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


This is version 1.3 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: 10.1021/jm050548m
  • Structures With Same Primary Citation

  • 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 exhibite ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replicase polyprotein 1ab
A
306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 2.1.1 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt)
Find proteins for P0C6X7 (Human SARS coronavirus)
Go to UniProtKB:  P0C6X7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CY6
Query on CY6

Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CY6IC50:  70000   nM  BindingDB
CY6IC50:  70000   nM  PDBBind
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



Entry History 

Deposition Data

Revision History 

  • 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