8PXM

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (1R,1'R)-7,7'-(pentane-1,5-diylbis(oxy))bis(1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 

Starting Model: experimental
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Literature

Design and Characterization of 1,3-Dihydro-2 H -benzo[ d ]azepin-2-ones as Rule-of-5 Compliant Bivalent BET Inhibitors.

Bamborough, P.Chung, C.W.Goodwin, N.C.Mitchell, D.J.Neipp, C.E.Phillipou, A.Preston, A.Prinjha, R.K.Soden, P.E.Watson, R.J.Demont, E.H.

(2023) ACS Med Chem Lett 14: 1231-1236

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00242
  • Primary Citation of Related Structures:  
    8PXM, 8PXN

  • PubMed Abstract: 

    The 1,3-dihydro-2 H -benzo[ d ]azepin-2-ones are potent and ligand-efficient pan-BET bromodomain inhibitors. Here we describe the extension of this template to exploit a bivalent mode of action, binding simultaneously to both bromodomains. Initially the linker length and attachment vectors compatible with bivalent binding were explored, leading to the discovery of exceptionally potent bivalent BET inhibitors within druglike rule-of-5 space.


  • Organizational Affiliation

    GlaxoSmithKline, Medicines Research Centre, 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 4
A, B
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
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZTY
Query on ZTY

Download Ideal Coordinates CCD File 
C [auth A](1R)-7-[5-[[(1R)-1,3-dimethyl-2-oxidanylidene-1H-3-benzazepin-7-yl]oxy]pentoxy]-1,3-dimethyl-1H-3-benzazepin-2-one
C29 H34 N2 O4
LPZBOHUHUQVYMM-NHCUHLMSSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
D [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.936α = 90
b = 59.766β = 90
c = 105.287γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-10-04 
  • Deposition Author(s): Chung, C.W.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release