2POB

PPARgamma Ligand binding domain complexed with a farglitazar analogue gw4709

• PDB DOI: https://doi.org/10.2210/pdb2POB/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-26 Released: 2008-03-18 
• Deposition Author(s): Nolte, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 

Starting Model: experimental

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

• PubMed: 17533125 
• DOI: https://doi.org/10.1016/j.bmcl.2007.04.111
• Primary Citation of 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.

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Organizational Affiliation: 

Drug Discovery, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	272	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GW4	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	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GW4	BindingDB:  2POB	Ki: 138 (nM) from 1 assay(s)
		IC50: 1585 (nM) from 1 assay(s)
		EC50: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.273 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.916	α = 90
b = 62.006	β = 101.94
c = 118.172	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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