8PP0 | pdb_00008pp0

Crystal structure of Retinoic Acid Receptor alpha (RXRA) in complexed with JP147

• PDB DOI: https://doi.org/10.2210/pdb8PP0/pdb

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


• Deposited: 2023-07-05 Released: 2024-02-07 
• Deposition Author(s): Chaikuad, A., Pollinger, J., Merk, D., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.223 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Design of a Highly Potent Partial RXR Agonist with Superior Physicochemical Properties.

Lewandowski, M., Carmina, M., Knumann, L., Sai, M., Willems, S., Kasch, T., Pollinger, J., Knapp, S., Marschner, J.A., Chaikuad, A., Merk, D.

(2024) J Med Chem 67: 2152-2164

• PubMed: 38237049 
• DOI: https://doi.org/10.1021/acs.jmedchem.3c02095
• Primary Citation Related Structures: 
  8PP0


• PubMed Abstract: 
  

  Retinoid X receptors (RXRs, NR2B1-3) hold therapeutic potential in oncology, neurodegeneration, and metabolic diseases, but traditional RXR agonists mimicking the natural ligand 9- cis retinoic acid exhibit poor physicochemical properties, pharmacokinetics, and safety profiles. Improved RXR ligands are needed to exploit RXR modulation as a promising therapeutic concept in various indications beyond its current role in second-line cancer treatment. Here, we report the co-crystal structure of RXR in complex with a novel pyrimidine-based ligand and the structure-informed optimization of this scaffold to highly potent and highly soluble RXR agonists. Focused structure-activity relationship elucidation and rigidization resulted in a substantially optimized partial RXR agonist with low nanomolar potency, no cytotoxic activity, and very favorable physicochemical properties highlighting this promising scaffold for the development of next-generation RXR targeting drugs.

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Organizational Affiliation: 
• Department of Pharmacy, Ludwig-Maximilians-Universität (LMU) München, 81377 Munich, Germany.
Department of Pharmaceutical Sciences, Università degli Studi di Perugia, 06123 Perugia, Italy.
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.2 kDa 
• Atom Count: 1,907 
• Modeled Residue Count: 227 
• Deposited Residue Count: 256 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A	242	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	B	14	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7QJ (Subject of Investigation/LOI)	C [auth A]	3-[4-[2,3-dihydro-1H-inden-4-yl(methyl)amino]-6-(trifluoromethyl)pyrimidin-2-yl]oxypropanoic acid C18 H18 F3 N3 O3 YMSJOQCCWIPKGF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7QJ	BindingDB:  8PP0	Kd: 95 (nM) from 1 assay(s)
		EC50: min: 93, max: 360 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.223 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.648	α = 90
b = 65.648	β = 90
c = 110.816	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Chaikuad, A., Pollinger, J., Merk, D., Knapp, S., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Database references