4KXJ

Crystal structure of HCoV-OC43 N-NTD complexed with PJ34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


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Literature

Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target

Lin, S.Y.Liu, C.L.Chang, Y.M.Zhao, J.Perlman, S.Hou, M.H.

(2014) J Med Chem 57: 2247-2257

  • DOI: 10.1021/jm500089r
  • Primary Citation of Related Structures:  
    4LI4, 4LMC, 4LM7, 4LM9, 4KXJ

  • PubMed Abstract: 
  • Coronaviruses (CoVs) cause numerous diseases, including Middle East respiratory syndrome and severe acute respiratory syndrome, generating significant health-related and economic consequences. CoVs encode the nucleocapsid (N) protein, a major structural protein that plays multiple roles in the virus replication cycle and forms a ribonucleoprotein complex with the viral RNA through the N protein's N-terminal domain (N-NTD) ...

    Coronaviruses (CoVs) cause numerous diseases, including Middle East respiratory syndrome and severe acute respiratory syndrome, generating significant health-related and economic consequences. CoVs encode the nucleocapsid (N) protein, a major structural protein that plays multiple roles in the virus replication cycle and forms a ribonucleoprotein complex with the viral RNA through the N protein's N-terminal domain (N-NTD). Using human CoV-OC43 (HCoV-OC43) as a model for CoV, we present the 3D structure of HCoV-OC43 N-NTD complexed with ribonucleoside 5'-monophosphates to identify a distinct ribonucleotide-binding pocket. By targeting this pocket, we identified and developed a new coronavirus N protein inhibitor, N-(6-oxo-5,6-dihydrophenanthridin-2-yl)(N,N-dimethylamino)acetamide hydrochloride (PJ34), using virtual screening; this inhibitor reduced the N protein's RNA-binding affinity and hindered viral replication. We also determined the crystal structure of the N-NTD-PJ34 complex. On the basis of these findings, we propose guidelines for developing new N protein-based antiviral agents that target CoVs.


    Organizational Affiliation

    College of Life Science, ‡Institute of Genomics and Bioinformatics, and §Agriculture Biotechnology Center, National Chung Hsing University , Taichung 40254, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NucleoproteinA136Human coronavirus OC43Mutation(s): 0 
Gene Names: N7a
UniProt
Find proteins for P33469 (Human coronavirus OC43)
Explore P33469 
Go to UniProtKB:  P33469
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P34 (Subject of Investigation/LOI)
Query on P34

Download Ideal Coordinates CCD File 
B [auth A]N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE
C17 H17 N3 O2
UYJZZVDLGDDTCL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.684α = 90
b = 81.684β = 90
c = 42.95γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2013-05-27 
  • Released Date: 2014-05-28 
  • Deposition Author(s): Lin, S.Y., Hou, M.H.

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release