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Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures.
(2009) Acta Crystallogr D Biol Crystallogr 65
PubMed: 19622862 | PubMedCentral: PMC2714719 | DOI: 10.1107/S0907444909015935
A database examination revealed that our PPAR LBD–TIPP complex structures resemble those of PPARα with AZ 242 (PDB code 1i7g ; Cronet et al. , 2001 ▶ ) and with a PPARα... γ dual agonist, α-acyl-β-phenylpropanioic acid (PDB code 2npa ; Han et al. , 2007 ▶ ), of PPARγ with rosiglitazone (PDB code 2prg ; Nolte et al. , 1998 ▶ ) and with a PPARα/γ dual agonist, a phenylpropanoic acid derivative (PDB code 2q8s ; Casimiro-Garcia et al. , 2008 ▶ ), and of PPARδ with GW2331 (PDB code 1y0s ; Takada et al. , 2000 ▶ ) and with a 3,4,5-trisubstituted isoxazole (PDB code 2j14 ; Epple et al. , 2006 ▶ ) (see Supplementary Fig. 2 1 ).
Publication Year: 2009
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
Anti-diabetic drugs inhibit obesity-linked phosphorylation of PPARgamma by Cdk5.
(2010) Nature 466
PubMed: 20651683 | PubMedCentral: PMC2987584 | DOI: 10.1038/nature09291
b , HDX data for the four peptides of interest are plotted over the structures of PPARγ-LBD bound with rosiglitazone (left, PDB:2PRG) and MRL24 (right, PDB:2Q5P).
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.
Publication Year: 2011
Peroxisome proliferator-activated receptor ? is a target for halogenated analogs of bisphenol A.
(2011) Environ Health Perspect 119
PubMed: 21561829 | PubMedCentral: PMC3230400 | DOI: 10.1289/ehp.1003328
( B ) Superimposition of the co-crystal structure of TBBPA-bound PPARγ LBD on the structure with rosiglitazone (PDB code 2PRG; Nolte et al. 1998).
Nuclear hormone receptor co-repressors: structure and function.
(2012) Mol Cell Endocrinol 348
PubMed: 21925568 | PubMedCentral: PMC3315023 | DOI: 10.1016/j.mce.2011.08.033
(a) Structure of the LBD from PPARγ with a peptide from the co-activator SRC1 (shown in green) and the ligand rosiglitazone (yellow) bound (PDB code 2PRG ( Nolte et al., 1998 )).
Publication Year: 2012
Structural insights into human peroxisome proliferator activated receptor delta (PPAR-delta) selective ligand binding.
(2012) PLoS One 7
PubMed: 22606221 | PubMedCentral: PMC3350516 | DOI: 10.1371/journal.pone.0033643
Nearby PPARγ-specific substitutions (δIle327/αIle354/γPhe391 and δThr252/αThr279/γArg316) introduce residues with flexible side chains that are ... ot likely to block GW0742 binding; γPhe391 contacts Rosiglitazone (PDB id 2PRG), but faces away from ligand in the PPARγ:Indeglitazar structure (PDB id 3ET3) ( Figure S1 ) and γArg316 faces away from both ligands.
Potential Steric Hindrance to GW0742 Binding in PPARα and γ We next compared the PPARδ:GW0742 structure with analogous structures of PPARα and γ LBDs in complex with representative selective agonists (GW735 and Rosiglitazone) and the three PPARs with a pan agonist, indeglitazar (PDB ids: 2P54  , 2PRG  and 3ET2, 3ET3 and 3ET1, respectively  .
The α selective ligand, GW735 (PDBid: 2P54), the δ selective ligand, GW0742, and the γ selective ligand, rosiglitazone (PDBid: 2PRG), are shown as yellow, magenta and green sticks, respectively.
Superposition of the γ-selective ligand rosiglitazone (green stick), pan-agonist ligand indeglitazar (blue sticks) and the γPhe391 residue from the respective crystallographic structures for PDB id 2PRG (green lines) and 3ET3 (green lines).
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
A , although GQ-16 ( purple ) induces an overall structure similar to that of rosiglitazone ( blue , GQ-16·PPARγ; white , rosiglitazone·PPARγ) (Protein Data Bank entry ... PRG ), GQ-16 binds to PPARγ in a different orientation than traditional TZDs, such as rosiglitazone.
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
Phytol, phytanic acid, and pioglitazone were first docked on the crystal structures of PPARγ (2PRG), which is originally complexed with its ligand rosiglitazone, as found in RCSB Protein Data ... ank (PDB entry 2PRG)  .
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 ).
