9S71 | pdb_00009s71

Crystal structure of RXR alpha LBD bound to a partial agonist 35 and a coactivator fragment SRC1

• PDB DOI: https://doi.org/10.2210/pdb9S71/pdb

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


• Deposited: 2025-08-01 Released: 2025-10-29 
• Deposition Author(s): Morozov, V., Merk, D., Lewandowski, M.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: in silico

Literature

Structural Tuning of Partial RXR Agonism and Antagonism.

Lewandowski, M., Granger-Riviere, M., Mayer, D., Kasch, T., Nawa, F., Egner, M., Marschner, J.A., Morozov, V., Merk, D.

(2025) J Med Chem 68: 25255-25273

• PubMed: 41276988 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c02270
• Primary Citation of Related Structures:  
  9S70, 9S71


• PubMed Abstract: 
  

  Retinoid X receptors (RXRs) represent a central switch in nuclear receptor signaling and appear to hold therapeutic potential in diverse indications. However, the ability of RXR agonists to activate multiple nuclear receptor heterodimers gives rise to adverse effects, which may be avoided by partial RXR agonism. In exploring the SAR of a partial agonist scaffold, we identified a region that allowed tuning of RXR activation efficacy between various levels of partial agonism and antagonism. Co-crystal structure analysis revealed dual steric pressure and a combination of reciprocal structural effects to mediate partial agonist activity providing a molecular basis for structural tuning of RXR modulators.

---

Organizational Affiliation: 
• Ludwig-Maximilians-Universität München, Department of Pharmacy, Munich 81377, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.18 kDa 
• Atom Count: 1,817 
• Modeled Residue Count: 220 
• 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	235	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 1	B	21	Homo sapiens	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JL8	C [auth A]	3-[[4-(4,4-dimethyl-2,3-dihydroquinolin-1-yl)-6-(trifluoromethyl)pyrimidin-2-yl]amino]propanoic acid C19 H21 F3 N4 O2 XCSAYKLWHFZVRD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.1	α = 90
b = 78.1	β = 90
c = 81.889	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Morozov, V., Merk, D., Lewandowski, M.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release
  
• Version 1.1: 2025-12-24
  Changes: Database references