9FBX

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5-(1-benzyl-4-chloro-1H-imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure- and Property-Based Optimization of Efficient Pan-Bromodomain and Extra Terminal Inhibitors to Identify Oral and Intravenous Candidate I-BET787.

Hirst, D.J.Bamborough, P.Al-Mahdi, N.Angell, D.C.Barnett, H.A.Baxter, A.Bit, R.A.Brown, J.A.Chung, C.W.Craggs, P.D.Davis, R.P.Demont, E.H.Ferrie, A.Gordon, L.J.Harada, I.Ho, T.C.T.Holyer, I.D.Hooper-Greenhill, E.Jones, K.L.Lindon, M.J.Lovatt, C.Lugo, D.Maller, C.McGonagle, G.Messenger, C.Mitchell, D.J.Pascoe, D.D.Patel, V.K.Patten, C.Poole, D.L.Shah, R.R.Rioja, I.Stafford, K.A.J.Tape, D.Taylor, S.Theodoulou, N.H.Tomlinson, L.Wall, I.D.Wellaway, C.R.White, G.Prinjha, R.K.Humphreys, P.G.

(2024) J Med Chem 67: 10464-10489

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00959
  • Primary Citation of Related Structures:  
    9FBX, 9FBY

  • PubMed Abstract: 

    The bromodomain and extra terminal (BET) family of bromodomain-containing proteins are important epigenetic regulators that elicit their effect through binding histone tail N -acetyl lysine (KAc) post-translational modifications. Recognition of such markers has been implicated in a range of oncology and immune diseases and, as such, small-molecule inhibition of the BET family bromodomain-KAc protein-protein interaction has received significant interest as a therapeutic strategy, with several potential medicines under clinical evaluation. This work describes the structure- and property-based optimization of a ligand and lipophilic efficient pan-BET bromodomain inhibitor series to deliver candidate I-BET787 ( 70 ) that demonstrates efficacy in a mouse model of inflammation and suitable properties for both oral and intravenous (IV) administration. This focused two-phase explore-exploit medicinal chemistry effort delivered the candidate molecule in 3 months with less than 100 final compounds synthesized.


  • Organizational Affiliation

    GSK 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 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.755α = 90
b = 52.427β = 90
c = 31.92γ = 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: 2024-06-26 
  • Deposition Author(s): Chung, C.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Database references