7L5D | pdb_00007l5d

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

PDB DOI: https://doi.org/10.2210/pdb7L5D/pdb

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

Deposited: 2020-12-21 Released: 2020-12-30
Deposition Author(s): Tan, K., Maltseva, N.I., 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.201 (Depositor), 0.202 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 34285133 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abg5827
Primary Citation 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).

Organizational Affiliation

Pritzker School for Molecular Engineering, The University of Chicago, Chicago, IL, USA. tays@uchicago.edu nirdra@uchicago.edu.

Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA.

Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA.

Department of Chemistry, The University of Chicago, Chicago, IL, USA.

Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA.

Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France.

Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.

Department of Medicine, Division of Immunobiology, Larner College of Medicine, University of Vermont, Burlington, VT, USA.

Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.

Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.

Cellular Screening Center, The University of Chicago, Chicago, IL, USA.

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

Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.

Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont, Burlington, VT, USA.

Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.

Department of Pharmaceutical Sciences, College of Pharmacy, Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA.

Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT, USA.

Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.

Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA. tays@uchicago.edu nirdra@uchicago.edu.

Macromolecule Content

Total Structure Weight: 34.99 kDa
Atom Count: 2,668
Modeled Residue Count: 301
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

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
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XNJ (Subject of Investigation/LOI) Query on XNJ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-(4-methyl-3-{[4-(pyridin-3-yl)-1,3-thiazol-2-yl]amino}phenyl)-4-[(piperazin-1-yl)methyl]benzamide C₂₇ H₂₈ N₆ O S LBWSNUMFQJZFGI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]