6Z7L

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 with GSK789

• PDB DOI: https://doi.org/10.2210/pdb6Z7L/pdb

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


• Deposited: 2020-05-31 Released: 2020-07-29 
• Deposition Author(s): Chung, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.225 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.200 (DCC) 

Starting Model: other

Literature

GSK789: A Selective Inhibitor of the First Bromodomains (BD1) of the Bromo and Extra Terminal Domain (BET) Proteins.

Watson, R.J., Bamborough, P., Barnett, H., Chung, C.W., Davis, R., Gordon, L., Grandi, P., Petretich, M., Phillipou, A., Prinjha, R.K., Rioja, I., Soden, P., Werner, T., Demont, E.H.

(2020) J Med Chem 63: 9045-9069

• PubMed: 32691589 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c00614
• Primary Citation of Related Structures:  
  6Z7L, 6Z7M


• PubMed Abstract: 
  

  Pan-bromodomain and extra terminal (BET) inhibitors interact equipotently with all eight bromodomains of the BET family of proteins. They have shown profound efficacy in vitro and in vivo in oncology and immunomodulatory models, and a number of them are currently in clinical trials where significant safety signals have been reported. It is therefore important to understand the functional contribution of each bromodomain to assess the opportunity to tease apart efficacy and toxicity. This article discloses the in vitro and cellular activity profiles of GSK789, a potent, cell-permeable, and highly selective inhibitor of the first bromodomains of the BET family.

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Organizational Affiliation: 

Molecular Discovery Research, GlaxoSmithKline, Cellzome GmbH, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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: 15.56 kDa 
• Atom Count: 1,327 
• Modelled 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 AAA]	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QAN	B [auth AAA]	(3~{R},4~{R})-~{N}-cyclohexyl-4-[[5-(furan-2-yl)-3-methyl-2-oxidanylidene-1~{H}-1,7-naphthyridin-8-yl]amino]-1-methyl-piperidine-3-carboxamide C26 H33 N5 O3 NDEORODKVUYMFQ-NHCUHLMSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QAN	BindingDB:  6Z7L	Kd: min: 6.3, max: 3.16e+4 (nM) from 4 assay(s)
		IC50: min: 32, max: 3.16e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.225 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.200 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.968	α = 90
b = 48.286	β = 90
c = 61.245	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Chung, C.

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description