6S25

Crystal Structure of the first bromodomain of BRD4 in complex with a benzodiazepine ligand

• PDB DOI: https://doi.org/10.2210/pdb6S25/pdb

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


• Deposited: 2019-06-20 Released: 2019-07-31 
• Deposition Author(s): Picaud, S., Traquete, R., Bernardes, G.J.L., Tobias, K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.145 
• R-Value Work: 0.124 
• R-Value Observed: 0.125 

Starting Model: experimental

Literature

Crystal Structure of the first bromodomain of BRD4 in complex with a benzodiazepine ligand

Picaud, S., Traquete, R., Bernardes, G.J.L., Tobias, K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.84 kDa 
• Atom Count: 1,355 
• Modelled 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): 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KSZ (Subject of Investigation/LOI)	E [auth A]	~{tert}-butyl ~{N}-[3-[2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]ethanoylamino]propyl]carbamate C28 H33 Cl N6 O4 VWFMCFRXMUQNOU-QFIPXVFZSA-N
EDO (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.145 
• R-Value Work: 0.124 
• R-Value Observed: 0.125 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.247	α = 90
b = 44.228	β = 90
c = 78.512	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Picaud, S., Traquete, R., Bernardes, G.J.L., Tobias, K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	095751/Z/11/Z

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description