6KL5

Structure of The N-terminal domain of Middle East respiratory syndrome coronavirus Nucleocapsid Protein complexed with Benzyl 2-(Hydroxymethyl)-1-Indolinecarboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 
    0.299 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.281 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 
    0.283 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Structure-Based Stabilization of Non-native Protein-Protein Interactions of Coronavirus Nucleocapsid Proteins in Antiviral Drug Design.

Lin, S.M.Lin, S.C.Hsu, J.N.Chang, C.K.Chien, C.M.Wang, Y.S.Wu, H.Y.Jeng, U.S.Kehn-Hall, K.Hou, M.H.

(2020) J Med Chem 63: 3131-3141

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01913
  • Primary Citation of Related Structures:  
    6KL2, 6KL5, 6KL6

  • PubMed Abstract: 

    Structure-based stabilization of protein-protein interactions (PPIs) is a promising strategy for drug discovery. However, this approach has mainly focused on the stabilization of native PPIs, and non-native PPIs have received little consideration. Here, we identified a non-native interaction interface on the three-dimensional dimeric structure of the N-terminal domain of the MERS-CoV nucleocapsid protein (MERS-CoV N-NTD). The interface formed a conserved hydrophobic cavity suitable for targeted drug screening. By considering the hydrophobic complementarity during the virtual screening step, we identified 5-benzyloxygramine as a new N protein PPI orthosteric stabilizer that exhibits both antiviral and N-NTD protein-stabilizing activities. X-ray crystallography and small-angle X-ray scattering showed that 5-benzyloxygramine stabilizes the N-NTD dimers through simultaneous hydrophobic interactions with both partners, resulting in abnormal N protein oligomerization that was further confirmed in the cell. This unique approach based on the identification and stabilization of non-native PPIs of N protein could be applied toward drug discovery against CoV diseases.


  • Organizational Affiliation

    Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein
A, B, C, D
144Middle East respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for K9N4V7 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N4V7 
Go to UniProtKB:  K9N4V7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9N4V7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DJO (Subject of Investigation/LOI)
Query on DJO

Download Ideal Coordinates CCD File 
E [auth A](phenylmethyl) (2S)-2-(hydroxymethyl)-2,3-dihydroindole-1-carboxylate
C17 H17 N O3
QSMOQTIGILELKY-HNNXBMFYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free:  0.299 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.281 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 0.283 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.44α = 90
b = 109.897β = 101.1
c = 91.526γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DJOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description