4IOR

Crystal Structure of the first bromodomain of BRD4 in complex with DMSO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Different orientations of low-molecular-weight fragments in the binding pocket of a BRD4 bromodomain.

Lolli, G.Battistutta, R.

(2013) Acta Crystallogr.,Sect.D 69: 2161-2164

  • DOI: 10.1107/S090744491301994X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bromodomains are involved in the regulation of chromatin architecture and transcription through the recognition of acetylated lysines in histones and other proteins. Many of them are considered to be relevant pharmacological targets for different pat ...

    Bromodomains are involved in the regulation of chromatin architecture and transcription through the recognition of acetylated lysines in histones and other proteins. Many of them are considered to be relevant pharmacological targets for different pathologies. Three crystallographic structures of the N-terminal bromodomain of BRD4 in complex with low-molecular-weight fragments are presented. They show that similar molecules mimicking acetylated lysine bind the bromodomain with different orientations and exploit different interactions. It is also advised to avoid DMSO when searching for low-affinity fragments that interact with bromodomains since DMSO binds in the acetylated lysine-recognition pocket of BRD4.


    Organizational Affiliation

    Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A
127Homo sapiensMutation(s): 0 
Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens)
Go to Gene View: BRD4
Go to UniProtKB:  O60885
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.176α = 90.00
b = 44.119β = 90.00
c = 77.965γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references