7FAY | pdb_00007fay

Crystal structure of SARS-CoV-2 main protease in complex with (R)-1a

• PDB DOI: https://doi.org/10.2210/pdb7FAY/pdb

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


• Deposited: 2021-07-08 Released: 2021-07-21 
• Deposition Author(s): Zeng, R., Quan, B.X., Liu, X.L., Lei, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.234 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

An orally available M pro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron.

Quan, B.X., Shuai, H., Xia, A.J., Hou, Y., Zeng, R., Liu, X.L., Lin, G.F., Qiao, J.X., Li, W.P., Wang, F.L., Wang, K., Zhou, R.J., Yuen, T.T., Chen, M.X., Yoon, C., Wu, M., Zhang, S.Y., Huang, C., Wang, Y.F., Yang, W., Tian, C., Li, W.M., Wei, Y.Q., Yuen, K.Y., Chan, J.F., Lei, J., Chu, H., Yang, S.

(2022) Nat Microbiol 7: 716-725

• PubMed: 35477751 
• DOI: https://doi.org/10.1038/s41564-022-01119-7
• Primary Citation Related Structures: 
  7FAY, 7FAZ


• PubMed Abstract: 
  

  Emerging SARS-CoV-2 variants continue to cause waves of new infections globally. Developing effective antivirals against SARS-CoV-2 and its variants is an urgent task. The main protease (M ^pro ) of SARS-CoV-2 is an attractive drug target because of its central role in viral replication and its conservation among variants. We herein report a series of potent α-ketoamide-containing M ^pro inhibitors obtained using the Ugi four-component reaction. The prioritized compound, Y180, showed an IC ₅₀ of 8.1 nM against SARS-CoV-2 M ^pro and had oral bioavailability of 92.9%, 31.9% and 85.7% in mice, rats and dogs, respectively. Y180 protected against wild-type SARS-CoV-2, B.1.1.7 (Alpha), B.1.617.1 (Kappa) and P.3 (Theta), with EC ₅₀ of 11.4, 20.3, 34.4 and 23.7 nM, respectively. Oral treatment with Y180 displayed a remarkable antiviral potency and substantially ameliorated the virus-induced tissue damage in both nasal turbinate and lung of B.1.1.7-infected K18-human ACE2 (K18-hACE2) transgenic mice. Therapeutic treatment with Y180 improved the survival of mice from 0 to 44.4% (P = 0.0086) upon B.1.617.1 infection in the lethal infection model. Importantly, Y180 was also highly effective against the B.1.1.529 (Omicron) variant both in vitro and in vivo. Overall, our study provides a promising lead compound for oral drug development against SARS-CoV-2.

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Organizational Affiliation: 
• State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China.
Academician workstation of Hainan Province and Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China.
State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China. [e-mail].
Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China. [e-mail].
Academician workstation of Hainan Province and Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, China. [e-mail].
State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China. [e-mail].
National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China. [e-mail].
State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China. [e-mail].
State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China. [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: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.24 kDa 
• Atom Count: 2,577 
• Modeled Residue Count: 301 
• 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  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
2XI (Subject of Investigation/LOI)	B [auth A]	(2~{R})-~{N}-[(1~{R})-2-(~{tert}-butylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-~{N}-(4-~{tert}-butylphenyl)-2-oxidanyl-propanamide C24 H33 N3 O3 VNQJAMKKDIWKCG-OXQOHEQNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.234 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.474	α = 90
b = 53.472	β = 102.35
c = 45.132	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Zeng, R., Quan, B.X., Liu, X.L., Lei, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	00402354A1028/HX2019nCoV039/

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Advisory, Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary