6G0E

BRD4 (BD1) in complex with APSC-derived ligands

• PDB DOI: https://doi.org/10.2210/pdb6G0E/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.261 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.74 kDa 
• Atom Count: 1,163 
• Modelled Residue Count: 125 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EGN (Subject of Investigation/LOI)	B [auth A]	4-[2-(4-cyclohexylpiperazin-4-ium-1-yl)-2-oxidanylidene-ethyl]sulfanyl-1-ethyl-quinolin-2-one C23 H32 N3 O2 S ZOILQSINXFCIAF-UHFFFAOYSA-O
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.261 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.482	α = 90
b = 46.749	β = 90
c = 78.347	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-08 
Deposition Author(s): Pretzel, J., Humbeck, L.

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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  

• Version 1.0: 2020-01-08
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description