3SP6

Structural basis for iloprost as a dual PPARalpha/delta agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for iloprost as a dual peroxisome proliferator-activated receptor alpha/delta agonist.

Jin, L.Lin, S.Rong, H.Zheng, S.Jin, S.Wang, R.Li, Y.

(2011) J Biol Chem 286: 31473-31479

  • DOI: https://doi.org/10.1074/jbc.M111.266023
  • Primary Citation of Related Structures:  
    3SP6, 3SP9

  • PubMed Abstract: 

    Iloprost is a prostacyclin analog that has been used to treat many vascular conditions. Peroxisome proliferator-activated receptors (PPARs) are ligand-regulated transcription factors with various important biological effects such as metabolic and cardiovascular physiology. Here, we report the crystal structures of the PPARα ligand-binding domain and PPARδ ligand-binding domain bound to iloprost, thus providing unambiguous evidence for the direct interaction between iloprost and PPARs and a structural basis for the recognition of PPARα/δ by this prostacyclin analog. In addition to conserved contacts for all PPARα ligands, iloprost also initiates several specific interactions with PPARs using its unique structural groups. Structural and functional studies of receptor-ligand interactions reveal strong functional correlations of the iloprost-PPARα/δ interactions as well as the molecular basis of PPAR subtype selectivity toward iloprost ligand. As such, the structural mechanism may provide a more rational template for designing novel compounds targeting PPARs with more favorable pharmacologic impact based on existing iloprost drugs.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor alpha285Homo sapiensMutation(s): 0 
Gene Names: PPARANR1C1PPAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens)
Explore Q07869 
Go to UniProtKB:  Q07869
PHAROS:  Q07869
GTEx:  ENSG00000186951 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07869
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma coactivator 1-beta11Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q86YN6 (Homo sapiens)
Explore Q86YN6 
Go to UniProtKB:  Q86YN6
PHAROS:  Q86YN6
GTEx:  ENSG00000155846 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86YN6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IL2
Query on IL2

Download Ideal Coordinates CCD File 
C [auth A](5E)-5-[(3aS,4R,5R,6aS)-5-hydroxy-4-[(1E,3S,4R)-3-hydroxy-4-methyloct-1-en-6-yn-1-yl]hexahydropentalen-2(1H)-ylidene]pentanoic acid
C22 H32 O4
HIFJCPQKFCZDDL-GBSCXWAGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.837α = 90
b = 60.973β = 108.99
c = 54.16γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2012-06-20
    Changes: Database references
  • Version 1.2: 2014-04-16
    Changes: Other
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations