7OE8 | pdb_00007oe8

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N5-((1R,5S,6r)-3-oxabicyclo[3.1.0]hexan-6-yl)-3-(1H-indol-4-yl)-N7-methyl-2,3-dihydrobenzofuran-5,7-dicarboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.215 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Optimization of a Series of 2,3-Dihydrobenzofurans as Highly Potent, Second Bromodomain (BD2)-Selective, Bromo and Extra-Terminal Domain (BET) Inhibitors.

Lucas, S.C.C.Atkinson, S.J.Chung, C.W.Davis, R.Gordon, L.Grandi, P.Gray, J.J.R.Grimes, T.Phillipou, A.Preston, A.G.Prinjha, R.K.Rioja, I.Taylor, S.Tomkinson, N.C.O.Wall, I.Watson, R.J.Woolven, J.Demont, E.H.

(2021) J Med Chem 64: 10711-10741

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00344
  • Primary Citation Related Structures: 
    7OE8, 7OE9

  • PubMed Abstract: 

    Herein, a series of 2,3-dihydrobenzofurans have been developed as highly potent bromo and extra-terminal domain (BET) inhibitors with 1000-fold selectivity for the second bromodomain (BD2) over the first bromodomain (BD1). Investment in the development of two orthogonal synthetic routes delivered inhibitors that were potent and selective but had raised in vitro clearance and suboptimal solubility. Insertion of a quaternary center into the 2,3-dihydrobenzofuran core blocked a key site of metabolism and improved the solubility. This led to the development of inhibitor 71 (GSK852): a potent, 1000-fold-selective, highly soluble compound with good in vivo rat and dog pharmacokinetics.


  • Organizational Affiliation
    • IVIVT Cellzome, Platform Technology and Science, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 13.97 kDa 
  • Atom Count: 1,143 
  • Modeled Residue Count: 112 
  • Deposited Residue Count: 115 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2115Homo 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
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.215 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.934α = 90
b = 52.389β = 90
c = 31.998γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-07-28 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description