7JKY | pdb_00007jky

Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with YF3-126


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 
    0.176 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7JKY

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Novel Pyrrolopyridone Bromodomain and Extra-Terminal Motif (BET) Inhibitors Effective in Endocrine-Resistant ER+ Breast Cancer with Acquired Resistance to Fulvestrant and Palbociclib.

Li, Y.Zhao, J.Gutgesell, L.M.Shen, Z.Ratia, K.Dye, K.Dubrovskyi, O.Zhao, H.Huang, F.Tonetti, D.A.Thatcher, G.R.J.Xiong, R.

(2020) J Med Chem 63: 7186-7210

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00456
  • Primary Citation Related Structures: 
    6P05, 7JKW, 7JKY, 7JKZ

  • PubMed Abstract: 

    Acquired resistance to fulvestrant and palbociclib is a new challenge to treatment of estrogen receptor positive (ER+) breast cancer. ER is expressed in most resistance settings; thus, bromodomain and extra-terminal protein inhibitors (BETi) that target BET-amplified ER-mediated transcription have therapeutic potential. Novel pyrrolopyridone BETi leveraged novel interactions with L92/L94 confirmed by a cocrystal structure of 27 with BRD4. Optimization of BETi using growth inhibition in fulvestrant-resistant (MCF-7:CFR) cells was confirmed in endocrine-resistant, palbociclib-resistant, and ESR1 mutant cell lines. 27 was more potent in MCF-7:CFR cells than six BET inhibitors in clinical trials. Transcriptomic analysis differentiated 27 from the benchmark BETi, JQ-1, showing downregulation of oncogenes and upregulation of tumor suppressors and apoptosis. The therapeutic approach was validated by oral administration of 27 in orthotopic xenografts of endocrine-resistant breast cancer in monotherapy and in combination with fulvestrant. Importantly, at an equivalent dose in rats, thrombocytopenia was mitigated.


  • Organizational Affiliation
    • UICentre (Drug Discovery @ UIC), University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States.

Macromolecule Content 

  • Total Structure Weight: 15.76 kDa 
  • Atom Count: 1,367 
  • Modeled Residue Count: 127 
  • Deposited Residue Count: 127 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4127Homo 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
GTEx:  ENSG00000141867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YF6
(Subject of Investigation/LOI)

Query on YF6



Download:Ideal Coordinates CCD File
B [auth A]N-(1-[1,1-di(pyridin-2-yl)ethyl]-6-{1-methyl-6-oxo-5-[(piperidin-4-yl)amino]-1,6-dihydropyridin-3-yl}-1H-indol-4-yl)ethanesulfonamide
C33 H37 N7 O3 S
RDWRDUFEWMSPGQ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free:  0.176 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.196α = 90
b = 42.303β = 90
c = 91.235γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
SCALEPACKdata scaling
Aimlessdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesUL1RR029879

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description