4EMA

Human peroxisome proliferator-activated receptor gamma in complex with rosiglitazone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report



Literature

Medium chain fatty acids are selective peroxisome proliferator activated receptor (PPAR) Gamma activators and pan-PPAR partial agonists

Liberato, M.V.Nascimento, A.S.Ayers, S.D.Lin, J.Z.Cvoro, A.Silveira, R.L.Martinez, L.Souza, P.C.Saidemberg, D.Deng, T.Amato, A.A.Togashi, M.Hsueh, W.A.Phillips, K.Palma, M.S.Neves, F.A.Skaf, M.S.Webb, P.Polikarpov, I.

(2012) PLoS One 7: e36297-e36297

  • DOI: 10.1371/journal.pone.0036297
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Thiazolidinediones (TZDs) act through peroxisome proliferator activated receptor (PPAR) γ to increase insulin sensitivity in type 2 diabetes (T2DM), but deleterious effects of these ligands mean that selective modulators with improved clinical profil ...

    Thiazolidinediones (TZDs) act through peroxisome proliferator activated receptor (PPAR) γ to increase insulin sensitivity in type 2 diabetes (T2DM), but deleterious effects of these ligands mean that selective modulators with improved clinical profiles are needed. We obtained a crystal structure of PPARγ ligand binding domain (LBD) and found that the ligand binding pocket (LBP) is occupied by bacterial medium chain fatty acids (MCFAs). We verified that MCFAs (C8-C10) bind the PPARγ LBD in vitro and showed that they are low-potency partial agonists that display assay-specific actions relative to TZDs; they act as very weak partial agonists in transfections with PPARγ LBD, stronger partial agonists with full length PPARγ and exhibit full blockade of PPARγ phosphorylation by cyclin-dependent kinase 5 (cdk5), linked to reversal of adipose tissue insulin resistance. MCFAs that bind PPARγ also antagonize TZD-dependent adipogenesis in vitro. X-ray structure B-factor analysis and molecular dynamics (MD) simulations suggest that MCFAs weakly stabilize C-terminal activation helix (H) 12 relative to TZDs and this effect is highly dependent on chain length. By contrast, MCFAs preferentially stabilize the H2-H3/β-sheet region and the helix (H) 11-H12 loop relative to TZDs and we propose that MCFA assay-specific actions are linked to their unique binding mode and suggest that it may be possible to identify selective PPARγ modulators with useful clinical profiles among natural products.


    Organizational Affiliation

    São Carlos Physics Institute, University of São Paulo, São Carlos, Sao Paulo, Brazil.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
275Homo 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
BRL
Query on BRL

Download CCD File 
A
2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
C18 H19 N3 O3 S
YASAKCUCGLMORW-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BRLEC50:  87   nM  BindingDB
BRLKd:  1.2000000476837158   nM  BindingDB
BRLIC50:  292   nM  BindingDB
BRLEC50:  95   nM  BindingDB
BRLEC50:  89   nM  BindingDB
BRLKi:  27   nM  BindingDB
BRLEC50:  1100   nM  BindingDB
BRLEC50:  10   nM  BindingDB
BRLIC50:  38   nM  BindingDB
BRLKi:  47   nM  BindingDB
BRLEC50:  117   nM  BindingDB
BRLEC50:  114   nM  BindingDB
BRLKd:  0.14000000059604645   nM  BindingDB
BRLKi:  8   nM  BindingDB
BRLEC50:  326   nM  BindingDB
BRLEC50:  332   nM  BindingDB
BRLEC50:  316   nM  BindingDB
BRLEC50:  300   nM  BindingDB
BRLIC50:  76   nM  BindingDB
BRLEC50:  260   nM  BindingDB
BRLEC50:  1   nM  BindingDB
BRLEC50:  39   nM  BindingDB
BRLEC50:  40   nM  BindingDB
BRLEC50:  52   nM  BindingDB
BRLIC50:  1   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.511α = 90
b = 61.958β = 100.7
c = 117.601γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release