Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.59 kDa 
• Atom Count: 2612 
• Modelled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

7JU7

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

• PDB DOI: 10.2210/pdb7JU7/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-19 Released: 2020-09-09 
• Deposition Author(s): Tan, K., Maltseva, N.I., Welk, L.F., Jedrzejczak, R.P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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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 

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

• PubMed: 34285133 
• 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. 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).

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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 --: --

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-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), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G65 (Subject of Investigation/LOI)	B [auth A]	Masitinib C28 H30 N6 O S WJEOLQLKVOPQFV-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

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 = 98.591	α = 90
b = 81.299	β = 114.62
c = 51.859	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-08-19 
• Released Date: 2020-09-09 
Deposition Author(s): Tan, K., Maltseva, N.I., Welk, L.F., Jedrzejczak, R.P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201 700060C

Revision History  

• 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