2AMP

Crystal Structure Of Porcine Transmissible Gastroenteritis Virus Mpro in Complex with an Inhibitor N1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


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: 10.1371/journal.pbio.0030324
  • Primary Citation of Related Structures:  

  • 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 infect ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3C-like proteinase
A, B
304Porcine transmissible gastroenteritis coronavirus (strain Purdue)Mutation(s): 0 
Gene Names: rep
Find proteins for P0C6Y5 (Porcine transmissible gastroenteritis coronavirus (strain Purdue))
Go to UniProtKB:  P0C6Y5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I12
Query on I12

Download SDF File 
Download CCD File 
A, B
N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]-L-ALANYL-L-VALYL-N~1~-((1S)-4-ETHOXY-4-OXO-1-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
(E)-(S)-4-[(S)-4-METHYL-2-((S)-3-METHYL-2{(S)-2-[(5-METHYL-ISOXAZOLE-3- CARBONYL)-AMINO]-PROPIONYLAMINO}-BUTYRYLAMINO)-PENTANOYLAMINO]-5-((S)-2- OXO-PYRROLIDIN-3-YL)-PENT-2-ENOIC ACID ETHYL ESTER
C30 H46 N6 O8
LIVSSCDUYUOZEL-GLXPMXKMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.589α = 90.00
b = 90.239β = 90.00
c = 110.345γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
CNSphasing
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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