Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor Boceprevir at 1.35 A Resolution

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.

Andi, B.Kumaran, D.Kreitler, D.F.Soares, A.S.Keereetaweep, J.Jakoncic, J.Lazo, E.O.Shi, W.Fuchs, M.R.Sweet, R.M.Shanklin, J.Adams, P.D.Schmidt, J.G.Head, M.S.McSweeney, S.

(2022) Sci Rep 12: 12197-12197

  • DOI: https://doi.org/10.1038/s41598-022-15930-z
  • Primary Citation of Related Structures:  
    7JYC, 7K3T, 7K40, 7K6D, 7K6E, 7MNG, 7MRR

  • PubMed Abstract: 

    Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (M pro also known as 3CL pro ) is a primary drug target, due to its essential role in maturation of the viral polyproteins. In this study, we provide crystallographic evidence, along with some binding assay data, that three clinically approved anti hepatitis C virus drugs and two other drug-like compounds covalently bind to the M pro Cys145 catalytic residue in the active site. Also, molecular docking studies can provide additional insight for the design of new antiviral inhibitors for SARS-CoV-2 using these drugs as lead compounds. One might consider derivatives of these lead compounds with higher affinity to the M pro as potential COVID-19 therapeutics for further testing and possibly clinical trials.

  • Organizational Affiliation

    Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe 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
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.279α = 90
b = 53.321β = 101.7
c = 45.835γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM133893
Department of Energy (DOE, United States)United StatesKP1605010
Brookhaven National Laboratory (BNL)United StatesLDRD 20-042
National Virtual Biotechnology Laboratory (NVBL)United StatesCoronavirus CARES Act

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description