6DL2 | pdb_00006dl2

BRD4 bromodomain 1 in complex with HYB157

• PDB DOI: https://doi.org/10.2210/pdb6DL2/pdb

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


• Deposited: 2018-05-31 Released: 2019-04-17 
• Deposition Author(s): Meagher, J.L., Stuckey, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.216 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Discovery of QCA570 as an Exceptionally Potent and Efficacious Proteolysis Targeting Chimera (PROTAC) Degrader of the Bromodomain and Extra-Terminal (BET) Proteins Capable of Inducing Complete and Durable Tumor Regression.

Qin, C., Hu, Y., Zhou, B., Fernandez-Salas, E., Yang, C.Y., Liu, L., McEachern, D., Przybranowski, S., Wang, M., Stuckey, J., Meagher, J., Bai, L., Chen, Z., Lin, M., Yang, J., Ziazadeh, D.N., Xu, F., Hu, J., Xiang, W., Huang, L., Li, S., Wen, B., Sun, D., Wang, S.

(2018) J Med Chem 61: 6685-6704

• PubMed: 30019901 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b00506
• Primary Citation Related Structures: 
  6DL2


• PubMed Abstract: 
  

  Proteins of the bromodomain and extra-terminal (BET) family are epigenetics "readers" and promising therapeutic targets for cancer and other human diseases. We describe herein a structure-guided design of [1,4]oxazepines as a new class of BET inhibitors and our subsequent design, synthesis, and evaluation of proteolysis-targeting chimeric (PROTAC) small-molecule BET degraders. Our efforts have led to the discovery of extremely potent BET degraders, exemplified by QCA570, which effectively induces degradation of BET proteins and inhibits cell growth in human acute leukemia cell lines even at low picomolar concentrations. QCA570 achieves complete and durable tumor regression in leukemia xenograft models in mice at well-tolerated dose-schedules. QCA570 is the most potent and efficacious BET degrader reported to date.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.53 kDa 
• Atom Count: 1,220 
• Modeled Residue Count: 128 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	128	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
GUJ	B [auth A]	3-benzyl-2,9-dimethyl-4H,6H-thieno[2,3-e][1,2,4]triazolo[3,4-c][1,4]oxazepine C17 H17 N3 O S QLGVMPYXPORRCO-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.216 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.512	α = 90
b = 43.13	β = 90
c = 79.306	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Meagher, J.L., Stuckey, J.A.

Revision History  

• Version 1.0: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description