Structure of SARS 3CL protease with peptidic aldehyde inhibitor

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structure-Based Design, Synthesis, and Evaluation of Peptide-Mimetic SARS 3CL Protease Inhibitors.

Akaji, K.Konno, H.Mitsui, H.Teruya, K.Shimamoto, Y.Hattori, Y.Ozaki, T.Kusunoki, M.Sanjoh, A.

(2011) J Med Chem 54: 7962-7973

  • DOI: https://doi.org/10.1021/jm200870n
  • Primary Citation of Related Structures:  
    3ATW, 3AVZ, 3AW0, 3AW1

  • PubMed Abstract: 

    The design and evaluation of low molecular weight peptide-based severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL) protease inhibitors are described. A substrate-based peptide aldehyde was selected as a starting compound, and optimum side-chain structures were determined, based on a comparison of inhibitory activities with Michael type inhibitors. For the efficient screening of peptide aldehydes containing a specific C-terminal residue, a new approach employing thioacetal to aldehyde conversion mediated by N-bromosuccinimide was devised. Structural optimization was carried out based on X-ray crystallographic analyses of the R188I SARS 3CL protease in a complex with each inhibitor to provide a tetrapeptide aldehyde with an IC(50) value of 98 nM. The resulting compound carried no substrate sequence, except for a P(3) site directed toward the outside of the protease. X-ray crystallography provided insights into the protein-ligand interactions.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-Like Proteinase306Severe acute respiratory syndrome-related coronavirusMutation(s): 1 
Gene Names: 1a
Find proteins for P0C6U8 (Severe acute respiratory syndrome coronavirus)
Explore P0C6U8 
Go to UniProtKB:  P0C6U8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6U8
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide ACE-SER-ALA-VAL-LEU-HIS-H6N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on HSV
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.384α = 90
b = 81.606β = 104.24
c = 53.33γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Other
  • Version 1.2: 2015-07-01
    Changes: Structure summary
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection