7OET

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,5-dimethyl-N-(2-(methylamino)-2-oxo-1-(tetrahydro-2H-pyran-4-yl)ethyl)-6-oxo-N-(2-phenyl-2-(pyridin-2-yl)ethyl)-1,6-dihydropyridine-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.180 

Starting Model: other
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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 Highly Selective BET BD2 Inhibitor from a DNA-Encoded Library Technology Screening Hit.

Rianjongdee, F.Atkinson, S.J.Chung, C.W.Grandi, P.Gray, J.R.J.Kaushansky, L.J.Medeiros, P.Messenger, C.Phillipou, A.Preston, A.Prinjha, R.K.Rioja, I.Satz, A.L.Taylor, S.Wall, I.D.Watson, R.J.Yao, G.Demont, E.H.

(2021) J Med Chem 64: 10806-10833

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00412
  • Primary Citation of Related Structures:  
    7OEO, 7OEP, 7OER, 7OES, 7OET

  • PubMed Abstract: 

    Second-generation bromodomain and extra terminal (BET) inhibitors, which selectively target one of the two bromodomains in the BET proteins, have begun to emerge in the literature. These inhibitors aim to help determine the roles and functions of each domain and assess whether they can demonstrate an improved safety profile in clinical settings compared to pan-BET inhibitors. Herein, we describe the discovery of a novel BET BD2-selective chemotype using a structure-based drug design from a hit identified by DNA-encoded library technologies, showing a structural differentiation from key previously reported greater than 100-fold BD2-selective chemotypes GSK620, GSK046, and ABBV-744. Following a structure-based hypothesis for the selectivity and optimization of the physicochemical properties of the series, we identified 60 (GSK040), an in vitro ready and in vivo capable BET BD2-inhibitor of unprecedented selectivity (5000-fold) against BET BD1, excellent selectivity against other bromodomains, and good physicochemical properties. This novel chemical probe can be added to the toolbox used in the advancement of epigenetics research.


  • Organizational Affiliation

    IVIVT Cellzome, Platform Technology and Science, GlaxoSmithKline, Meyerhofstr. 1, Heidelberg 69117, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2A [auth AAA]115Homo 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
80Z (Subject of Investigation/LOI)
Query on 80Z

Download Ideal Coordinates CCD File 
B [auth AAA]1,5-dimethyl-~{N}-[(1~{R})-2-(methylamino)-1-(oxan-4-yl)-2-oxidanylidene-ethyl]-6-oxidanylidene-~{N}-[(2~{S})-2-phenyl-2-pyridin-2-yl-ethyl]pyridine-3-carboxamide
C29 H34 N4 O4
MDCZQITXTAMNNV-AOYPEHQESA-N
PE4
Query on PE4

Download Ideal Coordinates CCD File 
F [auth AAA]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.62α = 90
b = 52.39β = 90
c = 31.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-10-13 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Derived calculations, Refinement description