8R00 | pdb_00008r00

Crystal structure of the human PXR ligand-binding domain in complex with furanodienone

• PDB DOI: https://doi.org/10.2210/pdb8R00/pdb

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


• Deposited: 2023-10-30 Released: 2025-04-16 
• Deposition Author(s): Bourguet, W., Carivenc, C., Sirounian, S.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.215 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

An abundant ginger compound furanodienone alleviates gut inflammation via the xenobiotic nuclear receptor PXR in mice.

Wang, X., Zhang, G., Bian, Z., Chow, V., Grimaldi, M., Carivenc, C., Sirounian, S., Li, H., Sladekova, L., Motta, S., Luperi, Y., Gong, Y., Costello, C., Li, L., Jachimowicz, M., Guo, M., Hu, S., Wilson, D., Balaguer, P., Bourguet, W., Mani, S., Bonati, L., Peng, H., March, J., Wang, H., Wang, S., Krause, H.M., Liu, J.

(2025) Nat Commun 16: 1280-1280

• PubMed: 39900639 
• DOI: https://doi.org/10.1038/s41467-025-56624-0
• Primary Citation Related Structures: 
  8R00


• PubMed Abstract: 
  

  The literature documenting the value of drug-like molecules found in natural products is vast. Although many dietary and herbal remedies have been found to be effective for treating intestinal inflammation, the identification of their active components has lagged behind. In this study, we find that a major ginger component, furanodienone (FDN), is a selective pregnane X receptor (PXR) ligand with agonistic transcriptional outcomes. We show that FDN binds within a sub-pocket of the PXR ligand binding domain (LBD), with subsequent alterations in LBD structure. Using male mice, we show that orally provided FDN has potent PXR-dependant anti-inflammatory outcomes that are colon-specific. Increased affinity and target gene activation in the presence of synergistically acting agonists indicates further opportunities for augmenting FDN activity, efficacy and safety. Collectively, these results support the translational potential of FDN as a therapeutic agent for the treatment and prevention of colonic diseases.

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Organizational Affiliation: 
• School of Pharmacy, Lanzhou University, Lanzhou, Gansu, People's Republic of China.
State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, People's Republic of China.
Department of Chemistry, York University, Toronto, ON, Canada.
Institut de Recherche en Cancérologie de Montpellier (IRCM), Université Montpellier, Institut régional du Cancer de Montpellier (ICM), Montpellier, France.
Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France.
Department of Molecular Pharmacology; Department of Genetics; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic.
Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy.
Department of Chemistry, University of Toronto, Toronto, ON, Canada.
College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China.
Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA.
Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA.
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
School of the Environment, University of Toronto, Toronto, ON, Canada.
State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, People's Republic of China. [e-mail].
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada. [e-mail].
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. [e-mail].
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.98 kDa 
• Atom Count: 2,364 
• Modeled Residue Count: 273 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 1 group I member 2	A	320	Homo sapiens	Mutation(s): 0  Gene Names: NR1I2, PXR
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens) Explore O75469  Go to UniProtKB:  O75469
PHAROS:  O75469 GTEx:  ENSG00000144852

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XFQ (Subject of Investigation/LOI)	B [auth A]	furanodienone C15 H18 O2 XVOHELPNOXGRBQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.215 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.826	α = 90
b = 91.826	β = 90
c = 85.731	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Bourguet, W., Carivenc, C., Sirounian, S.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-18-CE34-0009-01

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release