4WVD

Identification of a novel FXR ligand that regulates metabolism

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

  • 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: 2.90 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.279 

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


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:  
    4WVD

  • 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 screen ...

    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 LengthOrganismDetailsImage
Nuclear receptor corepressor 1 C, D17Homo sapiensMutation(s): 0 
Gene Names: NCOR1, KIAA1047
Find proteins for O75376 (Homo sapiens)
Explore O75376 
Go to UniProtKB:  O75376
NIH Common Fund Data Resources
PHAROS:  O75376
GTEx:  ENSG00000141027
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bile acid receptor A, B211Homo sapiensMutation(s): 0 
Gene Names: NR1H4, BAR, FXR, HRR1, RIP14
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
NIH Common Fund Data Resources
PHAROS:  Q96RI1
GTEx:  ENSG00000012504
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IVM
Query on IVM
Download Ideal Coordinates 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]benzodioxacy clooctadecine-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
C48 H74 O14
AZSNMRSAGSSBNP-XPNPUAGNSA-N		 Ligand Interaction
FMT
Query on FMT
Download Ideal Coordinates CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.279 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.008α = 90
b = 161.759β = 90
c = 169.018γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing

Structure Validation

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View more in-depth experimental data

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
    Changes: Data collection
  • Version 1.2: 2017-09-27
    Changes: Data collection, Derived calculations