3R8I

Crystal Structure of PPARgamma with an achiral ureidofibrate derivative (RT86)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Synthesis, characterization and biological evaluation of ureidofibrate-like derivatives endowed with peroxisome proliferator-activated receptor activity.

Porcelli, L.Gilardi, F.Laghezza, A.Piemontese, L.Mitro, N.Azzariti, A.Altieri, F.Cervoni, L.Fracchiolla, G.Giudici, M.Guerrini, U.Lavecchia, A.Montanari, R.Di Giovanni, C.Paradiso, A.Pochetti, G.Simone, G.M.Tortorella, P.Crestani, M.Loiodice, F.

(2012) J Med Chem 55: 37-54

  • DOI: 10.1021/jm201306q
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A series of ureidofibrate-like derivatives was prepared and assayed for their PPAR functional activity. A calorimetric approach was used to characterize PPARγ-ligand interactions, and docking experiments and X-ray studies were performed to explain th ...

    A series of ureidofibrate-like derivatives was prepared and assayed for their PPAR functional activity. A calorimetric approach was used to characterize PPARγ-ligand interactions, and docking experiments and X-ray studies were performed to explain the observed potency and efficacy. R-1 and S-1 were selected to evaluate several aspects of their biological activity. In an adipogenic assay, both enantiomers increased the expression of PPARγ target genes and promoted the differentiation of 3T3-L1 fibroblasts to adipocytes. In vivo administration of these compounds to insulin resistant C57Bl/6J mice fed a high fat diet reduced visceral fat content and body weight. Examination of different metabolic parameters showed that R-1 and S-1 are insulin sensitizers. Notably, they also enhanced the expression of hepatic PPARα target genes indicating that their in vivo effects stemmed from an activation of both PPARα and γ. Finally, the capability of R-1 and S-1 to inhibit cellular proliferation in colon cancer cell lines was also evaluated.


    Related Citations: 
    • Insights into the mechanism of partial agonism: crystal structures of the peroxisome proliferator-activated receptor gamma ligand-binding domain in the complex with two enantiomeric ligands.
      Pochetti, G., Godio, C., Mitro, N., Caruso, D., Galmozzi, A., Scurati, S., Loiodice, F., Fracchiolla, G., Tortorella, P., Laghezza, A., Lavecchia, A., Novellino, E., Mazza, F., Crestani, M.
      (2007) J Biol Chem 282: 17314
    • Structural insight into peroxisome proliferator-activated receptor gamma binding of two ureidofibrate-like enantiomers by molecular dynamics, cofactor interaction analysis, and site-directed mutagenesis.
      Pochetti, G., Mitro, N., Lavecchia, A., Gilardi, F., Besker, N., Scotti, E., Aschi, M., Re, N., Fracchiolla, G., Laghezza, A., Tortorella, P., Montanari, R., Novellino, E., Mazza, F., Crestani, M., Loiodice, F.
      (2010) J Med Chem 53: 4354

    Organizational Affiliation

    Laboratorio di Oncologia Sperimentale Clinica, Istituto Tumori "Giovanni Paolo II", 70124 Bari, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
287Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XCX
Query on XCX

Download CCD File 
A
2-(4-{2-[1,3-benzoxazol-2-yl(heptyl)amino]ethyl}phenoxy)-2-methylpropanoic acid
C26 H34 N2 O4
MMVUCPZZXMPIPE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XCXKd:  4500   nM  BindingDB
XCXKd:  4500   nM  Binding MOAD
XCXEC50:  110   nM  BindingDB
XCXKd :  4500   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.589α = 90
b = 62.398β = 102.11
c = 118.392γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references