3G8I

Aleglitazar, a new, potent, and balanced PPAR alpha/gamma agonist for the treatment of type II diabetes

• PDB DOI: https://doi.org/10.2210/pdb3G8I/pdb

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


• Deposited: 2009-02-12 Released: 2009-06-02 
• Deposition Author(s): Benz, J., Bernardeau, A., Binggeli, A., Blum, D., Boehringer, M., Grether, U., Hilpert, H., Kuhn, B., Maerki, H.P., Meyer, M., Puentener, K., Raab, S., Ruf, A., Schlatter, D., Gsell, B., Stihle, M., Mohr, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

Aleglitazar, a new, potent, and balanced dual PPARalpha/gamma agonist for the treatment of type II diabetes.

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

(2009) Bioorg Med Chem Lett 19: 2468-2473

• PubMed: 19349176 
• DOI: https://doi.org/10.1016/j.bmcl.2009.03.036
• Primary Citation of Related Structures:  
  3G8I, 3G9E


• PubMed Abstract: 
  

  Design, synthesis, and SAR of novel alpha-alkoxy-beta-arylpropionic acids as potent and balanced PPARalphagamma coagonists are described. One representative thereof, Aleglitazar ((S)-2Aa), was chosen for clinical development. Its X-ray structure in complex with both receptors as well as its high efficacy in animal models of T2D and dyslipidemia are also presented.

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Organizational Affiliation: 

F. Hoffmann-La Roche Ltd, Pharma Research, CH-4070 Basel, Switzerland.

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: 32.67 kDa 
• Atom Count: 2,289 
• Modelled Residue Count: 262 
• Deposited Residue Count: 283 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor alpha	A	270	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
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
RO7	C [auth A]	(2S)-2-methoxy-3-{4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]-1-benzothiophen-7-yl}propanoic acid C24 H23 N O5 S DAYKLWSKQJBGCS-NRFANRHFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RO7	BindingDB:  3G8I	IC50: min: 28, max: 38 (nM) from 2 assay(s)
		EC50: min: 50, max: 2340 (nM) from 4 assay(s)
	Binding MOAD:  3G8I	IC50: 38 (nM) from 1 assay(s)
	PDBBind:  3G8I	IC50: 38 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.405	α = 90
b = 76.033	β = 90
c = 98.495	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Benz, J., Bernardeau, A., Binggeli, A., Blum, D., Boehringer, M., Grether, U., Hilpert, H., Kuhn, B., Maerki, H.P., Meyer, M., Puentener, K., Raab, S., Ruf, A., Schlatter, D., Gsell, B., Stihle, M., Mohr, P.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description