Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 15.49 kDa 
• Atom Count: 1370 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

3U5L

Crystal Structure of the first bromodomain of human BRD4 in complex with a benzo-triazepine ligand (BzT-7)

• DOI: 10.2210/pdb3U5L/pdb

• Classification: SIGNALING PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-11 Released: 2011-11-23 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Bracher, F., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.142 
• R-Value Work: 0.111 
• R-Value Observed: 0.112 

Literature

Benzodiazepines and benzotriazepines as protein interaction inhibitors targeting bromodomains of the BET family.

Filippakopoulos, P., Picaud, S., Fedorov, O., Keller, M., Wrobel, M., Morgenstern, O., Bracher, F., Knapp, S.

(2012) Bioorg Med Chem 20: 1878-1886

• PubMed: 22137933 
• DOI: 10.1016/j.bmc.2011.10.080
• Primary Citation of Related Structures:  
  3U5K, 3U5L, 3U5J


• PubMed Abstract: 
  

Benzodiazepines are psychoactive drugs with anxiolytic, sedative, skeletal muscle relaxant and amnestic properties. Recently triazolo-benzodiazepines have been also described as potent and highly selective protein interaction inhibitors of bromodomain and extra-terminal (BET) proteins, a family of transcriptional co-regulators that play a key role in cancer cell survival and proliferation, but the requirements for high affinity interaction of this compound class with bromodomains has not been described. Here we provide insight into the structure-activity relationship (SAR) and selectivity of this versatile scaffold. In addition, using high resolution crystal structures we compared the binding mode of a series of benzodiazepine (BzD) and related triazolo-benzotriazepines (BzT) derivatives including clinically approved drugs such as alprazolam and midazolam. Our analysis revealed the importance of the 1-methyl triazolo ring system for BET binding and suggests modifications for the development of further high affinity bromodomain inhibitors.

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Organizational Affiliation: 

University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK.

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
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
08K	A	8-chloro-1,4-dimethyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,3,4]benzotriazepine C17 H14 Cl N5 UYIVCPRWMLOCSB-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
08K	Kd :  640   nM  PDBBind
08K	Kd:  640   nM  BindingDB
08K	Kd:  640   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.142 
• R-Value Work: 0.111 
• R-Value Observed: 0.112 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.36	α = 90
b = 44.13	β = 90
c = 78.38	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-11 
• Released Date: 2011-11-23 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Bracher, F., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-11-23
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Database references
• Version 1.2: 2012-03-21
  Changes: Database references