6TPY

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1,3-dimethyl-5-(1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-2-yl)pyridin-2(1H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.199 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of a Bromodomain and Extraterminal Inhibitor with a Low Predicted Human Dose through Synergistic Use of Encoded Library Technology and Fragment Screening.

Wellaway, C.R.Amans, D.Bamborough, P.Barnett, H.Bit, R.A.Brown, J.A.Carlson, N.R.Chung, C.W.Cooper, A.W.J.Craggs, P.D.Davis, R.P.Dean, T.W.Evans, J.P.Gordon, L.Harada, I.L.Hirst, D.J.Humphreys, P.G.Jones, K.L.Lewis, A.J.Lindon, M.J.Lugo, D.Mahmood, M.McCleary, S.Medeiros, P.Mitchell, D.J.O'Sullivan, M.Le Gall, A.Patel, V.K.Patten, C.Poole, D.L.Shah, R.R.Smith, J.E.Stafford, K.A.J.Thomas, P.J.Vimal, M.Wall, I.D.Watson, R.J.Wellaway, N.Yao, G.Prinjha, R.K.

(2020) J Med Chem 63: 714-746

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01670
  • Primary Citation of Related Structures:  
    6TPX, 6TPY, 6TPZ, 6TQ1, 6TQ2

  • PubMed Abstract: 

    The bromodomain and extraterminal (BET) family of bromodomain-containing proteins are important regulators of the epigenome through their ability to recognize N -acetyl lysine (KAc) post-translational modifications on histone tails. These interactions have been implicated in various disease states and, consequently, disruption of BET-KAc binding has emerged as an attractive therapeutic strategy with a number of small molecule inhibitors now under investigation in the clinic. However, until the utility of these advanced candidates is fully assessed by these trials, there remains scope for the discovery of inhibitors from new chemotypes with alternative physicochemical, pharmacokinetic, and pharmacodynamic profiles. Herein, we describe the discovery of a candidate-quality dimethylpyridone benzimidazole compound which originated from the hybridization of a dimethylphenol benzimidazole series, identified using encoded library technology, with an N -methyl pyridone series identified through fragment screening. Optimization via structure- and property-based design led to I-BET469, which possesses favorable oral pharmacokinetic properties, displays activity in vivo, and is projected to have a low human efficacious dose.


  • Organizational Affiliation

    GSK , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A [auth AAA]127Homo 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
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.694α = 90
b = 43.252β = 90
c = 79.181γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-01-15 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description