6FFD

Human BRD4 C-terminal bromodomain with 1-(4-(3-methylbenzyl)-3,4-dihydroquinoxalin-1(2H)-yl)ethanone

PDB DOI: https://doi.org/10.2210/pdb6FFD/pdb

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

Deposited: 2018-01-06 Released: 2019-01-30
Deposition Author(s): Chung, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.253
R-Value Work: 0.185
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design and Synthesis of Tetrahydroquinoxalines as Domain Selective BET Inhibitors

Chung, C.

To be published.

Macromolecule Content

Total Structure Weight: 13.92 kDa
Atom Count: 1,062
Modelled Residue Count: 113
Deposited Residue Count: 117
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	117	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
D7T Query on D7T Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1-(4-(3-methylbenzyl)-3,4-dihydroquinoxalin-1(2H)-yl)ethanone C₁₈ H₂₀ N₂ O GJDUNGUDLCUYKF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
D7T	BindingDB: 6FFD	IC50: min: 501, max: 1.58e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.253
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.31	α = 90
b = 57.15	β = 90
c = 73.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release

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.