9FBX | pdb_00009fbx

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 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.160 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IBVClick on this verticalbar to view details

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 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.160 (DCC) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IBVClick on this verticalbar to view details

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