4WVD

Identification of a novel FXR ligand that regulates metabolism

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)

  • Deposited: 2014-11-05 Released: 2015-02-11 
  • Deposition Author(s): Wang, R., Li, Y.
  • Funding Organization(s): National Basic Research Program of China; National Natural Science Foundation of China; Programme of Introducing Talents of Discipline to Universities 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.277 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 4II6 - determined by Wang, R., Li, Y.  

Literature

The antiparasitic drug ivermectin is a novel FXR ligand that regulates metabolism.

Jin, L.Feng, X.Rong, H.Pan, Z.Inaba, Y.Qiu, L.Zheng, W.Lin, S.Wang, R.Wang, Z.Wang, S.Liu, H.Li, S.Xie, W.Li, Y.

(2013) Nat Commun 4: 1937

  • DOI: 10.1038/ncomms2924
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Farnesoid X receptor (FXR) has important roles in maintaining bile acid and cholesterol homeostasis. Here we report that the antiparasitic drug ivermectin is a ligand for nuclear FXR. We identify ivermectin using a high-throughput compound library sc ...

    Farnesoid X receptor (FXR) has important roles in maintaining bile acid and cholesterol homeostasis. Here we report that the antiparasitic drug ivermectin is a ligand for nuclear FXR. We identify ivermectin using a high-throughput compound library screening and show that it induces the transcriptional activity of the FXR with distinctive properties in modulating coregulator recruitment. The crystal structure of ivermectin complexed with the ligand-binding domain of FXR reveals a unique binding mode of ivermectin in the FXR ligand-binding pocket, including the highly dynamic AF-2 helix and an expanded ligand-binding pocket. Treatment of wild-type mice, but not of FXR-null mice, with ivermectin decreases serum glucose and cholesterol levels, suggesting that ivermectin regulates metabolism through FXR. Our results establish FXR as the first mammalian protein targeted by ivermectin with high selectivity. Considering that ivermectin is a widely used clinical drug, our findings reveal a safe template for the design of novel FXR ligands.


    Organizational Affiliation

    State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Fujian 361005, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor corepressor 1
C, D
17Homo sapiensMutation(s): 0 
Gene Names: NCOR1 (KIAA1047)
Find proteins for O75376 (Homo sapiens)
Go to Gene View: NCOR1
Go to UniProtKB:  O75376
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bile acid receptor
A, B
211Homo 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
IVM
Query on IVM

Download SDF File 
Download CCD File 
A, B
(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17-oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacyclooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside
22,23-DIHYDROAVERMECTIN B1A; IVERMECTIN
C48 H74 O14
AZSNMRSAGSSBNP-XPNPUAGNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.277 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.008α = 90.00
b = 161.759β = 90.00
c = 169.018γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
Cootmodel building
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-11-05 
  • Released Date: 2015-02-11 
  • Deposition Author(s): Wang, R., Li, Y.
  • This entry supersedes: 4II6

Funding OrganizationLocationGrant Number
National Basic Research Program of ChinaChina973 Program: 2012CB910104
National Natural Science Foundation of ChinaChina81273567
National Natural Science Foundation of ChinaChina31270776
Programme of Introducing Talents of Discipline to UniversitiesChinaB12001

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Data collection
  • Version 1.2: 2017-09-27
    Type: Data collection, Derived calculations