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Intestinal antiinflammatory effect of 5-aminosalicylic acid is dependent on peroxisome proliferator-activated receptor-gamma.
(2005) J Exp Med 201
PubMed: 15824083 | PubMedCentral: PMC2213148 | DOI: 10.1084/jem.20041948
The structure of the human PPAR-γ ligand-binding domain was obtained from its complexed X-ray crystal structure with the rosiglitazone available in the Research Collaboratory for Structural Bi... informatics Protein Data Bank (1FM6) ( 38 ).
Publication Year: 2005
Active nuclear receptors exhibit highly correlated AF-2 domain motions.
(2008) PLoS Comput Biol 4
PubMed: 18617990 | PubMedCentral: PMC2432469 | DOI: 10.1371/journal.pcbi.1000111
The PXR-RXR heterodimer model was created by superimposing the PXR LBD onto the LBD of PPARγ in the PPARγ-RXRα heterodimer crystal structure (PDBID: 1FM6).
Publication Year: 2008
Binding-site assessment by virtual fragment screening.
(2010) PLoS One 5
PubMed: 20404926 | PubMedCentral: PMC2852417 | DOI: 10.1371/journal.pone.0010109
Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) ACE 1uze 0.60 HIVRT 1vrt 1.66 1o86 0.17 0.37 0.4... 1rt1 1.51 2.45 1.75 1uzf 0.35 0.79 0.69 1c1c a 1.88 3.12 1.61 Alr2 1ah0 1.42 1rth a 1.62 2.28 1.61 1ah3 a 1.06 3.19 1.27 HMGR 1hw8 1.39 2acr a , b 0.88 1.72 1.10 1hwk 0.61 1.49 1.31 CDK2 1aq1 a 1.32 NA 1a4g 0.57 1buh a , b 1.77 3.20 1.44 1a4q a 0.48 2.11 0.52 1dm2 a 1.75 4.49 1.62 1nsc a 0.34 1.49 0.52 COX-2 1cvu 1.51 P38 MAPK 1a9u 1.00 1cx2 a 1.24 3.78 1.53 1kv1 3.84 10.41 1.16 3pgh a 1.11 3.96 1.64 1kv2 3.54 11.26 1.61 DHFR 3dfr 1.01 PDE5 1xoz 1.18 6dfr b 1.47 1.96 1.02 1xp0 0.79 2.23 1.24 ER 1l2i 1.69 PPARg 1fm6 1.46 3ert a 2.61 4.47 1.55 1fm9 a 1.47 4.64 1.62 1err a 2.01 4.39 1.61 2prg a 0.71 1.27 1.43 Fxa 1f0r 1.64 Thrombin 1ba8 1.53 1fjs 1.09 2.57 1.59 1hgt b 0.69 1.85 1.55 1ksn a 0.67 1.65 1.59 TK 1kim a 1.58 1xka a 1.27 2.46 1.56 1ki4 a 1.78 2.90 1.40 RMSD ave was defined as the sidechain RMSD based on binding site residues within a cutoff distance of 4.5 Å from crystallographic ligands; RMSD max is defined as the largest sidechain RMSD value among all the binding site residues.
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
Supporting Information Figure S1 Colored ribbon representation of PPARγ showing three layers of helical “sandwich”, and co-crystallized rosiglitazone (PDB ID 1FM6  ).
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.
Publication Year: 2011
Low-resolution molecular models reveal the oligomeric state of the PPAR and the conformational organization of its domains in solution.
(2012) PLoS One 7
PubMed: 22363753 | PubMedCentral: PMC3283691 | DOI: 10.1371/journal.pone.0031852
The two monomers from the crystallographic structure (PDB id 1FM6) were separated and their relative position and orientation were minimized.
Experimental data (open black circles with errors bars), simulated curves corresponding to the high-resolution model obtained by the use of the PDB id 1FM6 (black solid line) and the rigid body model (gray line).
‡ Values of hPPARγ LBD monomer and hPPARγ/hRXRα LBD heterodimer from the crystallographic model data (PDB id 1FM6) .
Three orthogonal views of the SAXS ab initio models for A) hPPARγ LBD, obtained by Gasbor (shaded spheres), superposed to the hPPARγ LBD monomeric part of the high-resolution model PDB id 1FM6 (cartoon) and B) hPPARγ/hRXRα LBD heterodimer, obtained by Gasbor (shaded spheres), superposed to the rigid body model from PDB id 1FM6 (cartoon).
