6G0D

BRD4 (BD1) in complex with APSC-derived ligands (e.g. LY294002)

PDB DOI: https://doi.org/10.2210/pdb6G0D/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-03-18 Released: 2020-01-08
Deposition Author(s): Pretzel, J., Humbeck, L.
Funding Organization(s): German Research Foundation, German Federal Ministry for Education and Research (BMBF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.236
R-Value Work: 0.202
R-Value Observed: 0.204

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 of an Unexpected Similarity in Ligand Binding Between BRD4 and PPARgamma

Humbeck, L., Pretzel, J., Spitzer, S., Koch, O.

(2019) ChemRxiv

DOI: https://doi.org/10.26434/chemrxiv.11472618

Macromolecule Content

Total Structure Weight: 15.47 kDa
Atom Count: 1,258
Modelled Residue Count: 127
Deposited Residue Count: 127
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 1 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LY2 (Subject of Investigation/LOI) Query on LY2 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-MORPHOLIN-4-YL-7-PHENYL-4H-CHROMEN-4-ONE C₁₉ H₁₇ N O₃ CZQHHVNHHHRRDU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
LY2	BindingDB: 6G0D	IC50: min: 5330, max: 1.24e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.236
R-Value Work: 0.202
R-Value Observed: 0.204
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.295	α = 90
b = 42.868	β = 90
c = 79.582	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-01-08

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	SPP 1736
German Federal Ministry for Education and Research (BMBF)	Germany	BMBF Grant 1316053

Revision History (Full details and data files)

Version 1.0: 2020-01-08
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, 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.