Primary Citation PubMed: 15976031
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Virtual Screening as a Technique for PPAR Modulator Discovery.
(2010) PPAR Res 2010
PubMed: 19746174 | PubMedCentral: PMC2738858 | DOI: 10.1155/2010/861238
All PDB IDs list Homo sapiens as the protein source except 1ZGY ( Rattus norvegicus ).
Publication Year: 2010
Dietary ?-eleostearic acid ameliorates experimental inflammatory bowel disease in mice by activating peroxisome proliferator-activated receptor-?.
(2011) PLoS One 6
PubMed: 21904603 | PubMedCentral: PMC3164124 | DOI: 10.1371/journal.pone.0024031
The selected structure IDs were 1FM6  , 1ZGY  , 2PRG  , 3CS8  , and 3DZY  .
The average pose RMSD values for three structures, 1FM6, 1ZGY, and 2PRG, were within 2.0 Å of the crystal structure position.
Examination of the poses for all five structures revealed that the lowest RMSD value (0.99 Å) for all rosiglitazone poses was in the 1ZGY pose group as was the pose with the highest RMSD value (3.05 Å).
Thus, we favored the 1ZGY structure for further docking studies because this structure enabled docking at the known rosiglitazone binding position as well as docking at other energetically favorable positions within the binding site, suggesting that it might accommodate ligands of diverse structure.
Publication Year: 2011
Identification of PPARgamma partial agonists of natural origin (I): development of a virtual screening procedure and in vitro validation.
(2012) PLoS One 7
PubMed: 23226391 | PubMedCentral: PMC3511273 | DOI: 10.1371/journal.pone.0050816
Full agonists Partial agonists cluster 1 cluster 2 cluster 3 cluster 4 cluster 5 1FM9 1I7I 1FM6 2GTK 2G0G 4PRG 2Q6R 2FVJ 2Q6S 1RDT 1KNU 1ZGY 3B3K 2G0H 2Q61 2WM0 1K74 2F4B 2PRG 2ATH 2Q5S 3BC5 2HWQ 2FVJ... 1NYX 2Q5P 2Q8S 2HWR 1ZEO 2HFP 2P4Y Generation of Structure-Based Pharmacophores LigandScout v2.03 (Inte:ligand, Vienna, Austria, http://www.inteligand.com/ligandscout/ )  ,  was used for the analysis of the 31 PPARγ structures from Table 5 and the analysis of the possible interactions between the crystallized ligands and the ligand-binding pocket of PPARγ.
Publication Year: 2012
Molecular modelling study of the PPAR? receptor in relation to the mode of action/adverse outcome pathway framework for liver steatosis.
(2014) Int J Mol Sci 15
PubMed: 24857909 | PubMedCentral: PMC4057697 | DOI: 10.3390/ijms15057651
This complex was selected as an appropriate template in the subsequent modelling steps, because of the following reasons: (i) the complex represents a physiologically relevant heterodimer of the human... RXRα and PPARγ LBDs, respectively, bound with 9-cis retinoic acid and rosiglitazone and co-activator peptides; (ii) rosiglitazone is one of the most active agonists among the PPARγ ligands ( Table S1 ), thus providing a relevant structure for the purposes of pharmacophore modelling; (iii) the LBD of the complex consists of 272 residues (from Pro206 to Tyr477), thus fully covering the main structural elements of the domain; (iv) compared to other complexes of PPARγ with rosiglitazone (4EMA, 3DZY, 2PRG, 3CS8, [ 19 – 22 ]) available in PDB, that selected has the lowest resolution of 2.1 Å (the complex with PDB ID 1ZGY [ 23 ] has been resolved at 1.80 Å; however, it is not crystallised with RXRα and, thus, does not reflect physiological conditions).
Publication Year: 2014
PubMed ID is not available.
Published in 2015
We used the 3GZ9 [ 27 ] structure as PPARδ model and 1ZGY [ 48 ] as PPARγ model.
Publication Year: 2015
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