Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 15.46 kDa 
• Atom Count: 1383 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

4QB3

Crystal structure of the first bromodomain of human BRD4 in complex with Olinone

• PDB DOI: 10.2210/pdb4QB3/pdb

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


• Deposited: 2014-05-06 Released: 2015-04-22 
• Deposition Author(s): Plotnikov, A.N., Joshua, J., Zhou, M.-M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.155 
• R-Value Work: 0.136 
• R-Value Observed: 0.137 

Literature

Selective chemical modulation of gene transcription favors oligodendrocyte lineage progression.

Gacias, M., Gerona-Navarro, G., Plotnikov, A.N., Zhang, G., Zeng, L., Kaur, J., Moy, G., Rusinova, E., Rodriguez, Y., Matikainen, B., Vincek, A., Joshua, J., Casaccia, P., Zhou, M.M.

(2014) Chem Biol 21: 841-854

• PubMed: 24954007 
• DOI: 10.1016/j.chembiol.2014.05.009
• Primary Citation of Related Structures:  
  4QB3


• PubMed Abstract: 
  

Lysine acetylation regulates gene expression through modulating protein-protein interactions in chromatin. Chemical inhibition of acetyl-lysine binding bromodomains of the major chromatin regulators BET (bromodomain and extraterminal domain) proteins has been shown to effectively block cell proliferation in cancer and inflammation. However, whether selective inhibition of individual BET bromodomains has distinctive functional consequences remains only partially understood. In this study, we show that selective chemical inhibition of the first bromodomain of BET proteins using our small-molecule inhibitor, Olinone, accelerated the progression of mouse primary oligodendrocyte progenitors toward differentiation, whereas inhibition of both bromodomains of BET proteins hindered differentiation. This effect was target specific, as it was not detected in cells treated with inactive analogs and independent of any effect on proliferation. Therefore, selective chemical modulation of individual bromodomains, rather than use of broad-based inhibitors, may enhance regenerative strategies in disorders characterized by myelin loss such as aging and neurodegeneration.

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Organizational Affiliation: 

Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
30M	B [auth A]	N-[4-(1-oxo-1,2,3,4-tetrahydro-5H-pyrido[4,3-b]indol-5-yl)butyl]acetamide C17 H21 N3 O2 RYVLOOXFFIFQEN-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
30M	BindingDB:  4QB3	Ki: 1.72e+4 (nM) from 1 assay(s)
		Kd: min: 3300, max: 3.00e+5 (nM) from 4 assay(s)
	Binding MOAD:  4QB3	Kd: 3400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.155 
• R-Value Work: 0.136 
• R-Value Observed: 0.137 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.943	α = 90
b = 44.126	β = 90
c = 78.455	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-06 
• Released Date: 2015-04-22 
Deposition Author(s): Plotnikov, A.N., Joshua, J., Zhou, M.-M.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release