2Q8S | pdb_00002q8s

X-ray Crystal structure of the nuclear hormone receptor PPAR-gamma in a complex with a PPAR gamma/alpha dual agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.282 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Effects of modifications of the linker in a series of phenylpropanoic acid derivatives: Synthesis, evaluation as PPARalpha/gamma dual agonists, and X-ray crystallographic studies.

Casimiro-Garcia, A.Bigge, C.F.Davis, J.A.Padalino, T.Pulaski, J.Ohren, J.F.McConnell, P.Kane, C.D.Royer, L.J.Stevens, K.A.Auerbach, B.J.Collard, W.T.McGregor, C.Fakhoury, S.A.Schaum, R.P.Zhou, H.

(2008) Bioorg Med Chem 16: 4883-4907

  • DOI: https://doi.org/10.1016/j.bmc.2008.03.043
  • Primary Citation Related Structures: 
    2Q8S

  • PubMed Abstract: 

    A new series of alpha-aryl or alpha-heteroarylphenyl propanoic acid derivatives was synthesized that incorporate acetylene-, ethylene-, propyl-, or nitrogen-derived linkers as a replacement of the commonly used ether moiety that joins the central phenyl ring with the lipophilic tail. The effect of these modifications in the binding and activation of PPARalpha and PPARgamma was first evaluated in vitro. Compounds possessing suitable profiles were then evaluated in the ob/ob mouse model of type 2 diabetes. The propylene derivative 40 and the propyl derivative 53 demonstrated robust plasma glucose lowering activity in this model. Compound 53 was also evaluated in male Zucker diabetic fatty rats and was found to achieve normalization of glucose, triglycerides, and insulin levels. An X-ray crystal structure of the complex of 53 with the PPARgamma-ligand-binding domain was obtained and discussed in this report.


  • Organizational Affiliation
    • Department of Chemistry, Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. agustin.casimiro-garcia@pfizer.com

Macromolecule Content 

  • Total Structure Weight: 62.41 kDa 
  • Atom Count: 4,153 
  • Modeled Residue Count: 507 
  • Deposited Residue Count: 542 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
271Homo 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
GTEx:  ENSG00000132170 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L92

Query on L92



Download:Ideal Coordinates CCD File
C [auth A](2S)-3-{4-[3-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)PROPYL]PHENYL}-2-(1H-PYRROL-1-YL)PROPANOIC ACID
C26 H26 N2 O3
QPJVYLQOALFBLJ-DEOSSOPVSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.282 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.455α = 90
b = 62.016β = 102.54
c = 118.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2008-10-14 
  • Deposition Author(s): Ohren, J.F.

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description