7JT4

Crystal Structure of BPTF bromodomain labelled with 5-fluoro-tryptophan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Selectivity, ligand deconstruction, and cellular activity analysis of a BPTF bromodomain inhibitor

Kirberger, S.E.Ycas, P.D.Johnson, J.A.Chen, C.Ciccone, M.F.Woo, R.W.L.Urick, A.K.Zahid, H.Shi, K.Aihara, H.McAllister, S.D.Kashani-Sabet, M.Shi, J.Dickson, A.Dos Santos, C.O.Pomerantz, W.C.K.

(2019) Org Biomol Chem 17: 2020-2027

  • DOI: https://doi.org/10.1039/c8ob02599a
  • Primary Citation of Related Structures:  
    7JT4

  • PubMed Abstract: 

    Bromodomain and PHD finger containing protein transcription factor (BPTF) is an epigenetic protein involved in chromatin remodelling and is a potential anticancer target. The BPTF bromodomain has one reported small molecule inhibitor (AU1, rac-1). Here, advances made on the structure-activity relationship of a BPTF bromodomain ligand are reported using a combination of experimental and molecular dynamics simulations leading to the active enatiomer (S)-1. Additionally, a ligand deconstruction analysis was conducted to characterize important pharmacophores for engaging the BPTF bromodomain. These studies have been enabled by a protein-based fluorine NMR approach, highlighting the versatility of the method for selectivity, ligand deconstruction, and ligand binding. To enable future analysis of biological activity, cell growth analyses in a panel of cancer cell lines were carried out using CRISPR-Cas9 and (S)-1 to identify cell-based model systems that are sensitive to BPTF inhibition.


  • Organizational Affiliation

    Department of Chemistry, University of Minnesota, 207 Pleasant St. SE., Minneapolis, MN 55455, USA. wcp@umn.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleosome-remodeling factor subunit BPTF131Homo sapiensMutation(s): 0 
Gene Names: BPTFFAC1FALZ
UniProt & NIH Common Fund Data Resources
Find proteins for Q12830 (Homo sapiens)
Explore Q12830 
Go to UniProtKB:  Q12830
PHAROS:  Q12830
GTEx:  ENSG00000171634 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12830
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FTR
Query on FTR
A
L-PEPTIDE LINKINGC11 H11 F N2 O2TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.335α = 90
b = 66.763β = 105.02
c = 39.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047
National Institutes of Health/National Library of Medicine (NIH/NLM)United States5T32GM008347-23

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description