7MLG | pdb_00007mlg

Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C63

• PDB DOI: https://doi.org/10.2210/pdb7MLG/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-04-28 Released: 2021-12-22 
• Deposition Author(s): Sharon, I., Stille, J., Tjutrins, J., Wang, G., Venegas, F.A., Hennecker, C., Rueda, A.M., Miron, C.E., Pinus, S., Labarre, A., Patrascu, M.B., Vlaho, D., Huot, M., Mittermaier, A.K., Moitessier, N., Schmeing, T.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.268 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors.

Stille, J.K., Tjutrins, J., Wang, G., Venegas, F.A., Hennecker, C., Rueda, A.M., Sharon, I., Blaine, N., Miron, C.E., Pinus, S., Labarre, A., Plescia, J., Burai Patrascu, M., Zhang, X., Wahba, A.S., Vlaho, D., Huot, M.J., Schmeing, T.M., Mittermaier, A.K., Moitessier, N.

(2021) Eur J Med Chem 229: 114046-114046

• PubMed: 34995923 
• DOI: https://doi.org/10.1016/j.ejmech.2021.114046
• Primary Citation Related Structures: 
  7MLF, 7MLG


• PubMed Abstract: 
  

  Severe diseases such as the ongoing COVID-19 pandemic, as well as the previous SARS and MERS outbreaks, are the result of coronavirus infections and have demonstrated the urgent need for antiviral drugs to combat these deadly viruses. Due to its essential role in viral replication and function, 3CL ^pro (main coronaviruses cysteine-protease) has been identified as a promising target for the development of antiviral drugs. Previously reported SARS-CoV 3CL ^pro non-covalent inhibitors were used as a starting point for the development of covalent inhibitors of SARS-CoV-2 3CL ^pro . We report herein our efforts in the design and synthesis of submicromolar covalent inhibitors when the enzymatic activity of the viral protease was used as a screening platform.

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Organizational Affiliation: 
• Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8.
Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler Montreal, QC, Canada, H3G 0B1.
Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8. Electronic address: [e-mail].
Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada, H3A 0B8. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 34.28 kDa 
• Atom Count: 2,407 
• Modeled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

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
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZJ1 (Subject of Investigation/LOI)	B [auth A]	(2R)-2-[(4-tert-butylphenyl)(ethanesulfonyl)amino]-N-cyclohexyl-2-(pyridin-3-yl)acetamide C25 H35 N3 O3 S ZCSLMPKXGXMPHB-HSZRJFAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.268 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.45	α = 90
b = 53.318	β = 101.88
c = 45.474	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Sharon, I., Stille, J., Tjutrins, J., Wang, G., Venegas, F.A., Hennecker, C., Rueda, A.M., Miron, C.E., Pinus, S., Labarre, A., Patrascu, M.B., Vlaho, D., Huot, M., Mittermaier, A.K., Moitessier, N., Schmeing, T.M.

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2022-01-19
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary