6TPZ

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 5-(1-(1,3-dimethoxypropan-2-yl)-5-morpholino-1H-benzo[d]imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.9b01670
  • Primary Citation of Related Structures:  
    6TQ2, 6TQ1, 6TPZ, 6TPY, 6TPX

  • 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 int ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4AAA127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NV2
Query on NV2

Download CCD File 
AAA
5-[1-(1,3-dimethoxypropan-2-yl)-5-morpholin-4-yl-benzimidazol-2-yl]-1,3-dimethyl-pyridin-2-one
C23 H30 N4 O4
DDSHVVXWYKDTTQ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
AAA
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.493α = 90
b = 49.533β = 90
c = 58.213γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-12-15 
  • Released Date: 2020-01-15 
  • Deposition Author(s): Chung, C.

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references