6TQ1

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: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: 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 2A [auth AAA],
B [auth BBB],
C [auth CCC]
155Homo sapiensMutation(s): 0 
Gene Names: BRD2KIAA9001RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
GTEx:  ENSG00000204256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NUH (Subject of Investigation/LOI)
Query on NUH

Download Ideal Coordinates CCD File 
F [auth AAA],
H [auth BBB],
L [auth CCC]
5-(3-methoxyphenyl)-1-methyl-pyridin-2-one
C13 H13 N O2
WBOQDJCUHPQCRG-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth AAA],
E [auth AAA],
K [auth CCC]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth AAA],
I [auth BBB],
J [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.931α = 90
b = 55.606β = 94.434
c = 68.023γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



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