C) Superposition of the rigid body model with the crystallographic structure (PDB id 1FM6) showing the opening angle imposed on the rigid body model being larger than the crystallographic structure.
Conversely, SAXS scattering data for hPPARγ/hRXRα LBD complex are not fully compatible with the simulated scattering data computed from the hPPARγ/hRXRα LBD heterodimer crystallographic structure (PDB id 1FM6)  ( Table 2 ).
This means that the solution dimer interface is likely to be considerably smaller than that observed in the crystal structure (PDB id 1FM6).
Fitting of DAMs with crystallographic structures The crystallographic structures of hPPARγ LBD monomer (PPAR monomer part from the PDB id 1FM6)  , hPPARγ/hRXRα LBD complex (PDB id 1FM6), hPPARγ DBD-LBD monomer (PPAR monomer part from the PDB id 3DZU) and hPPARγ/hRXRα DBD-LBD complex (PDB id 3DZU)  were used to generate the simulated scattering curves by Crysol package  and to determine the R g and D max .
Publication Year: 2012
GQ-16, a novel peroxisome proliferator-activated receptor ? (PPAR?) ligand, promotes insulin sensitization without weight gain.
(2012) J Biol Chem 287
PubMed: 22584573 | PubMedCentral: PMC3431672 | DOI: 10.1074/jbc.M111.332106
Molecular Dynamics Simulations The simulations started from the crystallographic structure presented in this work (chain B of the GQ-16 complex) and from the structure 1FM6 ( 19 ) (chain D of the rosi... litazone complex) from the PDB.
Comparative molecular profiling of the PPAR?/? activator aleglitazar: PPAR selectivity, activity and interaction with cofactors.
(2012) ChemMedChem 7
PubMed: 22489042 | PubMedCentral: PMC3504387 | DOI: 10.1002/cmdc.201100598
For comparison, models of fenofibrate in PPARα (based on the X-ray complex with GW735, PDB: 2P54) 53 and pioglitazone in PPARγ (based on the X-ray complex with rosiglitazone, PDB: 1FM6... 54 are overlaid onto aleglitazar in the right panels.
Identification of PPARgamma partial agonists of natural origin (I): development of a virtual screening procedure and in vitro validation.
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.
Phytol/Phytanic acid and insulin resistance: potential role of phytanic acid proven by docking simulation and modulation of biochemical alterations.
(2013) PLoS One 8
PubMed: 23300941 | PubMedCentral: PMC3534692 | DOI: 10.1371/journal.pone.0045638
In addition, we performed another docking study of phytanic acid and/or pioglitazone into the crystal structures of the RXRα/PPARγ (1FM6) heterodimer, that was available through the RC... B Protein Data Bank (PDB entry 1FM6)  , and contains two binding sites for two ligands.
B. Generation of ligand and protein structures The crystal structures of target protein PPARγ (2PRG) and RXRα/PPARγ heterodimer (1FM6) active sites were retrieved from the Protein Data Bank ( http://www.rcsb.org/pdb/welcome.do ).
t003 Table 3 ICM scores of phytanic acid, retinoic acid, pioglitazone, and rosiglitazone docked in 1FM6 crystal structure binding site and hydrogen bonds formed with amino acid residues.
Publication Year: 2013
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
Superposed structures of rosiglitazone: the X-ray structure (PDB ID 1FM6) is shown in the atom type colour and the carbon atoms of the structure optimised by the MMFF94s force field are coloured in gr... en.
( a ) PPARγ and 58 agonists superposed on the template complex PDB ID 1FM6 with rosiglitazone (in space-filled rendering and C-atoms coloured in magenta); the other ligands are rendered in lines and coloured according to atom type; ( b ) surface map of the binding site (in constant grey colouring) of all agonists and rosiglitazone (in magenta); the coloured residues outline the corresponding arms within the binding site: Arm I, green; Arm II, cyan; Arm III, yellow; the entrance to the pocket (outlined with a black dotted line) is located between the arms; the protein backbone is rendered in ribbon and coloured according to the secondary structure: helix, red; strand, yellow; turn, blue; loop, white; H1–H12 assign the numbers of the helices in the PPARγ LBD structure.
Pharmacophore Development Prior to pharmacophore development, the full agonists’ complexes were superposed on the template structure of 1FM6.
