2D2D

Crystal Structure Of SARS-CoV Mpro in Complex with an Inhibitor I2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design of Wide-Spectrum Inhibitors Targeting Coronavirus Main Proteases.

Yang, H.Xie, W.Xue, X.Yang, K.Ma, J.Liang, W.Zhao, Q.Zhou, Z.Pei, D.Ziebuhr, J.Hilgenfeld, R.Yuen, K.Y.Wong, L.Gao, G.Chen, S.Chen, Z.Ma, D.Bartlam, M.Rao, Z.

(2005) PLoS Biol 3: 324-334

  • DOI: https://doi.org/10.1371/journal.pbio.0030324
  • Primary Citation of Related Structures:  
    1WOF, 2AMD, 2AMP, 2AMQ, 2D2D

  • PubMed Abstract: 

    The genus Coronavirus contains about 25 species of coronaviruses (CoVs), which are important pathogens causing highly prevalent diseases and often severe or fatal in humans and animals. No licensed specific drugs are available to prevent their infection. Different host receptors for cellular entry, poorly conserved structural proteins (antigens), and the high mutation and recombination rates of CoVs pose a significant problem in the development of wide-spectrum anti-CoV drugs and vaccines. CoV main proteases (M(pro)s), which are key enzymes in viral gene expression and replication, were revealed to share a highly conservative substrate-recognition pocket by comparison of four crystal structures and a homology model representing all three genetic clusters of the genus Coronavirus. This conclusion was further supported by enzyme activity assays. Mechanism-based irreversible inhibitors were designed, based on this conserved structural region, and a uniform inhibition mechanism was elucidated from the structures of Mpro-inhibitor complexes from severe acute respiratory syndrome-CoV and porcine transmissible gastroenteritis virus. A structure-assisted optimization program has yielded compounds with fast in vitro inactivation of multiple CoV M(pro)s, potent antiviral activity, and extremely low cellular toxicity in cell-based assays. Further modification could rapidly lead to the discovery of a single agent with clinical potential against existing and possible future emerging CoV-related diseases.


  • Organizational Affiliation

    Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
311Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
EC: 3.4.24
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
ENB
Query on ENB

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
ETHYL (2E,4S)-4-[((2R)-2-{[N-(TERT-BUTOXYCARBONYL)-L-VALYL]AMINO}-2-PHENYLETHANOYL)AMINO]-5-[(3S)-2-OXOPYRROLIDIN-3-YL]PENT-2-ENOATE
C29 H42 N4 O7
NUDVEHBHDBJSMD-XBEUYHOESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.703α = 90
b = 94.737β = 103.04
c = 66.204γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance