3FEI

Design and biological evaluation of novel, balanced dual PPARa/g agonists

• PDB DOI: https://doi.org/10.2210/pdb3FEI/pdb

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


• Deposited: 2008-11-30 Released: 2009-10-20 
• Deposition Author(s): Benz, J., Grether, U., Gsell, B., Binggeli, A., Hilpert, H., Maerki, H.P., Mohr, P., Ruf, A., Stihle, M., Schlatter, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.260 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

Design and biological evaluation of novel, balanced dual PPARalpha/gamma agonists

Grether, U., Benardeau, A., Benz, J., Binggeli, A., Blum, D., Hilpert, H., Kuhn, B., Maerki, H.P., Meyer, M., Mohr, P., Puntener, K., Raab, S., Ruf, A., Schlatter, D.

(2009) ChemMedChem 4: 951-956

• PubMed: 19326383 
• DOI: https://doi.org/10.1002/cmdc.200800425
• Primary Citation of Related Structures:  
  3FEI, 3FEJ


• PubMed Abstract: 
  

  An X-ray-guided design approach led to the identification of a novel, balanced class of alpha-ethoxy-phenylpropionic acid-derived dual PPARalpha/gamma agonists. The series shows a wide range of PPARalpha/gamma ratios within a rather narrow structural space. Advanced compounds possess favorable physicochemical and pharmacokinetic profiles and show a high efficacy in T2D and dyslipidemia animal models.

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Organizational Affiliation: 

Pharma Research, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 32.36 kDa 
• Atom Count: 2,213 
• Modelled Residue Count: 254 
• Deposited Residue Count: 280 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor alpha	A	267	Homo sapiens	Mutation(s): 0  Gene Names: PPARA, NR1C1, PPAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q07869 (Homo sapiens) Explore Q07869  Go to UniProtKB:  Q07869
PHAROS:  Q07869 GTEx:  ENSG00000186951

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide motif 5 of Nuclear receptor coactivator 1	B [auth Z]	13	N/A	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTM	C [auth A]	(2S)-3-(4-{[2-(4-chlorophenyl)-1,3-thiazol-4-yl]methoxy}-2-methylphenyl)-2-ethoxypropanoic acid C22 H22 Cl N O4 S OTUKSARQRIIQDU-FQEVSTJZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CTM	PDBBind:  3FEI	IC50: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.260 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.528	α = 90
b = 75.705	β = 90
c = 97.891	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Benz, J., Grether, U., Gsell, B., Binggeli, A., Hilpert, H., Maerki, H.P., Mohr, P., Ruf, A., Stihle, M., Schlatter, D.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations