6CKS

Crystal Structure of BRD4 with QC4956

• PDB DOI: https://doi.org/10.2210/pdb6CKS/pdb

• Classification: GENE REGULATION/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.211 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 

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

• PubMed: 29657099 
• 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.

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Organizational Affiliation: 

Celgene Quanticel Research, 10300 Campus Point Drive, Suite 100, San Diego, CA 92121, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.45 kDa 
• Atom Count: 1,254 
• Modelled Residue Count: 126 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	126	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F5Y	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 VFQXMHYHBXHDCR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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

• Method: X-RAY DIFFRACTION
• 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 = 41.83	α = 90
b = 49.12	β = 90
c = 56.673	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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