Development of Broad-Spectrum Halomethyl Ketone Inhibitors Against Coronavirus Main Protease 3CLpro

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report

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Development of broad-spectrum halomethyl ketone inhibitors against coronavirus main protease 3CL(pro).

Bacha, U.Barrila, J.Gabelli, S.B.Kiso, Y.Mario Amzel, L.Freire, E.

(2008) Chem Biol Drug Des 72: 34-49

  • DOI: https://doi.org/10.1111/j.1747-0285.2008.00679.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Coronaviruses comprise a large group of RNA viruses with diverse host specificity. The emergence of highly pathogenic strains like the SARS coronavirus (SARS-CoV), and the discovery of two new coronaviruses, NL-63 and HKU1, corroborates the high rate of mutation and recombination that have enabled them to cross species barriers and infect novel hosts. For that reason, the development of broad-spectrum antivirals that are effective against several members of this family is highly desirable. This goal can be accomplished by designing inhibitors against a target, such as the main protease 3CL(pro) (M(pro)), which is highly conserved among all coronaviruses. Here 3CL(pro) derived from the SARS-CoV was used as the primary target to identify a new class of inhibitors containing a halomethyl ketone warhead. The compounds are highly potent against SARS 3CL(pro) with K(i)'s as low as 300 nM. The crystal structure of the complex of one of the compounds with 3CL(pro) indicates that this inhibitor forms a thioether linkage between the halomethyl carbon of the warhead and the catalytic Cys 145. Furthermore, Structure Activity Relationship (SAR) studies of these compounds have led to the identification of a pharmacophore that accurately defines the essential molecular features required for the high affinity.

  • Organizational Affiliation

    Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase299Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep
EC: 3.4.22
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 959

Download Ideal Coordinates CCD File 
B [auth A]benzyl (2-oxopropyl)carbamate
C11 H13 N O3
Binding Affinity Annotations 
IDSourceBinding Affinity
959 PDBBind:  3D62 Kd: 800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.264 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.668α = 90
b = 45.16β = 90
c = 53.967γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2012-05-09
    Changes: Structure summary
  • Version 1.4: 2017-10-25
    Changes: Refinement description