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: 15.49 kDa 
• Atom Count: 1228 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

4XYA

Crystal Structure of the first bromodomain of human BRD4 in complex with a 2-amine-9H-purine ligand

• PDB DOI: 10.2210/pdb4XYA/pdb

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


• Deposited: 2015-02-02 Released: 2015-03-11 
• Deposition Author(s): Picaud, S., von Delft, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.207 
• R-Value Work: 0.147 
• R-Value Observed: 0.150 

Literature

9H-Purine Scaffold Reveals Induced-Fit Pocket Plasticity of the BRD9 Bromodomain.

Picaud, S., Strocchia, M., Terracciano, S., Lauro, G., Mendez, J., Daniels, D.L., Riccio, R., Bifulco, G., Bruno, I., Filippakopoulos, P.

(2015) J Med Chem 58: 2718-2736

• PubMed: 25703523 
• DOI: 10.1021/jm501893k
• Primary Citation of Related Structures:  
  4XY8, 4XY9, 4XYA


• PubMed Abstract: 
  

The 2-amine-9H-purine scaffold was identified as a weak bromodomain template and was developed via iterative structure based design into a potent nanomolar ligand for the bromodomain of human BRD9 with small residual micromolar affinity toward the bromodomain of BRD4. Binding of the lead compound 11 to the bromodomain of BRD9 results in an unprecedented rearrangement of residues forming the acetyllysine recognition site, affecting plasticity of the protein in an induced-fit pocket. The compound does not exhibit any cytotoxic effect in HEK293 cells and displaces the BRD9 bromodomain from chromatin in bioluminescence proximity assays without affecting the BRD4/histone complex. The 2-amine-9H-purine scaffold represents a novel template that can be further modified to yield highly potent and selective tool compounds to interrogate the biological role of BRD9 in diverse cellular systems.

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Organizational Affiliation: 

∥Nuffield Department of Clinical Medicine, Ludwig Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.

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
43S	B [auth A]	6-(5-bromo-1-benzofuran-7-yl)-9H-purin-2-amine C13 H8 Br N5 O BEMKXMYIKPJVHA-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
43S	Binding MOAD:  4XYA	Kd: 1370 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.207 
• R-Value Work: 0.147 
• R-Value Observed: 0.150 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.242	α = 90
b = 44.373	β = 90
c = 79.015	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-02-02 
• Released Date: 2015-03-11 
Deposition Author(s): Picaud, S., von Delft, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	095751/Z/11/Z

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 1.2: 2015-04-08
  Changes: Database references