5A7C

Crystal structure of the second bromodomain of human BRD3 in complex with compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cancer Differentiating Agent Hexamethylene Bisacetamide Inhibits Bet Bromodomain Proteins.

Nilsson, L.M.Green, L.C.Muralidharan, S.V.Demir, D.Welin, M.Bhadury, J.Logan, D.T.Walse, B.Nilsson, J.A.

(2016) Cancer Res. 76: 2376

  • DOI: 10.1158/0008-5472.CAN-15-2721

  • PubMed Abstract: 
  • Agents that trigger cell differentiation are highly efficacious in treating certain cancers, but such approaches are not generally effective in most malignancies. Compounds such as DMSO and hexamethylene bisacetamide (HMBA) have been used to induce d ...

    Agents that trigger cell differentiation are highly efficacious in treating certain cancers, but such approaches are not generally effective in most malignancies. Compounds such as DMSO and hexamethylene bisacetamide (HMBA) have been used to induce differentiation in experimental systems, but their mechanisms of action and potential range of uses on that basis have not been developed. Here, we show that HMBA, a compound first tested in the oncology clinic over 25 years ago, acts as a selective bromodomain inhibitor. Biochemical and structural studies revealed an affinity of HMBA for the second bromodomain of BET proteins. Accordingly, both HMBA and the prototype BET inhibitor JQ1 induced differentiation of mouse erythroleukemia cells. As expected of a BET inhibitor, HMBA displaced BET proteins from chromatin, caused massive transcriptional changes, and triggered cell-cycle arrest and apoptosis in Myc-induced B-cell lymphoma cells. Furthermore, HMBA exerted anticancer effects in vivo in mouse models of Myc-driven B-cell lymphoma. This study illuminates the function of an early anticancer agent and suggests an intersection with ongoing clinical trials of BET inhibitor, with several implications for predicting patient selection and response rates to this therapy and starting points for generating BD2-selective BET inhibitors. Cancer Res; 76(8); 2376-83. ©2016 AACR.


    Organizational Affiliation

    Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center at University of Gothenburg, Gothenburg, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BROMODOMAIN-CONTAINING PROTEIN 3
A, B, C, D
113Homo sapiensMutation(s): 0 
Gene Names: BRD3 (KIAA0043, RING3L)
Find proteins for Q15059 (Homo sapiens)
Go to Gene View: BRD3
Go to UniProtKB:  Q15059
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5D4
Query on 5D4

Download SDF File 
Download CCD File 
A, B, C, D
N-(6-ACETAMIDOHEXYL)ACETAMIDE
C10 H20 N2 O2
BNQSTAOJRULKNX-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.365α = 90.00
b = 92.013β = 95.35
c = 64.898γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection