7X6T

Discovery of Selective BRD4 BD1 Inhibitor Based on [1,2,4] triazolo [4,3-b] pyridazine Scaffold

PDB DOI: https://doi.org/10.2210/pdb7X6T/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-08 Released: 2023-03-22
Deposition Author(s): Cao, D., Xiong, B.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.198
R-Value Work: 0.185
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of Selective BRD4 BD1 Inhibitor Based on [1,2,4] triazolo [4,3-b] pyridazine Scaffold

Hanyue, Z., Cao, D., Li, Y., Du, Z., Xiong, B.

To be published.

Macromolecule Content

Total Structure Weight: 15.13 kDa
Atom Count: 1,220
Modelled Residue Count: 124
Deposited Residue Count: 124
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform C of Bromodomain-containing protein 4	A	124	Homo sapiens	Mutation(s): 0 Gene Names: BRD4, HUNK1
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60885
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
97F (Subject of Investigation/LOI) Query on 97F Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(2~{R})-2-[[3-methyl-6-(2-phenoxyphenyl)-[1,2,4]triazolo[4,3-b]pyridazin-8-yl]amino]propanamide C₂₁ H₂₀ N₆ O₂ KJEVFPWGGUKRKQ-CYBMUJFWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.198
R-Value Work: 0.185
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.264	α = 90
b = 43.064	β = 90
c = 79.041	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	China	81703340

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.