7F5D

Crystal structure of BPTF-BRD with ligand DC-BPi-03 bound

• PDB DOI: https://doi.org/10.2210/pdb7F5D/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-21 Released: 2022-06-29 
• Deposition Author(s): Lu, T., Lu, H.B., Wang, J., Lin, H., Lu, W., Luo, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Discovery and Optimization of Small-Molecule Inhibitors for the BPTF Bromodomains Proteins

Lu, T., Lu, H.B., Wang, J., Han, J., Xiao, S., Jiang, H., Chen, Y., Yang, F., Li, Q., Jiang, H.L., Chen, K.X., Lu, W.C., Lin, H., Luo, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.75 kDa 
• Atom Count: 1,091 
• Modelled Residue Count: 108 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome-remodeling factor subunit BPTF	A	115	Homo sapiens	Mutation(s): 0  Gene Names: BPTF
UniProt & NIH Common Fund Data Resources
Find proteins for Q12830 (Homo sapiens) Explore Q12830  Go to UniProtKB:  Q12830
PHAROS:  Q12830 GTEx:  ENSG00000171634

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EUO (Subject of Investigation/LOI)	B [auth A]	6-(1H-indol-5-yl)-N-methyl-2-methylsulfonyl-pyrimidin-4-amine C14 H14 N4 O2 S RTONKOFFKFVXAW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EUO	BindingDB:  7F5D	Kd: 2810 (nM) from 1 assay(s)
		IC50: 698 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.651	α = 90
b = 27.139	β = 96.649
c = 37.907	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Lu, T., Lu, H.B., Wang, J., Lin, H., Lu, W., Luo, C.

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description