2ALV

X-ray structural analysis of SARS coronavirus 3CL proteinase in complex with designed anti-viral inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Design and synthesis of peptidomimetic severe acute respiratory syndrome chymotrypsin-like protease inhibitors.

Ghosh, A.K.Xi, K.Ratia, K.Santarsiero, B.D.Fu, W.Harcourt, B.H.Rota, P.A.Baker, S.C.Johnson, M.E.Mesecar, A.D.

(2005) J Med Chem 48: 6767-6771

  • DOI: https://doi.org/10.1021/jm050548m
  • Primary Citation of Related Structures:  
    2ALV

  • PubMed Abstract: 

    Design, synthesis, and biological evaluation of peptidomimetic severe acute respiratory syndrome chymotrypsin-like protease (SARS-3CLpro) inhibitors for severe acute respiratory syndrome coronavirus (SARS-CoV) are described. These inhibitors exhibited antiviral activity against SARS-CoV in infected cells in the micromolar range. An X-ray crystal structure of our lead inhibitor (4) bound to SARS-3CLpro provided important drug-design templates for the design of small-molecule inhibitors.


  • Organizational Affiliation

    Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA. akghosh@purdue.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replicase polyprotein 1ab306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
EC: 3.4.22
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CY6
Query on CY6

Download Ideal Coordinates CCD File 
B [auth A]N-((3S,6R)-6-((S,E)-4-ETHOXYCARBONYL-1-((S)-2-OXOPYRROLIDIN-3-YL)BUT-3-EN-2-YLCARBAMOYL)-2,9-DIMETHYL-4-OXODEC-8-EN-3-YL)-5-METHYLISOXAZOLE-3-CARBOXAMIDE
C29 H42 N4 O7
CSNQHKJCKPMZCY-YFUAOJPXSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CY6 BindingDB:  2ALV IC50: min: 7.00e+4, max: 8.00e+5 (nM) from 2 assay(s)
PDBBind:  2ALV IC50: 7.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.098α = 90
b = 83.24β = 104.409
c = 53.696γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
EPMRphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-08-23
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description