6G0F | pdb_00006g0f

BRD4 (BD1) in complex with docking-derived ligand

• PDB DOI: https://doi.org/10.2210/pdb6G0F/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: 1.62 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

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: 15.57 kDa 
• Atom Count: 1,208 
• Modeled Residue Count: 127 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EGH (Subject of Investigation/LOI)	C [auth A]	(4~{R})-4-(5-bromanyl-2-fluoranyl-phenyl)-5,6,7-trimethoxy-3,4-dihydro-1~{H}-quinolin-2-one C18 H17 Br F N O4 PWBKGPVHXOKOOE-NSHDSACASA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.529	α = 90
b = 44.329	β = 90
c = 78.517	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	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, Refinement description