6FFE

Human BRD2 C-terminal bromodomain with 2-((4-acetyl-3-cyclopropyl-3,4-dihydroquinoxalin-1(2H)-yl)methyl)benzoic acid

• PDB DOI: https://doi.org/10.2210/pdb6FFE/pdb

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


• Deposited: 2018-01-07 Released: 2019-01-30 
• Deposition Author(s): Chung, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.230 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 

Literature

Discovery of Tetrahydroquinoxalines as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the Second Bromodomain.

Law, R.P., Atkinson, S.J., Bamborough, P., Chung, C.W., Demont, E.H., Gordon, L.J., Lindon, M., Prinjha, R.K., Watson, A.J.B., Hirst, D.J.

(2018) J Med Chem 61: 4317-4334

• PubMed: 29656650 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b01666
• Primary Citation of Related Structures:  
  6FFE, 6FFF, 6FFG


• PubMed Abstract: 
  

  The bromodomain and extra-terminal domain (BET) family of proteins bind acetylated lysine residues on histone proteins. The four BET bromodomains-BRD2, BRD3, BRD4, and BRDT-each contain two bromodomain modules. BET bromodomain inhibition is a potential therapy for various cancers and immunoinflammatory diseases, but few reported inhibitors show selectivity within the BET family. Inhibitors with selectivity for the first or second bromodomain are desired to aid investigation of the biological function of these domains. Focused library screening identified a series of tetrahydroquinoxalines with selectivity for the second bromodomains of the BET family (BD2). Structure-guided optimization of the template improved potency, selectivity, and physicochemical properties, culminating in potent BET inhibitors with BD2 selectivity.

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Organizational Affiliation: 

WestCHEM, Department of Pure and Applied Chemistry , University of Strathclyde, Thomas Graham Building , 295 Cathedral Street , Glasgow , G1 1XL , U.K.

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: 14.12 kDa 
• Atom Count: 1,194 
• Modelled Residue Count: 113 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A	115	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D7Q	F [auth A]	2-((4-acetyl-3-cyclopropyl-3,4-dihydroquinoxalin-1(2H)-yl)methyl)benzoic acid C21 H22 N2 O3 PPKDQAUERJXIAY-HXUWFJFHSA-N
PEG	B [auth A], C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.230 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.401	α = 90
b = 52.795	β = 90
c = 31.945	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Chung, C.

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2020-02-12
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references