Crystal Structure of BRD4 with QC4956

Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4126Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on F5Y

Download Ideal Coordinates CCD File 
B [auth A]4-[5-(ethylsulfonyl)-2-methoxyphenyl]-2-methyl-6-(1-methyl-1H-pyrazol-4-yl)isoquinolin-1(2H)-one
C23 H23 N3 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
F5Y BindingDB:  6CKS IC50: min: 15, max: 500 (nM) from 3 assay(s)
Binding MOAD:  6CKS IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.72 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.83α = 90
b = 49.12β = 90
c = 56.673γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description