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: 2.30 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

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
  • Primary Citation of Related Structures:  
    5EC9

  • 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 ...

    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

    Chemical Biology & Therapeutics, Department of Experimental Medical Science, Lund University , Sölvegatan 19, BMC DIO, SE-221 84 Lund, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha A210Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS:  P19793
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP B11Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS:  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5LO
Query on 5LO

Download Ideal Coordinates 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5LOEC50:  25   nM  BindingDB
5LOEC50:  6.300000190734863   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.252α = 90
b = 68.252β = 90
c = 106.273γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

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