7Z59 | pdb_00007z59

SARS-CoV-2 main protease (Mpro) covalently modified with a penicillin derivative

• PDB DOI: https://doi.org/10.2210/pdb7Z59/pdb

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


• Deposited: 2022-03-08 Released: 2022-06-29 
• Deposition Author(s): Owen, C.D., Malla, T.R., Brewitz, L., Lukacik, P., Strain-Damerell, C., Mikolajek, H., Muntean, D.G., Aslam, H., Salah, E., Tumber, A., Schofield, C.J., Walsh, M.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.252 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.230 (DCC) 

Starting Model: experimental

Literature

Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine.

Malla, T.R., Brewitz, L., Muntean, D.G., Aslam, H., Owen, C.D., Salah, E., Tumber, A., Lukacik, P., Strain-Damerell, C., Mikolajek, H., Walsh, M.A., Schofield, C.J.

(2022) J Med Chem 65: 7682-7696

• PubMed: 35549342 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c02214
• Primary Citation Related Structures: 
  7Z59


• PubMed Abstract: 
  

  The SARS-CoV-2 main protease (M ^pro ) is a medicinal chemistry target for COVID-19 treatment. Given the clinical efficacy of β-lactams as inhibitors of bacterial nucleophilic enzymes, they are of interest as inhibitors of viral nucleophilic serine and cysteine proteases. We describe the synthesis of penicillin derivatives which are potent M ^pro inhibitors and investigate their mechanism of inhibition using mass spectrometric and crystallographic analyses. The results suggest that β-lactams have considerable potential as M ^pro inhibitors via a mechanism involving reaction with the nucleophilic cysteine to form a stable acyl-enzyme complex as shown by crystallographic analysis. The results highlight the potential for inhibition of viral proteases employing nucleophilic catalysis by β-lactams and related acylating agents.

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Organizational Affiliation: 
• Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.
Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom.
Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom.

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)

Macromolecule Content 

• Total Structure Weight: 34.27 kDa 
• Atom Count: 2,537 
• Modeled Residue Count: 305 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	305	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IFO (Subject of Investigation/LOI)	B [auth A]	(3S)-4-[[2,4-bis(fluoranyl)phenyl]methoxy]-2-methyl-4-oxidanylidene-3-[[(Z)-3-oxidanylidene-2-(2-phenoxyethanoylamino)prop-1-enyl]amino]butane-2-sulfinic acid C23 H24 F2 N2 O7 S YLWXTKUTNLREPM-LRJKXPEMSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.252 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.230 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.341	α = 90
b = 53.808	β = 100.649
c = 44.703	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BUSTER	refinement
Aimless	data scaling
xia2	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Owen, C.D., Malla, T.R., Brewitz, L., Lukacik, P., Strain-Damerell, C., Mikolajek, H., Muntean, D.G., Aslam, H., Salah, E., Tumber, A., Schofield, C.J., Walsh, M.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary