Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 15485.23 
• Atom Count: 1152 
• 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


• 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 

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, 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens) Go to Gene View: BRD4 Go to UniProtKB:  O60885

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
08K	Kd: 640 nM (99) BINDINGDB
08K	Kd: 640 nM BINDINGMOAD
08K	Kd: 640 nM PDBBIND

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 37.360	α = 90.00
b = 44.130	β = 90.00
c = 78.380	γ = 90.00

Software Package:

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

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
  Type: Database references
• Version 1.2: 2012-03-21
  Type: Database references