5D3P

First bromodomain of BRD4 bound to inhibitor XD41


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1).

Hugle, M.Lucas, X.Weitzel, G.Ostrovskyi, D.Breit, B.Gerhardt, S.Einsle, O.Gunther, S.Wohlwend, D.

(2016) J.Med.Chem. 59: 1518-1530

  • DOI: 10.1021/acs.jmedchem.5b01267
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Several human diseases, including cancer, show altered signaling pathways resulting from changes in the activity levels of epigenetic modulators. In the past few years, small-molecule inhibitors against specific modulators, including the bromodomain ...

    Several human diseases, including cancer, show altered signaling pathways resulting from changes in the activity levels of epigenetic modulators. In the past few years, small-molecule inhibitors against specific modulators, including the bromodomain and extra-terminal (BET) bromodomain family of acetylation readers, have shown early promise in the treatment of the genetically defined midline carcinoma and hematopoietic malignancies. We have recently developed a novel potent inhibitor of BET proteins, 1 (XD14[ Angew. Chem., Int. Ed. 2013, 52, 14055]), which exerts a strong inhibitory potential on the proliferation of specific leukemia cell lines. In the study presented here, we designed analogues of 1 to study the potential of substitutions on the 4-acyl pyrrole backbone to occupy additional sites within the substrate recognition site of BRD4(1). The compounds were profiled using ITC, DSF, and X-ray crystallography. We could introduce several substitutions that address previously untargeted areas of the substrate recognition site. This work may substantially contribute to the development of therapeutics with increased target specificity against BRD4-related malignancies.


    Organizational Affiliation

    Institut für Biochemie, Albert-Ludwigs-Universität Freiburg , Albertstrasse 21, D-79104 Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A
127Homo sapiensMutation(s): 1 
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
57E
Query on 57E

Download SDF File 
Download CCD File 
A
1-[(4-acetyl-3-ethyl-5-methyl-1H-pyrrol-2-yl)carbonyl]-N-methyl-1H-indole-6-sulfonamide
C19 H21 N3 O4 S
FRIHRFHOIOFYKK-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.700α = 90.00
b = 44.550β = 90.00
c = 78.620γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyWO2012/1-1

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence