Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25460.84 
• Atom Count: 1795 
• Residue Count: 221 
• Unique protein chains: 2

5EC9

Retinoic acid receptor alpha in complex with chiral dihydrobenzofuran benzoic acid 9a and a fragment of the coactivator TIF2

• DOI: 10.2210/pdb5EC9/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2015-10-20 Released: 2016-03-09 
• Deposition Author(s): Leysen, S., Ottmann, C., Schafer, A., Scheepstra, M., Brunsveld, L., Sunden, R., Ma, J.N., Burnstein, E.S., Olsson, R.
• Funding Organization(s): Michael J. Fox Foundation; Netherlands Organisation for Scientific Research; ECHO; Marie Curie Action 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.214 
• R-Value Work: 0.161 

Literature

Chiral Dihydrobenzofuran Acids Show Potent Retinoid X Receptor-Nuclear Receptor Related 1 Protein Dimer Activation.

Sunden, H., Schafer, A., Scheepstra, M., Leysen, S., Malo, M., Ma, J.N., Burstein, E.S., Ottmann, C., Brunsveld, L., Olsson, R.

(2016) J.Med.Chem. 59: 1232-1238

• PubMed: 26820900 
• DOI: 10.1021/acs.jmedchem.5b01702


• PubMed Abstract: 
  

The nuclear receptor Nurr1 can be activated by RXR via heterodimerization (RXR-Nurr1) and is a promising target for treating neurodegenerative diseases. We herein report the enantioselective synthesis and SAR of sterically constricted benzofurans at RXR. The established SAR, using whole cell functional assays, lead to the full agonist 9a at RXR (pEC50 of 8.2) and RXR-Nurr1. The X-ray structure shows enantiomeric discrimination where 9a optimally addresses the ligand binding pocket of RXR.

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Organizational Affiliation: 

Department of Chemistry and Molecular Biology, Medicinal Chemistry, University of Gothenburg , SE-41296 Gothenburg, Sweden.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Retinoic acid receptor RXR-alpha	A	210	Homo sapiens	Mutation(s): 0  Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens) Go to Gene View: RXRA Go to UniProtKB:  P19793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP	B	11	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens) Go to Gene View: NCOA2 Go to UniProtKB:  Q15596

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
5LO	A	4-[(11S,15R)-4,4,7,7-Tetramethyl-16-oxatetracyclo[8.6.0.03,8.011,15]hexadeca-1(10),2,8-trien-11-yl]benzoic acid C26 H30 O3 PLLRIXHLFVZTMU-GJZUVCINSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.214 
• R-Value Work: 0.161 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 68.252	α = 90.00
b = 68.252	β = 90.00
c = 106.273	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-10-20 
• Released Date: 2016-03-09 
• Deposition Author(s): Leysen, S., Ottmann, C., Schafer, A., Scheepstra, M., Brunsveld, L., Sunden, R., Ma, J.N., Burnstein, E.S., Olsson, R.

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Funding Organization	Location	Grant Number
Michael J. Fox Foundation	United States	--
Netherlands Organisation for Scientific Research	Netherlands	024.00.035
ECHO	Netherlands	711011017
Marie Curie Action	Netherlands	--

Revision History 

• Version 1.0: 2016-03-09
  Type: Initial release
• Version 1.1: 2017-09-13
  Type: Author supporting evidence, Data collection