4UIT

BROMODOMAIN OF HUMAN BRD9 WITH 7-(3,4-dimethoxyphenyl)-2-(4- methanesulfonylpiperazine-1-carbonyl)-5-methyl-4H,5H-thieno-3,2-c- pyridin-4-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

  • 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 brom ...

    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

    Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BROMODOMAIN-CONTAINING PROTEIN 9A106Homo sapiensMutation(s): 0 
Gene Names: BRD9UNQ3040/PRO9856
Find proteins for Q9H8M2 (Homo sapiens)
Explore Q9H8M2 
Go to UniProtKB:  Q9H8M2
NIH Common Fund Data Resources
PHAROS  Q9H8M2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N1D
Query on N1D

Download CCD File 
A
7-(3,4-dimethoxyphenyl)-5-methyl-2-(4-methylsulfonylpiperazin-1-yl)carbonyl-thieno[3,2-c]pyridin-4-one
C22 H25 N3 O6 S2
BEIFGZXXCPXAAY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N1DIC50:  200   nM  BindingDB
N1DIC50:  19950   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.7α = 70.26
b = 34.11β = 73.8
c = 39.68γ = 74.24
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2019-05-15
    Changes: Advisory, Data collection, Experimental preparation, Other