2POB | pdb_00002pob

PPARgamma Ligand binding domain complexed with a farglitazar analogue gw4709

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.273 (Depositor), 0.324 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Cocrystal structure guided array synthesis of PPARgamma inverse agonists

Trump, R.P., Cobb, J.E., Shearer, B.G., Lambert, M.H., Nolte, R.T., Willson, T.M., Buckholtz, R.G., Zhao, S.M., Leesnitzer, L.M., Iannone, M.A., Pearce, K.H., Billin, A.N., Hoekstra, W.J.

(2007) Bioorg Med Chem Lett 17: 3916-3920

  • DOI: https://doi.org/10.1016/j.bmcl.2007.04.111
  • Primary Citation Related Structures: 
    2POB

  • PubMed Abstract: 

    PPARgamma-activating thiazolidinediones and carboxylic acids such as farglitazar exert their anti-diabetic effects in part in PPARgamma rich adipose. Both pro- and anti-adipogenic PPARgamma ligands promote glucose and lipid lowering in animal models of diabetes. Herein, we disclose representatives of an array of 160 farglitazar analogues with atypical inverse agonism of PPARgamma in mature adipocytes.

    • Organizational Affiliation: 
    • Drug Discovery, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.

Macromolecule Content 

  • Total Structure Weight: 62.85 kDa 
  • Atom Count: 4,278 
  • Modeled Residue Count: 502 
  • Deposited Residue Count: 544 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
272Homo sapiensMutation(s): 0 
Gene Names: PPARG, NR1C3
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GW4

Query on GW4


Download:Ideal Coordinates CCD File
C [auth A]N-[(2S)-2-[(2-BENZOYLPHENYL)AMINO]-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL]ACETAMIDE
C36 H35 N3 O4
WCJXONGEWJNZQV-PMERELPUSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
D [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.273 (Depositor), 0.324 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.916α = 90
b = 62.006β = 101.94
c = 118.172γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2008-03-18 
    • Deposition Author(s): Nolte, R.T.

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2014-09-10
    Changes: Database references
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-04-03
    Changes: Refinement description