6DJC

Crystal structure of human Bromodomain-containing protein 4 (BRD4) bromodomain with MS645


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Spatially constrained tandem bromodomain inhibition bolsters sustained repression of BRD4 transcriptional activity for TNBC cell growth.

Ren, C.Zhang, G.Han, F.Fu, S.Cao, Y.Zhang, F.Zhang, Q.Meslamani, J.Xu, Y.Ji, D.Cao, L.Zhou, Q.Cheung, K.L.Sharma, R.Babault, N.Yi, Z.Zhang, W.Walsh, M.J.Zeng, L.Zhou, M.M.

(2018) Proc Natl Acad Sci U S A 115: 7949-7954

  • DOI: 10.1073/pnas.1720000115
  • Primary Citation of Related Structures:  
    6DJC, 6DNE

  • PubMed Abstract: 
  • The importance of BET protein BRD4 in gene transcription is well recognized through the study of chemical modulation of its characteristic tandem bromodomain (BrD) binding to lysine-acetylated histones and transcription factors. However, while monovalent inhibition of BRD4 by BET BrD inhibitors such as JQ1 blocks growth of hematopoietic cancers, it is much less effective generally in solid tumors ...

    The importance of BET protein BRD4 in gene transcription is well recognized through the study of chemical modulation of its characteristic tandem bromodomain (BrD) binding to lysine-acetylated histones and transcription factors. However, while monovalent inhibition of BRD4 by BET BrD inhibitors such as JQ1 blocks growth of hematopoietic cancers, it is much less effective generally in solid tumors. Here, we report a thienodiazepine-based bivalent BrD inhibitor, MS645, that affords spatially constrained tandem BrD inhibition and consequently sustained repression of BRD4 transcriptional activity in blocking proliferation of solid-tumor cells including a panel of triple-negative breast cancer (TNBC) cells. MS645 blocks BRD4 binding to transcription enhancer/mediator proteins MED1 and YY1 with potency superior to monovalent BET inhibitors, resulting in down-regulation of proinflammatory cytokines and genes for cell-cycle control and DNA damage repair that are largely unaffected by monovalent BrD inhibition. Our study suggests a therapeutic strategy to maximally control BRD4 activity for rapid growth of solid-tumor TNBC cells.


    Organizational Affiliation

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029; ming-ming.zhou@mssm.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A, B132Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CF6 (Subject of Investigation/LOI)
Query on CF6

Download Ideal Coordinates CCD File 
C [auth A]N,N'-(decane-1,10-diyl)bis{2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetamide}
C48 H54 Cl2 N10 O2 S2
VFGPQYYCEGAFLY-UWXQCODUSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CF6 Binding MOAD:  6DJC Ki: 232.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54α = 90
b = 59.72β = 90
c = 95.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-05-25 
  • Released Date: 2018-07-25 
  • Deposition Author(s): Ren, C., Zhou, M.M.

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-15
    Changes: Data collection, Database references