5WZX

Structural basis for a pentacyclic oleanane-type triterpenoid as a ligand of FXR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of an Oleanane-Type Triterpene Hedragonic Acid as a Novel Farnesoid X Receptor Ligand with Liver Protective Effects and Anti-inflammatory Activity

Lu, Y.Zheng, W.Lin, S.Guo, F.Zhu, Y.Wei, Y.Liu, X.Jin, S.Jin, L.Li, Y.

(2018) Mol. Pharmacol. 93: 63-72

  • DOI: 10.1124/mol.117.109900

  • PubMed Abstract: 
  • Farnesoid X receptor (FXR) and G-protein-coupled bile acid receptor 1 (GPBAR1) are two important bile acid (BA) receptors. As non-BAs drug template for GPBAR1, none of the natural oleanane-type triterpenes have been reported as FXR ligands, despite F ...

    Farnesoid X receptor (FXR) and G-protein-coupled bile acid receptor 1 (GPBAR1) are two important bile acid (BA) receptors. As non-BAs drug template for GPBAR1, none of the natural oleanane-type triterpenes have been reported as FXR ligands, despite FXR and GPBAR1 having similar binding pockets for BAs. Here, we report the natural triterpene hedragonic acid that has been isolated from the stem and root of Celastrus orbiculatus Thunb. (COT) as an effective agonist for FXR. Both biochemical amplified luminescent proximity homogeneous assay and cell-based reporter assays showed that hedragonic acid regulated the transcriptional activity of FXR. Circular dichroism spectroscopy further suggested the conformational changes of FXR upon the binding of hedragonic acid. Interestingly, the crystal structure of hedragonic acid-bound FXR revealed a unique binding mode with hedragonic acid occupying a novel binding pocket different from the classic binding position. The structural comparison between hedragonic acid-bound FXR and oleanolic acid-bound GPBAR1 explained the molecular basis for the selectivity of oleanane-type triterpenes for FXR. Moreover, hedragonic acid treatment protected mice from liver injury induced by acetaminophen overdose and decreased hepatic inflammatory responses in an FXR-dependent manner, suggesting that hedragonic acid might be one of the major components of COT for its multifunctional pharmaceutical uses. In conclusion, our results provide novel structure templates for drug design based on natural triterpenes by targeting FXR and/or GPBAR1 with pharmaceutical values.


    Organizational Affiliation

    State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, China jinlh@xmu.edu.cn yongli@xmu.edu.cn.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bile acid receptor
A, B
228Homo sapiensMutation(s): 0 
Gene Names: NR1H4 (BAR, FXR, HRR1, RIP14)
Find proteins for Q96RI1 (Homo sapiens)
Go to Gene View: NR1H4
Go to UniProtKB:  Q96RI1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SRC2-3 peptide from Nuclear receptor coactivator 2
C, D
12Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU3
Query on BU3

Download SDF File 
Download CCD File 
A
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
7VX
Query on 7VX

Download SDF File 
Download CCD File 
A, B
(4aR,6aR,6aS,6bS,8aS,9R,12aR,14bR)-2,2,6a,6b,9,12a-hexamethyl-10-oxidanylidene-1,3,4,5,6,6a,7,8,8a,9,11,12,13,14b-tetradecahydropicene-4a-carboxylic acid
C29 H44 O3
USBFNWRNJYBPQP-IQJSWQEESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 74.561α = 90.00
b = 86.075β = 90.00
c = 177.300γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-01-19 
  • Released Date: 2018-01-03 
  • Deposition Author(s): Lu, Y., Li, Y.

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Database references