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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.228
R-Value Work: 0.194
R-Value Observed: 0.196

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12830
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EUO (Subject of Investigation/LOI) Query on EUO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-(1H-indol-5-yl)-N-methyl-2-methylsulfonyl-pyrimidin-4-amine C₁₄ H₁₄ N₄ O₂ S RTONKOFFKFVXAW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
EUO	BindingDB: 7F5D	Kd: 2810 (nM) from 1 assay(s)
EUO	BindingDB: 7F5D	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
R-Value Work: 0.194
R-Value Observed: 0.196
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.