8E3W | pdb_00008e3w

BRD4-D1 in complex with BET inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8E3W/pdb

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


• Deposited: 2022-08-17 Released: 2023-03-29 
• Deposition Author(s): Gorman, M.A., Fitzgerald, C.G.D., White, J.M., Parker, M.W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Bromodomain and extraterminal protein-targeted probe enables tumour visualisation in vivo using positron emission tomography.

Dickmann, C.G.F., McDonald, A.F., Huynh, N., Rigopoulos, A., Liu, Z., Guo, N., Osellame, L.D., Gorman, M.A., Parker, M.W., Gan, H.K., Scott, A.M., Ackermann, U., Burvenich, I.J.G., White, J.M.

(2023) Chem Commun (Camb) 59: 3126-3129

• PubMed: 36809538 
• DOI: https://doi.org/10.1039/d2cc04813b
• Primary Citation Related Structures: 
  8DYR, 8E17, 8E3W


• PubMed Abstract: 
  

  Bromodomain and extraterminal (BET) proteins, a family of epigenetic regulators, have emerged as important oncology drug targets. BET proteins have not been targeted for molecular imaging of cancer. Here, we report the development of a novel molecule radiolabelled with positron emitting fluorine-18, [ ¹⁸ F]BiPET-2, and its in vitro and preclinical evaluation in glioblastoma models.

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Organizational Affiliation: 
• Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia. [e-mail].
Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, and School of Cancer Medicine, La Trobe University, Heidelberg, Australia. [e-mail].
Department of Molecular Imaging and Therapy, Austin Hospital, Heidelberg, Australia.
ACRF Facility for Innovative Cancer Drug Discovery, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, VIC 3065, Australia.
Faculty of Medicine, University of Melbourne, Parkville, Australia.

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: 15.54 kDa 
• Atom Count: 1,259 
• Modeled 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 [auth B]	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
UHI (Subject of Investigation/LOI)	B	(4P)-4-[2-(cyclopropylmethoxy)-5-(methanesulfonyl)phenyl]-2-methylisoquinolin-1(2H)-one C21 H21 N O4 S UWZAJPITKGWMFJ-UHFFFAOYSA-N
EDO	C [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UHI	BindingDB:  8E3W	IC50: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.517	α = 90
b = 44.26	β = 90
c = 78.149	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-29 
Deposition Author(s): Gorman, M.A., Fitzgerald, C.G.D., White, J.M., Parker, M.W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-03-29
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description