The protein structures of the complexes were next superposed on the X-ray structure of the PPARγ-rosiglitazone complex (PDB ligand ID BRL; complex ID 1FM6, [ 18 ]).
In general, the superposition on the D-chain produced better RMSDs; thus, the superposition on the D-chain of the 1FM6 complex was selected to produce the overlay of all bioactive conformations of the PPARγ full agonists.
Considering the fact that the X-ray structure may represent a “tensed” conformation of the ligand due to the crystal packing forces, we compared the structure of rosiglitazone as extracted from the 1FM6 complex and the one that has been relaxed using the MMFF94s force field.
Binding poses of three full agonists (BRL (rosiglitazone), 544 (GW409544) 570 (farglitazar); in magenta) and three partial agonists (MRL24, SR145, SR147; in green) within the PPARγ binding pocket (template complex 1FM6).
Figure 4a illustrates the PPARγ LBD and 58 full and partial agonists superposed on the template complex 1FM6 with rosiglitazone.
Figure 6 illustrates the ligand-protein interactions of rosiglitazone in the PPARγ complex 1FM6 and GW409544 (PDB ligand ID 544) in complex 1K74 [ 25 ].
Publication Year: 2014
Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.
(2014) PLoS Comput Biol 10
PubMed: 25079060 | PubMedCentral: PMC4117425 | DOI: 10.1371/journal.pcbi.1003741
Target Structural data Docking-based druggability Protein flexibility Variation PDB ID RMSD ave (Å) [A] dock hit rate [B] DScore+ [A] [B] CDK2 1aq1 1.32 1.7 21% 11% 1buh 1.8 1.44 1.7 1dm2 1.8 ... .62 1.9 ER 1l2i 1.69 2.9 9% 7% 3ert 2.6 1.55 2.7 1err 2.0 1.61 2.8 HIV RT 1vrt 1.66 2.5 8% 13% 1rt1 1.5 1.75 2.3 1c1c 1.9 1.61 2.2 1rth 1.6 1.61 2.3 p38α 1a9u 1.00 1.8 49% 15% kinase 1kv1 3.8 1.16 2.1 1kv2 3.5 1.61 2.1 PPARγ 1fm6 1.46 2.9 13% 34% 1fm9 1.5 1.62 3.0 2prg 0.7 1.43 2.1 TK 1kim 1.58 2.7 12% 4% 1ki4 1.8 1.40 2.6 IL-2 1z92 0.13 * 107% 13% 1py2 2.6 0.62 * 1m48 2.5 0.62 * Bcl-XL 2bzw 1.04 2.4 21% 4% 2yxj 2.5 0.84 2.5 TNF 1tnf 0.95 2.4 1% 18% 2az5 2.9 0.96 2.0 MDM2 1ycr 0.45 2.5 69% 18% 1rv1 1.8 0.92 2.2 1t4e 1.6 0.66 2.1 HPV E2 1tue -0.24 * 323% 31% 1r6n 2.8 1.02 * Targets are from Huang and Jacobson  , and include all targets where at least two structures have an RMSD ave greater than 1.5 Å.
Design and Synthesis of Pyrazole-3-one Derivatives as Hypoglycaemic Agents.
(2015) Int J Med Chem 2015
PubMed: 25734015 | PubMedCentral: PMC4334925 | DOI: 10.1155/2015/670181
The X-ray crystal of peroxisome proliferator-activated receptor gamma (PPARgamma) in complex with rosiglitazone (PDB entry code 1FM6) [ 19 ] was obtained from the RCSB Protein Data Bank (PDB) and util... zed in order to get the detailed insights of ligand-protein structure in this study.
Out of four chains in the reported protein structure 1FM6, only single monomer chain with rosiglitazone was selected for further work.
Docking study was performed in single monomer by replacing rosiglitazone from reported crystal structure 1FM6.
Figures 2 , 3 , 4 , 5 , 6 , and 7 show the docked compounds (1, 3, 4, 5, and 6, rosiglitazone) in the active site of 1FM6, respectively.
Publication Year: 2015
PubMed ID is not available.
Published in 2015
The ligands MEKT-21 (PDB ID 3VSO, Table 1 ) and rosiglitazone (PDB ID 1FM6) were used as references.
We were able to successfully regenerate not only the pose of the original ligand but also of rosiglitazone (PDB ID 1FM6) and MEKT-75 (PDB ID 3WMH).
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