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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 16.56 kDa 
• Atom Count: 1290 
• Modelled Residue Count: 133 
• Deposited Residue Count: 135 
• Unique protein chains: 1

6AJV

Crystal structure of BRD4 in complex with isoliquiritigenin and DMSO (Cocktail No. 3)

• PDB DOI: 10.2210/pdb6AJV/pdb

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


• Deposited: 2018-08-28 Released: 2019-06-12 
• Deposition Author(s): Yokoyama, T., Matsumoto, K., Nabeshima, Y., Mizuguchi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.

Yokoyama, T., Matsumoto, K., Ostermann, A., Schrader, T.E., Nabeshima, Y., Mizuguchi, M.

(2019) FEBS J 286: 1656-1667

• PubMed: 30565859 
• DOI: 10.1111/febs.14736
• Primary Citation of Related Structures:  
  6AJV, 6AJW, 6AJX, 6AJY, 6AJZ


• PubMed Abstract: 
  

Bromodomain-containing protein 4 (BRD4) recognizes the acetylated lysine of histone H4 via its bromodomains, leading to the recruitment of positive transcription elongation factor b. Small molecules that inhibit BRD4 have potential as anticancer agents by leading to the downregulation of specific oncogenes. Using X-ray crystallographic screening, we identified the BRD4 inhibitory activity of isoliquiritigenin (ISL), a natural chalcone found in licorice. Structural analysis revealed that ISL bound to BRD4 with a novel binding mode and squeezed out one of the six conserved water molecules that form a strong hydrogen bond network. The thermodynamic analysis revealed that the binding of ISL is enthalpy driven, suggesting that strong hydrogen bonds would compensate for the desolvation penalty. Neutron protein crystallography further suggested that the favorable binding enthalpy originates from the stabilization and optimization of the hydrogen bond network of the conserved water molecules. Here, we describe the novelty and potential of ISL as a template for new BRD4 inhibitors.

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Organizational Affiliation: 

Graduate School of Innovative Life Science, University of Toyama, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	135	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCC (Subject of Investigation/LOI)	C [auth A]	2',4,4'-TRIHYDROXYCHALCONE C15 H12 O4 DXDRHHKMWQZJHT-FPYGCLRLSA-N
DMS (Subject of Investigation/LOI)	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	B [auth A], E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HCC	Binding MOAD:  6AJV	Kd: 9100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.227 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.784	α = 90
b = 47.147	β = 90
c = 78.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-08-28 
• Released Date: 2019-06-12 
Deposition Author(s): Yokoyama, T., Matsumoto, K., Nabeshima, Y., Mizuguchi, M.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release