4NR8

Crystal structure of the first bromodomain of human BRD4 in complex with an isoxazolyl-benzimidazole ligand

• PDB DOI: https://doi.org/10.2210/pdb4NR8/pdb

• Classification: TRANSCRIPTION/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-26 Released: 2013-12-25 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Hay, D., Fedorov, O., Martin, S., von Delft, F., Brennan, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.246 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Crystal structure of the first bromodomain of human BRD4 in complex with an isoxazolyl-benzimidazole ligand

Filippakopoulos, P., Hay, D., von Delft, F., Edwards, A.M., Picaud, S., Fedorov, O., Brennan, P., Bountra, C.

To be published.

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: 15.63 kDa 
• Atom Count: 1,204 
• 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): 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2LL	C [auth A]	5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazole C26 H30 N4 O2 ZVYCZICBBIUVHC-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.246 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.052	α = 90
b = 50.755	β = 90
c = 58.661	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Hay, D., Fedorov, O., Martin, S., von Delft, F., Brennan, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description