8IGO | pdb_00008igo

Crystal structure of apo SARS-CoV-2 main protease

• PDB DOI: https://doi.org/10.2210/pdb8IGO/pdb

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


• Deposited: 2023-02-21 Released: 2023-04-05 
• Deposition Author(s): Huang, X., Zhou, B., Xu, J., Yang, Z., Zhong, N., Xiong, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), National Key Research and Development Program of China, Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Preclinical evaluation of the SARS-CoV-2 M pro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir.

Chen, X., Huang, X., Ma, Q., Kuzmic, P., Zhou, B., Zhang, S., Chen, J., Xu, J., Liu, B., Jiang, H., Zhang, W., Yang, C., Wu, S., Huang, J., Li, H., Long, C., Zhao, X., Xu, H., Sheng, Y., Guo, Y., Niu, C., Xue, L., Xu, Y., Liu, J., Zhang, T., Spencer, J., Zhu, Z., Deng, W., Chen, X., Chen, S.H., Zhong, N., Xiong, X., Yang, Z.

(2024) Nat Microbiol 9: 1075-1088

• PubMed: 38553607 
• DOI: https://doi.org/10.1038/s41564-024-01618-9
• Primary Citation of Related Structures:  
  8IGN, 8IGO


• PubMed Abstract: 
  

  Although vaccines are available for SARS-CoV-2, antiviral drugs such as nirmatrelvir are still needed, particularly for individuals in whom vaccines are less effective, such as the immunocompromised, to prevent severe COVID-19. Here we report an α-ketoamide-based peptidomimetic inhibitor of the SARS-CoV-2 main protease (M ^pro ), designated RAY1216. Enzyme inhibition kinetic analysis shows that RAY1216 has an inhibition constant of 8.4 nM and suggests that it dissociates about 12 times slower from M ^pro compared with nirmatrelvir. The crystal structure of the SARS-CoV-2 M ^pro :RAY1216 complex shows that RAY1216 covalently binds to the catalytic Cys145 through the α-ketoamide group. In vitro and using human ACE2 transgenic mouse models, RAY1216 shows antiviral activities against SARS-CoV-2 variants comparable to those of nirmatrelvir. It also shows improved pharmacokinetics in mice and rats, suggesting that RAY1216 could be used without ritonavir, which is co-administered with nirmatrelvir. RAY1216 has been approved as a single-component drug named 'leritrelvir' for COVID-19 treatment in China.

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Organizational Affiliation: 
• School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China.
Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China.
State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
BioKin Ltd, Watertown, MA, USA.
Guangzhou National Laboratory, Guangzhou, China.
Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), Guangzhou, China.
School of Life Sciences, University of Science and Technology of China, Hefei, China.
School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
WuXi AppTec, Shanghai, China.
State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
WuXi AppTec, Shanghai, China. [e-mail].
State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China. [e-mail].
Guangzhou National Laboratory, Guangzhou, China. [e-mail].
State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China. [e-mail].
State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. [e-mail].
State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China. [e-mail].
Guangzhou National Laboratory, Guangzhou, China. [e-mail].
State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), 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: 33.83 kDa 
• Atom Count: 2,414 
• 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 nsp5	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.393	α = 90
b = 82.488	β = 115.52
c = 51.421	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-05 
Deposition Author(s): Huang, X., Zhou, B., Xu, J., Yang, Z., Zhong, N., Xiong, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82341085
National Key Research and Development Program of China	China	2021YFA1300903
National Natural Science Foundation of China (NSFC)	China	82341099
National Key Research and Development Program of China	China	2021YFA1300904
National Key Research and Development Program of China	China	2022YFC0868700
Ministry of Science and Technology (MoST, China)	China	2021YFA1300900

Revision History  

• Version 1.0: 2023-04-05
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2024-04-10
  Changes: Database references
• Version 1.3: 2024-04-17
  Changes: Database references