7QDL

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 with I-BET567


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis, and Characterization of I-BET567, a Pan-Bromodomain and Extra Terminal (BET) Bromodomain Oral Candidate.

Humphreys, P.G.Atkinson, S.J.Bamborough, P.Bit, R.A.Chung, C.W.Craggs, P.D.Cutler, L.Davis, R.Ferrie, A.Gong, G.Gordon, L.J.Gray, M.Harrison, L.A.Hayhow, T.G.Haynes, A.Henley, N.Hirst, D.J.Holyer, I.D.Lindon, M.J.Lovatt, C.Lugo, D.McCleary, S.Molnar, J.Osmani, Q.Patten, C.Preston, A.Rioja, I.Seal, J.T.Smithers, N.Sun, F.Tang, D.Taylor, S.Theodoulou, N.H.Thomas, C.Watson, R.J.Wellaway, C.R.Zhu, L.Tomkinson, N.C.O.Prinjha, R.K.

(2022) J Med Chem 65: 2262-2287

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01747
  • Primary Citation of Related Structures:  
    7QDL

  • PubMed Abstract: 

    Through regulation of the epigenome, the bromodomain and extra terminal (BET) family of proteins represent important therapeutic targets for the treatment of human disease. Through mimicking the endogenous N -acetyl-lysine group and disrupting the protein-protein interaction between histone tails and the bromodomain, several small molecule pan-BET inhibitors have progressed to oncology clinical trials. This work describes the medicinal chemistry strategy and execution to deliver an orally bioavailable tetrahydroquinoline (THQ) pan-BET candidate. Critical to the success of this endeavor was a potency agnostic analysis of a data set of 1999 THQ BET inhibitors within the GSK collection which enabled identification of appropriate lipophilicity space to deliver compounds with a higher probability of desired oral candidate quality properties. SAR knowledge was leveraged via Free-Wilson analysis within this design space to identify a small group of targets which ultimately delivered I-BET567 ( 27 ), a pan-BET candidate inhibitor that demonstrated efficacy in mouse models of oncology and inflammation.


  • Organizational Affiliation

    GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom.


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
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
AKQ BindingDB:  7QDL Kd: min: 5, max: 25 (nM) from 2 assay(s)
IC50: min: 63, max: 126 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.222α = 90
b = 48.995β = 90
c = 60.865γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-12-14 
  • Deposition Author(s): Chung, C.

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-01
    Changes: Refinement description