7JT4 | pdb_00007jt4

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

• PDB DOI: https://doi.org/10.2210/pdb7JT4/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-17 Released: 2021-07-28 
• Deposition Author(s): Johnson, J.A., Shi, K., Aihara, H., Pomerantz, W.C.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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

• PubMed: 30706071 
• DOI: https://doi.org/10.1039/c8ob02599a
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, University of Minnesota, 207 Pleasant St. SE., Minneapolis, MN 55455, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.43 kDa 
• Atom Count: 1,228 
• Modeled Residue Count: 122 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome-remodeling factor subunit BPTF	A	131	Homo sapiens	Mutation(s): 0  Gene Names: BPTF, FAC1, FALZ
UniProt & NIH Common Fund Data Resources
Find proteins for Q12830 (Homo sapiens) Explore Q12830  Go to UniProtKB:  Q12830
PHAROS:  Q12830 GTEx:  ENSG00000171634

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FTR	A	L-PEPTIDE LINKING	C11 H11 F N2 O2		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.335	α = 90
b = 66.763	β = 105.02
c = 39.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Johnson, J.A., Shi, K., Aihara, H., Pomerantz, W.C.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	5T32GM008347-23

Revision History  

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