Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragment

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.150 

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Biophysical Screens Identify Fragments That Bind to the Viral DNA-Binding Proteins EBNA1 and LANA.

Messick, T.E.Tolvinski, L.Zartler, E.R.Moberg, A.Frostell, A.Smith, G.R.Reitz, A.B.Lieberman, P.M.

(2020) Molecules 25

  • DOI: https://doi.org/10.3390/molecules25071760
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The human gamma-herpesviruses Epstein-Barr virus (EBV) (HHV-4) and Kaposi's sarcoma-associated herpesvirus (KSHV) (HHV-8) are responsible for a number of diseases, including various types of cancer. Epstein-Barr nuclear antigen 1 (EBNA1) from EBV and latency-associated nuclear antigen (LANA) from KSHV are viral-encoded DNA-binding proteins that are essential for the replication and maintenance of their respective viral genomes during latent, oncogenic infection. As such, EBNA1 and LANA are attractive targets for the development of small-molecule inhibitors. To this end, we performed a biophysical screen of EBNA1 and LANA using a fragment library by saturation transfer difference (STD)-NMR spectroscopy and surface plasmon resonance (SPR). We identified and validated a number of unique fragment hits that bind to EBNA1 or LANA. We also determined the high-resolution crystal structure of one fragment bound to EBNA1. Results from this screening cascade provide new chemical starting points for the further development of potent inhibitors for this class of viral proteins.

  • Organizational Affiliation

    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epstein-Barr nuclear antigen 1
A, B
142Human herpesvirus 4 strain B95-8Mutation(s): 0 
Gene Names: EBNA1BKRF1
Find proteins for P03211 (Epstein-Barr virus (strain B95-8))
Explore P03211 
Go to UniProtKB:  P03211
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03211
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QX4 (Subject of Investigation/LOI)
Query on QX4

Download Ideal Coordinates CCD File 
C [auth B]4-hydroxy-6-methyl-2H-1-benzopyran-2-one
C10 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
QX4 Binding MOAD:  6VH6 Kd: 4.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.516α = 90
b = 68.344β = 90
c = 69.687γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT096496
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R01CA186775

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description