4UIZ | pdb_00004uiz

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)-2-(4-methanesulfonylpiperazine-1-carbonyl)-5-methyl-4H,5H-thieno-3,2-c- pyridin-4-one

• PDB DOI: https://doi.org/10.2210/pdb4UIZ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-03 Released: 2015-04-22 
• Deposition Author(s): Chung, C., Theodoulou, N.T., Bamborough, P., Humphreys, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 
  0.175 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

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

• PubMed: 25856009 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00256
• Primary Citation 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.

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Organizational Affiliation: 
• Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K.
WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K.
Computational & Structural Chemistry, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K.
Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K.
Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany.
Department of Chemical Biology, GlaxoSmithKline , Research Triangle Park, North Carolina 27709, United States.
Biological Sciences, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.72 kDa 
• Atom Count: 1,449 
• Modeled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 4	A	127	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N1D	D [auth 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
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free:  0.175 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.373	α = 90
b = 44.555	β = 90
c = 78.698	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Chung, C., Theodoulou, N.T., Bamborough, P., Humphreys, P.G.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other