3ATW

Structure-Based Design, Synthesis, Evaluation of Peptide-mimetic SARS 3CL Protease Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/jm200870n
  • Primary Citation of Related Structures:  

  • 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 o ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3C-Like Proteinase
A, B
306Human SARS coronavirusMutation(s): 1 
Find proteins for P0C6U8 (Human SARS coronavirus)
Go to UniProtKB:  P0C6U8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide ACE-THR-VAL-ALC-HIS-H
C, D
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000815
Query on PRD_000815
C,Dpeptide ACE-THR-VAL-ALC-HIS-HPeptide-like / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 54.517α = 94.29
b = 58.546β = 104.03
c = 67.745γ = 106.64
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Other
  • Version 1.2: 2015-07-01
    Type: Structure summary