N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH N-(1,1-dioxo-1-thian-4-yl)- 5-methyl-4-oxo-7-3-(trifluoromethyl)phenyl-4H,5H-thieno-3,2-c- pyridine-2-carboximidamide

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


The Discovery of I-Brd9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition.

Theodoulou, N.H.Bamborough, P.Bannister, A.J.Becher, I.Bit, R.A.Che, K.H.Chung, C.Dittmann, A.Drewes, G.Drewry, D.H.Gordon, L.Grandi, P.Leveridge, M.Lindon, M.Michon, A.Molnar, J.Robson, S.C.Tomkinson, N.C.O.Kouzarides, T.Prinjha, R.K.Humphreys, P.G.

(2016) J Med Chem 59: 1425

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00256
  • Primary Citation of Related Structures:  
    4UIT, 4UIU, 4UIV, 4UIW, 4UIX, 4UIY, 4UIZ

  • PubMed Abstract: 

    Acetylation of histone lysine residues is one of the most well-studied post-translational modifications of chromatin, selectively recognized by bromodomain "reader" modules. Inhibitors of the bromodomain and extra terminal domain (BET) family of bromodomains have shown profound anticancer and anti-inflammatory properties, generating much interest in targeting other bromodomain-containing proteins for disease treatment. Herein, we report the discovery of I-BRD9, the first selective cellular chemical probe for bromodomain-containing protein 9 (BRD9). I-BRD9 was identified through structure-based design, leading to greater than 700-fold selectivity over the BET family and 200-fold over the highly homologous bromodomain-containing protein 7 (BRD7). I-BRD9 was used to identify genes regulated by BRD9 in Kasumi-1 cells involved in oncology and immune response pathways and to the best of our knowledge, represents the first selective tool compound available to elucidate the cellular phenotype of BRD9 bromodomain inhibition.

  • Organizational Affiliation

    Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BROMODOMAIN-CONTAINING PROTEIN 4127Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5V2

Download Ideal Coordinates CCD File 
E [auth A]N-[1,1-bis(oxidanylidene)thian-4-yl]-5-methyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide
C21 H20 F3 N3 O3 S2
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
5V2 Binding MOAD:  4UIY IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.35α = 90
b = 44.24β = 90
c = 78.64γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Data collection