Crystal structure of the 2019-nCoV main protease complexed with Boceprevir

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

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This is version 2.3 of the entry. See complete history


Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease.

Fu, L.Ye, F.Feng, Y.Yu, F.Wang, Q.Wu, Y.Zhao, C.Sun, H.Huang, B.Niu, P.Song, H.Shi, Y.Li, X.Tan, W.Qi, J.Gao, G.F.

(2020) Nat Commun 11: 4417-4417

  • DOI: https://doi.org/10.1038/s41467-020-18233-x
  • Primary Citation of Related Structures:  
    7BRO, 7BRP, 7C6S, 7C6U, 7D1M

  • PubMed Abstract: 

    COVID-19 was declared a pandemic on March 11 by WHO, due to its great threat to global public health. The coronavirus main protease (M pro , also called 3CLpro) is essential for processing and maturation of the viral polyprotein, therefore recognized as an attractive drug target. Here we show that a clinically approved anti-HCV drug, Boceprevir, and a pre-clinical inhibitor against feline infectious peritonitis (corona) virus (FIPV), GC376, both efficaciously inhibit SARS-CoV-2 in Vero cells by targeting M pro . Moreover, combined application of GC376 with Remdesivir, a nucleotide analogue that inhibits viral RNA dependent RNA polymerase (RdRp), results in sterilizing additive effect. Further structural analysis reveals binding of both inhibitors to the catalytically active side of SARS-CoV-2 protease M pro as main mechanism of inhibition. Our findings may provide critical information for the optimization and design of more potent inhibitors against the emerging SARS-CoV-2 virus.

  • Organizational Affiliation

    University of Chinese Academy of Sciences, 100049, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinaseA [auth B],
B [auth A]
307Severe 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 B],
D [auth A]
boceprevir (bound form)
C27 H47 N5 O5
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.367α = 90
b = 53.551β = 101.663
c = 113.772γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2020-05-13 
  • Deposition Author(s): Fu, L.F.

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 2.0: 2020-11-04
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-11-25
    Changes: Database references
  • Version 2.2: 2021-03-10
    Changes: Structure summary
  • Version 2.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description