SARS-CoV-2 3CL protease (3CL pro) in complex with a novel inhibitor

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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This is version 1.3 of the entry. See complete history


Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients.

Su, H.X.Yao, S.Zhao, W.F.Li, M.J.Liu, J.Shang, W.J.Xie, H.Ke, C.Q.Hu, H.C.Gao, M.N.Yu, K.Q.Liu, H.Shen, J.S.Tang, W.Zhang, L.K.Xiao, G.F.Ni, L.Wang, D.W.Zuo, J.P.Jiang, H.L.Bai, F.Wu, Y.Ye, Y.Xu, Y.C.

(2020) Acta Pharmacol Sin 41: 1167-1177

  • DOI: https://doi.org/10.1038/s41401-020-0483-6
  • Primary Citation of Related Structures:  
    6M2N, 6M2Q

  • PubMed Abstract: 

    Human infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) and there is no cure currently. The 3CL protease (3CLpro) is a highly conserved protease which is indispensable for CoVs replication, and is a promising target for development of broad-spectrum antiviral drugs. In this study we investigated the anti-SARS-CoV-2 potential of Shuanghuanglian preparation, a Chinese traditional patent medicine with a long history for treating respiratory tract infection in China. We showed that either the oral liquid of Shuanghuanglian, the lyophilized powder of Shuanghuanglian for injection or their bioactive components dose-dependently inhibited SARS-CoV-2 3CLpro as well as the replication of SARS-CoV-2 in Vero E6 cells. Baicalin and baicalein, two ingredients of Shuanghuanglian, were characterized as the first noncovalent, nonpeptidomimetic inhibitors of SARS-CoV-2 3CLpro and exhibited potent antiviral activities in a cell-based system. Remarkably, the binding mode of baicalein with SARS-CoV-2 3CLpro determined by X-ray protein crystallography was distinctly different from those of known 3CLpro inhibitors. Baicalein was productively ensconced in the core of the substrate-binding pocket by interacting with two catalytic residues, the crucial S1/S2 subsites and the oxyanion loop, acting as a "shield" in front of the catalytic dyad to effectively prevent substrate access to the catalytic dyad within the active site. Overall, this study provides an example for exploring the in vitro potency of Chinese traditional patent medicines and effectively identifying bioactive ingredients toward a specific target, and gains evidence supporting the in vivo studies of Shuanghuanglian oral liquid as well as two natural products for COVID-19 treatment.

  • Organizational Affiliation

    CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B, C, D
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.957α = 74.09
b = 67.942β = 78.27
c = 95.046γ = 66.1
Software Package:
Software NamePurpose
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2021-02-03
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description