Crystal Structure of the First Bromodomain of Human BRD4 in Complex With Cyclic Vinylogous Amide Inhibitor MS402

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.137 

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BET N-terminal bromodomain inhibition selectively blocks Th17 cell differentiation and ameliorates colitis in mice.

Cheung, K.Lu, G.Sharma, R.Vincek, A.Zhang, R.Plotnikov, A.N.Zhang, F.Zhang, Q.Ju, Y.Hu, Y.Zhao, L.Han, X.Meslamani, J.Xu, F.Jaganathan, A.Shen, T.Zhu, H.Rusinova, E.Zeng, L.Zhou, J.Yang, J.Peng, L.Ohlmeyer, M.Walsh, M.J.Zhang, D.Y.Xiong, H.Zhou, M.M.

(2017) Proc Natl Acad Sci U S A 114: 2952-2957

  • DOI: https://doi.org/10.1073/pnas.1615601114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    T-helper 17 (Th17) cells have important functions in adaptor immunity and have also been implicated in inflammatory disorders. The bromodomain and extraterminal domain (BET) family proteins regulate gene transcription during lineage-specific differentiation of naïve CD4 + T cells to produce mature T-helper cells. Inhibition of acetyl-lysine binding of the BET proteins by pan-BET bromodomain (BrD) inhibitors, such as JQ1, broadly affects differentiation of Th17, Th1, and Th2 cells that have distinct immune functions, thus limiting their therapeutic potential. Whether these BET proteins represent viable new epigenetic drug targets for inflammatory disorders has remained an unanswered question. In this study, we report that selective inhibition of the first bromodomain of BET proteins with our newly designed small molecule MS402 inhibits primarily Th17 cell differentiation with a little or almost no effect on Th1 or Th2 and Treg cells. MS402 preferentially renders Brd4 binding to Th17 signature gene loci over those of housekeeping genes and reduces Brd4 recruitment of p-TEFb to phosphorylate and activate RNA polymerase II for transcription elongation. We further show that MS402 prevents and ameliorates T-cell transfer-induced colitis in mice by blocking Th17 cell overdevelopment. Thus, selective pharmacological modulation of individual bromodomains likely represents a strategy for treatment of inflammatory bowel diseases.

  • Organizational Affiliation

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4
A, B
127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5MJ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H19 Cl N2 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
5MJ Binding MOAD:  5ULA Ki: 77 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.137 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.66α = 90
b = 47.66β = 90
c = 124.21γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references