaluated the top hits against SARS-CoV-2 ...

    There is an urgent need for antiviral agents that treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We screened a library of 1900 clinically safe drugs against OC43, a human beta coronavirus that causes the common cold, and evaluated the top hits against SARS-CoV-2. Twenty drugs significantly inhibited replication of both viruses in cultured human cells. Eight of these drugs inhibited the activity of the SARS-CoV-2 main protease, 3CLpro, with the most potent being masitinib, an orally bioavailable tyrosine kinase inhibitor. X-ray crystallography and biochemistry show that masitinib acts as a competitive inhibitor of 3CLpro. Mice infected with SARS-CoV-2 and then treated with masitinib showed >200-fold reduction in viral titers in the lungs and nose, as well as reduced lung inflammation. Masitinib was also effective in vitro against all tested variants of concern (B.1.1.7, B.1.351, and P.1).


    Related Citations: 
    • Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro .
      Drayman, N., Jones, K.A., Azizi, S.A., Froggatt, H.M., Tan, K., Maltseva, N.I., Chen, S., Nicolaescu, V., Dvorkin, S., Furlong, K., Kathayat, R.S., Firpo, M.R., Mastrodomenico, V., Bruce, E.A., Schmidt, M.M., Jedrzejczak, R., Munoz-Alia, M.A., Schuster, B., Nair, V., Botten, J.W., Brooke, C.B., Baker, S.C., Mounce, B.C., Heaton, N.S., Dickinson, B.C., Jaochimiak, A., Randall, G., Tay, S.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G65 (Subject of Investigation/LOI)
Query on G65

Download Ideal Coordinates CCD File 
B [auth A]Masitinib
C28 H30 N6 O S
WJEOLQLKVOPQFV-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.591α = 90
b = 81.299β = 114.62
c = 51.859γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201 700060C

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2021-08-25
    Changes: Database references
  • Version 1.3: 2021-09-01
    Changes: Database references