5U6V | pdb_00005u6v

X-ray crystal structure of 1,2,3-triazolobenzodiazepine in complex with BRD2(D2)

• PDB DOI: https://doi.org/10.2210/pdb5U6V/pdb

• Classification: transcription/transcription inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-09 Released: 2017-12-13 
• Deposition Author(s): Hatfaludi, T., Sharp, P.P., Garnier, J.-M., Burns, C.J., Czabotar, P.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Design, Synthesis, and Biological Activity of 1,2,3-Triazolobenzodiazepine BET Bromodomain Inhibitors.

Sharp, P.P., Garnier, J.M., Hatfaludi, T., Xu, Z., Segal, D., Jarman, K.E., Jousset, H., Garnham, A., Feutrill, J.T., Cuzzupe, A., Hall, P., Taylor, S., Walkley, C.R., Tyler, D., Dawson, M.A., Czabotar, P., Wilks, A.F., Glaser, S., Huang, D.C.S., Burns, C.J.

(2017) ACS Med Chem Lett 8: 1298-1303

• PubMed: 29259751 
• DOI: https://doi.org/10.1021/acsmedchemlett.7b00389
• Primary Citation Related Structures: 
  5U6V


• PubMed Abstract: 
  

  A number of diazepines are known to inhibit bromo- and extra-terminal domain (BET) proteins. Their BET inhibitory activity derives from the fusion of an acetyl-lysine mimetic heterocycle onto the diazepine framework. Herein we describe a straightforward, modular synthesis of novel 1,2,3-triazolobenzodiazepines and show that the 1,2,3-triazole acts as an effective acetyl-lysine mimetic heterocycle. Structure-based optimization of this series of compounds led to the development of potent BET bromodomain inhibitors with excellent activity against leukemic cells, concomitant with a reduction in c- MYC expression. These novel benzodiazepines therefore represent a promising class of therapeutic BET inhibitors.

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Organizational Affiliation: 
• Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.
Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
Synthesis MedChem, 399 Royal Parade, Parkville, VIC 3052, Australia.
St. Vincent's Institute of Medical Research and Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, VIC 3052, Australia.
Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.
Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.
Sir Peter MacCallum Department of Oncology, The University of Melbourne, East Melbourne, VIC 3002, Australia.
School of Chemistry, The Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.

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: 13.63 kDa 
• Atom Count: 1,079 
• Modeled Residue Count: 109 
• Deposited Residue Count: 110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A	110	Homo sapiens	Mutation(s): 0  Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440  Go to UniProtKB:  P25440
PHAROS:  P25440 GTEx:  ENSG00000204256

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7WY	B [auth A]	5-[7-(4-chlorophenyl)-1-methyl-6,7-dihydro-5H-[1,2,3]triazolo[1,5-d][1,4]benzodiazepin-9-yl]pyridin-2-amine C22 H19 Cl N6 PUTQASIWNBKTDJ-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.617	α = 90
b = 71.743	β = 90
c = 31.935	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-13 
Deposition Author(s): Hatfaludi, T., Sharp, P.P., Garnier, J.-M., Burns, C.J., Czabotar, P.E.

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2018-01-03
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references