9MDQ | pdb_00009mdq

Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) Complex with Azapeptide Inhibitor 20a

• PDB DOI: https://doi.org/10.2210/pdb9MDQ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-12-05 Released: 2025-09-24 
• Deposition Author(s): Vishwakarma, J., Taylor, A.B., Harris, R.S.
• 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: 
  0.203 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Azapeptide-Based SARS-CoV-2 Main Protease Inhibitors: Design, Synthesis, Enzyme Inhibition, Structural Determination, and Antiviral Activity.

Flury, P., Vishwakarma, J., Sylvester, K., Higashi-Kuwata, N., Dabrowska, A.K., Delgado, R., Cuell, A., Basu, R., Taylor, A.B., de Oliveira, E.G., Magalhaes Serafim, M.S., Qiao, J., Chen, Y., Yang, S., O'Donoghue, A.J., Mitsuya, H., Gutschow, M., Laufer, S.A., Muller, C.E., Harris, R.S., Pillaiyar, T.

(2025) J Med Chem 68: 19339-19376

• PubMed: 40932417 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c01520
• Primary Citation Related Structures: 
  9MDQ


• PubMed Abstract: 
  

  M ^pro of SARS-CoV-2 plays a vital role in the replication and pathogenesis of virus. Additionally, its high conservation within the Coronaviridae family makes it an attractive therapeutic target for developing broad-spectrum agents. This study describes the design, synthesis, and structure-activity relationships of azapeptide-based SARS-CoV-2 M ^pro inhibitors, leading to several compounds with nanomolar IC ₅₀ values. Examples include 14r (IC ₅₀ = 13.3 nM), 14s (IC ₅₀ = 30.6 nM), 20a ( TPG-20a , IC ₅₀ = 28.0 nM), and 20g (IC ₅₀ = 30.4 nM). Some compounds inhibit MERS-CoV and SARS-CoV-1 M ^pro but not the human protease cathepsin L. Several inhibitors, such as 20a and 20f , exhibit antiviral activity with potencies comparable to nirmatrelvir and activity against the E166V-carrying SARS-CoV-2 variant (SARS-CoV-2 ^E166V ). An M ^pro cocrystal structure with 20a shows a covalent adduct with the catalytic Cys145. Overall, these new inhibitors are promising chemical tools that may contribute to the identification of future pan-anticoronaviral drugs.

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Organizational Affiliation: 
• Institute of Pharmaceutical Sciences, Department of Pharmaceutical and Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany.
Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany.
Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States.
PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany.
Department of Refractory Viral Diseases, National Institute of Global Health and Medicine, Japan Institute for Health Security, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan.
Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States.
Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive, San Diego, La Jolla, California 92093-0657, United States.
Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, 78229, United States.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.4 kDa 
• Atom Count: 2,539 
• Modeled Residue Count: 296 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BKV (Subject of Investigation/LOI)	B [auth A]	N-[(2S)-1-{2-(dichloroacetyl)-2-[(2-oxo-1,2-dihydropyridin-3-yl)methyl]hydrazin-1-yl}-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide C24 H27 Cl2 N5 O5 XAQBZJZQCBKCJV-KRWDZBQOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.203 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.889	α = 90
b = 83.076	β = 115.174
c = 52.011	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data scaling
autoPROC	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Vishwakarma, J., Taylor, A.B., Harris, R.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1U19AI171954

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release
  
• Version 1.1: 2025-10-08
  Changes: Database references