Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 1451 
• Residue Count: 127 
• Unique protein chains: 1

4CFL

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH LY303511

• DOI: 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.217 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

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: 10.1021/cb400789e
• Primary Citation of 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.

---

Organizational Affiliation: 

Cellzome GmbH , Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BRD4 PROTEIN	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885 GTEx  ENSG00000141867

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8DQ	A	8-phenyl-2-piperazin-1-yl-chromen-4-one C19 H18 N2 O2 NGAGMBNBKCDCDJ-UHFFFAOYSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
8DQ	Kd:  1330   nM  Binding MOAD
8DQ	IC50:  9050   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.217 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• 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

• Deposited Date: 2013-11-18 
• 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