5EC9

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

PDB DOI: https://doi.org/10.2210/pdb5EC9/pdb

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

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

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 2.1 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

PubMed: 26820900 Search on PubMed
DOI: https://doi.org/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 8.2) 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.

Macromolecule Content

Total Structure Weight: 25.46 kDa
Atom Count: 2,009
Modelled Residue Count: 221
Deposited Residue Count: 221
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A	210	Homo sapiens	Mutation(s): 0 Gene Names: RXRA, NR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens) Explore P19793 Go to UniProtKB: P19793
PHAROS: P19793 GTEx: ENSG00000186350
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19793
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP	B	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596 Go to UniProtKB: Q15596
PHAROS: Q15596 GTEx: ENSG00000140396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15596
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5LO Query on 5LO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth 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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
5LO	BindingDB: 5EC9	EC50: min: 6.3, max: 25 (nM) from 3 assay(s)

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 = 68.252	α = 90
b = 68.252	β = 90
c = 106.273	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

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 (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
Version 2.0: 2022-08-10
Changes: Atomic model, Database references, Derived calculations
Version 2.1: 2024-06-19
Changes: Data collection