9G0H | pdb_00009g0h

Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the noncovalently bound inhibitor C5N17A

• PDB DOI: https://doi.org/10.2210/pdb9G0H/pdb

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


• Deposited: 2024-07-08 Released: 2025-07-02 
• Deposition Author(s): Yang, C.-C., Strater, N., Sylvester, K., Muller, C.E., Yang, M., Lee, M.K., Gao, S., Song, L., Liu, X., Kim, M., Zhan, P.
• Funding Organization(s): Volkswagen Foundation, National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Miniaturized Modular Click Chemistry-enabled Rapid Discovery of Unique SARS-CoV-2 M pro Inhibitors With Robust Potency and Drug-like Profile.

Yang, M., Lee, M.K., Gao, S., Song, L., Jang, H.Y., Jo, I., Yang, C.C., Sylvester, K., Ko, C., Wang, S., Ye, B., Tang, K., Li, J., Gu, M., Muller, C.E., Strater, N., Liu, X., Kim, M., Zhan, P.

(2024) Adv Sci (Weinh) 11: e2404884-e2404884

• PubMed: 39319611 
• DOI: https://doi.org/10.1002/advs.202404884
• Primary Citation Related Structures: 
  9G0H, 9G0I


• PubMed Abstract: 
  

  The COVID-19 pandemic has required an expeditious advancement of innovative antiviral drugs. In this study, focused compound libraries are synthesized in 96- well plates utilizing modular click chemistry to rapidly discover potent inhibitors targeting the main protease (M ^pro ) of SARS-CoV-2. Subsequent direct biological screening identifies novel 1,2,3-triazole derivatives as robust M ^pro inhibitors with high anti-SARS-CoV-2 activity. Notably, C5N17B demonstrates sub-micromolar M ^pro inhibitory potency (IC ₅₀ = 0.12 µM) and excellent antiviral activity in Calu-3 cells determined in an immunofluorescence-based antiviral assay (EC ₅₀ = 0.078 µM, no cytotoxicity: CC ₅₀ > 100 µM). C5N17B shows superior potency to nirmatrelvir (EC ₅₀ = 1.95 µM) and similar efficacy to ensitrelvir (EC ₅₀ = 0.11 µM). Importantly, this compound displays high antiviral activities against several SARS-CoV-2 variants (Gamma, Delta, and Omicron, EC ₅₀ = 0.13 - 0.26 µM) and HCoV-OC43, indicating its broad-spectrum antiviral activity. It is worthy that C5N17B retains antiviral activity against nirmatrelvir-resistant strains with T21I/E166V and L50F/E166V mutations in M ^pro (EC ₅₀ = 0.26 and 0.15 µM, respectively). Furthermore, C5N17B displays favorable pharmacokinetic properties. Crystallography studies reveal a unique, non-covalent multi-site binding mode. In conclusion, these findings substantiate the potential of C5N17B as an up-and-coming drug candidate targeting SARS-CoV-2 M ^pro for clinical therapy.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, China.
Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea.
Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany.
PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113, Bonn, Germany.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 68.54 kDa 
• Atom Count: 5,166 
• Modeled Residue Count: 602 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IHT (Subject of Investigation/LOI)	D [auth A]	[(1~{S},5~{R})-8-[(~{S})-(3-fluorophenyl)-[1-(2-thiophen-3-ylethyl)-1,2,3-triazol-4-yl]methyl]-3,8-diazabicyclo[3.2.1]octan-3-yl]-(5-methylpyridin-3-yl)methanone C28 H29 F N6 O S SJCLQOKUUYZWNP-WEWMWRJBSA-N
DMS	C [auth A], F [auth B], G [auth B], H [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.887	α = 90
b = 99.889	β = 90
c = 104.104	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Yang, C.-C., Strater, N., Sylvester, K., Muller, C.E., Yang, M., Lee, M.K., Gao, S., Song, L., Liu, X., Kim, M., Zhan, P.

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Funding Organization	Location	Grant Number
Volkswagen Foundation	Germany	9A894
Volkswagen Foundation	Germany	9A850
National Natural Science Foundation of China (NSFC)	China	22307067
Ministry of Science and Technology (MoST, China)	China	2023YFC2606500

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release