4CFL | pdb_00004cfl

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH LY303511

• PDB DOI: https://doi.org/10.2210/pdb4CFL/pdb

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


• Deposited: 2013-11-18 Released: 2014-01-15 
• Deposition Author(s): Chung, C., Dittmann, A., Drewes, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.217 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

The Commonly Used Pi3-Kinase Probe Ly294002 is an Inhibitor of Bet Bromodomains.

Dittmann, A., Werner, T., Chung, C., Savitski, M.M., Falth Savitski, M., Grandi, P., Hopf, C., Lindon, M., Neubauer, G., Prinjha, R.K., Bantscheff, M., Drewes, G.

(2014) ACS Chem Biol 9: 495

• PubMed: 24533473 
• DOI: https://doi.org/10.1021/cb400789e
• Primary Citation Related Structures: 
  4CFK, 4CFL


• PubMed Abstract: 
  

  A commonly used small-molecule probe in cell-signaling research is the phosphoinositide 3-kinase inhibitor LY294002. Quantitative chemoproteomic profiling shows that LY294002 and LY303511, a close analogue devoid of PI3K activity, inhibit the BET bromodomain proteins BRD2, BRD3, and BRD4 that comprise a family of targets structurally unrelated to PI3K. Both compounds competitively inhibit acetyl-lysine binding of the first but not the second bromodomain of BET proteins in cell extracts. X-ray crystallography shows that the chromen-4-one scaffold represents a new bromodomain pharmacophore and establishes LY294002 as a dual kinase and BET-bromodomain inhibitor, whereas LY303511 exhibits anti-inflammatory and antiproliferative effects similar to the recently discovered BET inhibitors.

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Organizational Affiliation: 
• 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)

Macromolecule Content 

• Total Structure Weight: 15.56 kDa 
• Atom Count: 1,451 
• Modeled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BRD4 PROTEIN	A	127	Homo sapiens	Mutation(s): 0
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8DQ	B [auth A]	8-phenyl-2-piperazin-1-yl-chromen-4-one C19 H18 N2 O2 NGAGMBNBKCDCDJ-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.32 Å
• R-Value Free:  0.217 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.52	α = 90
b = 44.48	β = 90
c = 77.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Chung, C., Dittmann, A., Drewes, G.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Database references
• Version 1.2: 2014-03-05
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other