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


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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
  • Primary Citation of Related Structures:  
    4EM9, 4EMA

  • 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 profiles are needed ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaA, B275Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BRL (Subject of Investigation/LOI)
Query on BRL

Download Ideal Coordinates CCD File 
C [auth A]2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
C18 H19 N3 O3 S
YASAKCUCGLMORW-HNNXBMFYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BRL BindingDB:  4EMA Ki: min: 8, max: 59 (nM) from 4 assay(s)
Kd: min: 0.14, max: 1.2 (nM) from 2 assay(s)
IC50: min: 1, max: 298 (nM) from 8 assay(s)
EC50: min: 1, max: 1600 (nM) from 31 assay(s)
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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