8WQO

Crystal structure of BRD4-BD1 bound with DI106

PDB DOI: https://doi.org/10.2210/pdb8WQO/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-12 Released: 2024-07-24
Deposition Author(s): Cao, D., Xiong, B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free: 0.212
R-Value Work: 0.199
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Rational design and evaluation of BET-Aurora A dual-inhibitors for treatment of cancers

Xiong, B., Kaikai, L., Cao, D., Dong, G.

To be published.

Macromolecule Content

Total Structure Weight: 15.15 kDa
Atom Count: 1,236
Modelled Residue Count: 123
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
X3L (Subject of Investigation/LOI) Query on X3L 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]	(3~{R})-6-[[4-(3,5-dimethyl-1~{H}-pyrazol-4-yl)pyrimidin-2-yl]amino]-1,3-dimethyl-4-propan-2-yl-3~{H}-quinoxalin-2-one C₂₂ H₂₇ N₇ O QXGVEYHHHIIWTF-OAHLLOKOSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free: 0.212
R-Value Work: 0.199
R-Value Observed: 0.199
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.523	α = 90
b = 46.314	β = 90
c = 77.251	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release

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.