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

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: (PDB Primary Data), (UniProt), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U5G (Subject of Investigation/LOI)
Query on U5G

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
boceprevir (bound form)
C27 H47 N5 O5
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • 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 = 67.761α = 90
b = 99.426β = 90
c = 103.806γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2020YFS0010/HX2019nCoV039

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-11-29
    Changes: Data collection, Database references, Refinement description