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

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

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Structure-based design of small-molecule inhibitors of EBNA1 DNA binding blocks Epstein-Barr virus latent infection and tumor growth.

Messick, T.E.Smith, G.R.Soldan, S.S.McDonnell, M.E.Deakyne, J.S.Malecka, K.A.Tolvinski, L.van den Heuvel, A.P.J.Gu, B.W.Cassel, J.A.Tran, D.H.Wassermann, B.R.Zhang, Y.Velvadapu, V.Zartler, E.R.Busson, P.Reitz, A.B.Lieberman, P.M.

(2019) Sci Transl Med 11

  • DOI: https://doi.org/10.1126/scitranslmed.aau5612
  • Primary Citation of Related Structures:  
    6NPI, 6NPM, 6NPP

  • PubMed Abstract: 

    Epstein-Barr virus (EBV) is a DNA tumor virus responsible for 1 to 2% of human cancers including subtypes of Burkitt's lymphoma, Hodgkin's lymphoma, gastric carcinoma, and nasopharyngeal carcinoma (NPC). Persistent latent infection drives EBV-associated tumorigenesis. Epstein-Barr nuclear antigen 1 (EBNA1) is the only viral protein consistently expressed in all EBV-associated tumors and is therefore an attractive target for therapeutic intervention. It is a multifunctional DNA binding protein critical for viral replication, genome maintenance, viral gene expression, and host cell survival. Using a fragment-based approach and x-ray crystallography, we identify a 2,3-disubstituted benzoic acid series that selectively inhibits the DNA binding activity of EBNA1. We characterize these inhibitors biochemically and in cell-based assays, including chromatin immunoprecipitation and DNA replication assays. In addition, we demonstrate the potency of EBNA1 inhibitors to suppress tumor growth in several EBV-dependent xenograft models, including patient-derived xenografts for NPC. These inhibitors selectively block EBV gene transcription and alter the cellular transforming growth factor-β (TGF-β) signaling pathway in NPC tumor xenografts. These EBNA1-specific inhibitors show favorable pharmacological properties and have the potential to be further developed for the treatment of EBV-associated malignancies.

  • Organizational Affiliation

    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA. lieberman@wistar.org troymessick@gmail.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epstein-Barr nuclear antigen 1
A, B
141Human 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
Query on KVD

Download Ideal Coordinates CCD File 
C [auth B]5-(phenylethynyl)pyridine-3-carboxylic acid
C14 H9 N O2
Binding Affinity Annotations 
IDSourceBinding Affinity
KVD Binding MOAD:  6NPM Ki: 1.10e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.458α = 90
b = 67.951β = 90
c = 69.546γ = 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

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description