5EC9

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • 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 ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
A
210Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP
B
11Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5LO
Query on 5LO

Download SDF File 
Download CCD File 
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
 Ligand Interaction
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 = 68.252α = 90.00
b = 68.252β = 90.00
c = 106.273γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Michael J. Fox FoundationUnited States--
Netherlands Organisation for Scientific ResearchNetherlands024.00.035
ECHONetherlands711011017
Marie Curie ActionNetherlands--

Revision History 

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