6CZU

BRD4(BD1) complexed with 3219


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and Characterization of Novel Covalent Bromodomain and Extra-Terminal Domain (BET) Inhibitors Targeting a Methionine.

Kharenko, O.A.Patel, R.G.Brown, S.D.Calosing, C.White, A.Lakshminarasimhan, D.Suto, R.K.Duffy, B.C.Kitchen, D.B.McLure, K.G.Hansen, H.C.van der Horst, E.H.Young, P.R.

(2018) J. Med. Chem. 61: 8202-8211

  • DOI: 10.1021/acs.jmedchem.8b00666
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • BET proteins are key epigenetic regulators that regulate transcription through binding to acetylated lysine (AcLys) residues of histones and transcription factors through bromodomains (BDs). The disruption of this interaction with small molecule brom ...

    BET proteins are key epigenetic regulators that regulate transcription through binding to acetylated lysine (AcLys) residues of histones and transcription factors through bromodomains (BDs). The disruption of this interaction with small molecule bromodomain inhibitors is a promising approach to treat various diseases including cancer, autoimmune and cardiovascular diseases. Covalent inhibitors can potentially offer a more durable target inhibition leading to improved in vivo pharmacology. Here we describe the design of covalent inhibitors of BRD4(BD1) that target a methionine in the binding pocket by attaching an epoxide warhead to a suitably oriented noncovalent inhibitor. Using thermal denaturation, MALDI-TOF mass spectrometry, and an X-ray crystal structure, we demonstrate that these inhibitors selectively form a covalent bond with Met149 in BRD4(BD1) but not other bromodomains and provide durable transcriptional and antiproliferative activity in cell based assays. Covalent targeting of methionine offers a novel approach to drug discovery for BET proteins and other targets.


    Organizational Affiliation

    Xtal BioStructures, Inc. , 12 Michigan Drive , Natick , Massachusetts 01760 , United States.,AMRI , 26 Corporate Circle , P.O. Box 15098, Albany , New York 12212-5098 , United States.,Zenith Epigenetics , Suite 300, 4820 Richard Road SW , Calgary , Alberta T3E 6L1 , Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A
129Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FP7
Query on FP7

Download SDF File 
Download CCD File 
A
5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-({4-[(1R)-1-hydroxyethyl]phenyl}methyl)pyridin-2(1H)-one
C19 H20 N2 O3
GYFSAKAXGZYFTD-CYBMUJFWSA-N
 Ligand Interaction
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: 1.47 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.066α = 90.00
b = 48.967β = 90.00
c = 59.880γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-10
    Type: Data collection, Database references