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: 15.77 kDa 
• Atom Count: 1447 
• Residue Count: 127 
• Unique protein chains: 1

4YH4

Crystal structure of human BRD4(1) in complex with 4-[(5-phenylpyridin-3-yl)carbonyl]-3,4-dihydroquinoxalin-2(1H)-one (compound 19d)

• DOI: 10.2210/pdb4YH4/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-26 Released: 2016-01-13 
• Deposition Author(s): Lakshminarasimhan, D., White, A., Suto, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.147 
• R-Value Work: 0.107 
• R-Value Observed: 0.109 

Literature

Discovery of a new chemical series of BRD4(1) inhibitors using protein-ligand docking and structure-guided design.

Duffy, B.C., Liu, S., Martin, G.S., Wang, R., Hsia, M.M., Zhao, H., Guo, C., Ellis, M., Quinn, J.F., Kharenko, O.A., Norek, K., Gesner, E.M., Young, P.R., McLure, K.G., Wagner, G.S., Lakshminarasimhan, D., White, A., Suto, R.K., Hansen, H.C., Kitchen, D.B.

(2015) Bioorg Med Chem Lett 25: 2818-2823

• PubMed: 26022843 
• DOI: 10.1016/j.bmcl.2015.04.107
• Primary Citation of Related Structures:  
  4YH3, 4YH4


• PubMed Abstract: 
  

Bromodomains are key transcriptional regulators that are thought to be druggable epigenetic targets for cancer, inflammation, diabetes and cardiovascular therapeutics. Of particular importance is the first of two bromodomains in bromodomain containing 4 protein (BRD4(1)). Protein-ligand docking in BRD4(1) was used to purchase a small, focused screening set of compounds possessing a large variety of core structures. Within this set, a small number of weak hits each contained a dihydroquinoxalinone ring system. We purchased other analogs with this ring system and further validated the new hit series and obtained improvement in binding inhibition. Limited exploration by new analog synthesis showed that the binding inhibition in a FRET assay could be improved to the low μM level making this new core a potential hit-to-lead series. Additionally, the predicted geometries of the initial hit and an improved analog were confirmed by X-ray co-crystallography with BRD4(1).

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Organizational Affiliation: 

Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	129	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
Y81	A	4-[(5-phenylpyridin-3-yl)carbonyl]-3,4-dihydroquinoxalin-2(1H)-one C20 H15 N3 O2 JAGBWIHWQBQGAX-UHFFFAOYSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
Y81	IC50:  26000   nM  BindingDB
Y81	IC50:  26000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.147 
• R-Value Work: 0.107 
• R-Value Observed: 0.109 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.799	α = 90
b = 44.436	β = 90
c = 77.353	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PDB_EXTRACT	data extraction
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-26 
• Released Date: 2016-01-13 
Deposition Author(s): Lakshminarasimhan, D., White, A., Suto, R.K.

Revision History 

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description