Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
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: 68.69 kDa 
• Atom Count: 5,137 
• Modelled Residue Count: 599 
• Deposited Residue Count: 612 
• Unique protein chains: 1

 7COM

Crystal structure of the SARS-CoV-2 main protease in complex with Boceprevir (space group P212121)

• PDB DOI:  https://doi.org/10.2210/pdb7COM/pdb

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


• Deposited: 2020-08-04 Released: 2020-08-19 
• Deposition Author(s): Zeng, R., Qiao, J.X., Wang, Y.F., Li, Y.S., Yao, R., Liu, J.M., Zhou, Y.L., Chen, P., Yang, S.Y., Lei, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model.

Qiao, J., Li, Y.S., Zeng, R., Liu, F.L., Luo, R.H., Huang, C., Wang, Y.F., Zhang, J., Quan, B., Shen, C., Mao, X., Liu, X., Sun, W., Yang, W., Ni, X., Wang, K., Xu, L., Duan, Z.L., Zou, Q.C., Zhang, H.L., Qu, W., Long, Y.H., Li, M.H., Yang, R.C., Liu, X., You, J., Zhou, Y., Yao, R., Li, W.P., Liu, J.M., Chen, P., Liu, Y., Lin, G.F., Yang, X., Zou, J., Li, L., Hu, Y., Lu, G.W., Li, W.M., Wei, Y.Q., Zheng, Y.T., Lei, J., Yang, S.

(2021) Science 371: 1374-1378

• PubMed: 33602867 
• DOI: https://doi.org/10.1126/science.abf1611
• Primary Citation of Related Structures:  
  7C7P, 7COM, 7D3I


• PubMed Abstract: 
  

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continually poses serious threats to global public health. The main protease (M ^pro ) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing M ^pro inhibitors derived from either boceprevir or telaprevir, both of which are approved antivirals. All compounds inhibited SARS-CoV-2 M ^pro activity in vitro, with 50% inhibitory concentration values ranging from 7.6 to 748.5 nM. The cocrystal structure of M ^pro in complex with MI-23, one of the most potent compounds, revealed its interaction mode. Two compounds (MI-09 and MI-30) showed excellent antiviral activity in cell-based assays. In a transgenic mouse model of SARS-CoV-2 infection, oral or intraperitoneal treatment with MI-09 or MI-30 significantly reduced lung viral loads and lung lesions. Both also displayed good pharmacokinetic properties and safety in rats.

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Organizational Affiliation: 

State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
U5G (Subject of Investigation/LOI)	C [auth A], D [auth B]	boceprevir (bound form) C27 H47 N5 O5 FEBWCINGHXXUCV-GFLQDLJJSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002382 (U5G)	C [auth A], D [auth B]	Boceprevir (bound form)	Peptide-like / Enzyme inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.761	α = 90
b = 99.426	β = 90
c = 103.806	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Zeng, R., Qiao, J.X., Wang, Y.F., Li, Y.S., Yao, R., Liu, J.M., Zhou, Y.L., Chen, P., Yang, S.Y., Lei, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2020YFS0010/HX2019nCoV039

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2021-03-03
  Changes: Database references, Derived calculations
• Version 1.2: 2021-03-10
  Changes: Structure summary
• Version 1.3: 2021-04-14
  Changes: Database references