6MH7 | pdb_00006mh7

Crystal structure of the first bromodomain of human BRD4 in complex with SKT-68, a 1,4,5-trisubstituted imidazole analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.185 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Molecular Basis for the N-Terminal Bromodomain-and-Extra-Terminal-Family Selectivity of a Dual Kinase-Bromodomain Inhibitor.

Divakaran, A.Talluri, S.K.Ayoub, A.M.Mishra, N.K.Cui, H.Widen, J.C.Berndt, N.Zhu, J.Y.Carlson, A.S.Topczewski, J.J.Schonbrunn, E.K.Harki, D.A.Pomerantz, W.C.K.

(2018) J Med Chem 61: 9316-9334

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01248
  • Primary Citation Related Structures: 
    6MH1, 6MH7

  • PubMed Abstract: 

    As regulators of transcription, epigenetic proteins that interpret post-translational modifications to N-terminal histone tails are essential for maintaining cellular homeostasis. When dysregulated, "reader" proteins become drivers of disease. In the case of bromodomains, which recognize N-ε-acetylated lysine, selective inhibition of individual bromodomain-and-extra-terminal (BET)-family bromodomains has proven challenging. We describe the >55-fold N-terminal-BET bromodomain selectivity of 1,4,5-trisubstituted-imidazole dual kinase-bromodomain inhibitors. Selectivity for the BRD4 N-terminal bromodomain (BRD4(1)) over its second bromodomain (BRD4(2)) arises from the displacement of ordered waters and the conformational flexibility of lysine-141 in BRD4(1). Cellular efficacy was demonstrated via reduction of c-Myc expression, inhibition of NF-κB signaling, and suppression of IL-8 production through potential synergistic inhibition of BRD4(1) and p38α. These dual inhibitors provide a new scaffold for domain-selective inhibition of BRD4, the aberrant function of which plays a key role in cancer and inflammatory signaling.


  • Organizational Affiliation
    • Department of Medicinal Chemistry , University of Minnesota , 2231 6th Street SE , Minneapolis , Minnesota 55455 , United States.

Macromolecule Content 

  • Total Structure Weight: 31.41 kDa 
  • Atom Count: 2,444 
  • Modeled Residue Count: 254 
  • Deposited Residue Count: 254 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JQY
(Subject of Investigation/LOI)

Query on JQY



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
N-(3,4-dimethylphenyl)-4-[4-(4-fluorophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]pyrimidin-2-amine
C26 H27 F N6
OGDBBVMMKPWVLG-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
H [auth B],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.185 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.75α = 90
b = 59.37β = 90
c = 111.82γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1352019
American Heart AssociationUnited States15SDG25710427

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description