6CKR

Crystal Structure of BRD4 with QC4956


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design, synthesis and biological evaluation of novel 4-phenylisoquinolinone BET bromodomain inhibitors.

Bennett, M.J.Wu, Y.Boloor, A.Matuszkiewicz, J.O'Connell, S.M.Shi, L.Stansfield, R.K.Del Rosario, J.R.Veal, J.M.Hosfield, D.J.Xu, J.Kaldor, S.W.Stafford, J.A.Betancort, J.M.

(2018) Bioorg Med Chem Lett 28: 1811-1816

  • DOI: 10.1016/j.bmcl.2018.04.016
  • Primary Citation of Related Structures:  
    6CKR, 6CKS

  • PubMed Abstract: 
  • The bromodomain and extra-terminal (BET) family of epigenetic proteins has attracted considerable attention in drug discovery given its involvement in regulating gene transcription. Screening a focused small molecule library based on the bromodomain pharmacophore resulted in the identification of 2-methylisoquinoline-1-one as a novel BET bromodomain-binding motif ...

    The bromodomain and extra-terminal (BET) family of epigenetic proteins has attracted considerable attention in drug discovery given its involvement in regulating gene transcription. Screening a focused small molecule library based on the bromodomain pharmacophore resulted in the identification of 2-methylisoquinoline-1-one as a novel BET bromodomain-binding motif. Structure guided SAR exploration resulted in >10,000-fold potency improvement for the BRD4-BD1 bromodomain. Lead compounds exhibited excellent potencies in both biochemical and cellular assays in MYC-dependent cell lines. Compound 36 demonstrated good physicochemical properties and promising exposure levels in exploratory PK studies.


    Organizational Affiliation

    Celgene Quanticel Research, 10300 Campus Point Drive, Suite 100, San Diego, CA 92121, United States. Electronic address: jbetancort@celgene.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A, B126Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F5V (Subject of Investigation/LOI)
Query on F5V

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]N-{3-[2-methyl-6-(1-methyl-1H-pyrazol-4-yl)-1-oxo-1,2-dihydroisoquinolin-4-yl]phenyl}methanesulfonamide
C21 H20 N4 O3 S
XUAJCFLNMSRSIO-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
F5V BindingDB:  6CKR IC50: min: 50, max: 500 (nM) from 3 assay(s)
Binding MOAD:  6CKR IC50: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.37α = 100.72
b = 41.47β = 104.83
c = 57.66γ = 90.5
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-02-28 
  • Released Date: 2018-05-02 
  • Deposition Author(s): Hosfield, D.J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references