Results Table 2 , Figure 1A–C depict the docking results of phytanic acid in the crystal structures of PPARγ binding protein (2PRG) in terms of orientation, fitting and binding affinity as compared with rosiglitazone, pioglitazone and phytol.
Publication Year: 2013
A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding.
(2013) J Cheminform 5
PubMed: 23627990 | PubMedCentral: PMC3648400 | DOI: 10.1186/1758-2946-5-21
We can go to the crystallographic image of the rosiglitazone-PPARγ complex (PDB code: 2PRG) [ 35 ].
Around the bound structure of rosiglitazone (PDB: 2PRG), the ES symbol ssO can detect the key interaction between rosiglitazone ether oxygen and the two sulfurs of Cys285 (3.79 Å) and Met364 (4.70 Å).
Intrinsically semi-disordered state and its role in induced folding and protein aggregation.
(2013) Cell Biochem Biophys 67
PubMed: 23723000 | PubMedCentral: PMC3838602 | DOI: 10.1007/s12013-013-9638-0
( b ) Disorder probability profiles with zero ordered residues ( f o = 0) for the chain A of the PDB ID 2qt4 (2qt4A) in the control set, for DP00179 (chain B in PDB ID 1DPJ) in SL477,... and for chain C of PDB ID 2prg (2prgC) in DX4080.
Coffee component hydroxyl hydroquinone (HHQ) as a putative ligand for PPAR gamma and implications in breast cancer.
(2013) BMC Genomics 14 Suppl 5
PubMed: 24564733 | PubMedCentral: PMC3852186 | DOI: 10.1186/1471-2164-14-S5-S6
HHQ was observed to dock and form hydrogen bonds with PDB ID - 2PRG (PDB 3-D crystal structure of the Ligand-binding domain of the human peroxisome proliferator activated receptor gamma solved in comp... exation with Rosiglitazone, the PPAR gamma agonist/ligand).
The PDB file for the crystal structure of PPARγ (PDB ID - 2PRG) was downloaded from http://www.rcsb.org and transferred into the workspace keeping the orientation as a control.
Here, we used the PDB crystal structure 2PRG (PPARγ with ligand Rosiglitazone) for structure-based identification of HHQ as a potential ligand for PPARγ in breast cancer therapeutics.
Drugs Hydrogen bond score (kcal.mol-1) Number of hydrogen bonds Residues of PPARγ binding site interacting with the ligands Rerank score HHQ -9.46033 5 Gln286, His449, Tyr473, Ser289, His323 -33.3562 Rosiglitazone -5.48771 3 Gln286, His449, Ser289 -122.433 Figure 1 HHQ docked in the ligand binding domain of PPARγ protein crystal structure for PDB solved in conjunction with Rosiglitazone (PDBID: 2PRG) .
[A] Represents hydrogen bonds (in black dotted line) observed for Rosiglitazone (in red) with the active site residues in the ligand binding domain of PPARγ (2PRG).
[C] Represents superposition of the best conformation of Rosiglitazone (in red) and HHQ (in yellow) in the ligand binding domain of 2PRG.
Rosiglitazone (the ligand in the crystal structure 2PRG) forms 3 hydrogen bonds with the 2PRG (Gln286, His449, Ser289) and HHQ forms 5 hydrogen bonds with 2PRG (Gln286, His449, Tyr473, Ser289, His323).
Synthesis of PPAR-? activators inspired by the marine natural product, paecilocin A.
(2014) Mar Drugs 12
PubMed: 24531188 | PubMedCentral: PMC3944523 | DOI: 10.3390/md12020926
Protein coordinates were downloaded from the Protein Data Bank (accession code: 2PRG).
Publication Year: 2014
A conservation and biophysics guided stochastic approach to refining docked multimeric proteins.
(2013) BMC Struct Biol 13 Suppl 1
PubMed: 24565106 | PubMedCentral: PMC3952451 | DOI: 10.1186/1472-6807-13-S1-S7
In addition to these dimers, we produced multimeric input structures by running the Multi-LZerD multimeric docking program without refinement [ 11 ] for protein complexes with the following PDB IDs: 1... 3O , 1JYO , 1LOG , 1QGW , 1VCB , 1W88 , 1WWW , 2BBK , 2PRG and 6RLX .
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).
CMHX008, a novel peroxisome proliferator-activated receptor ? partial agonist, enhances insulin sensitivity in vitro and in vivo.
(2014) PLoS One 9
PubMed: 25004107 | PubMedCentral: PMC4087031 | DOI: 10.1371/journal.pone.0102102
The crystal structure of PPARγ was derived from PDB database (ID: 2PRG).
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.
Identification of novel multitargeted PPAR?/?/? pan agonists by core hopping of rosiglitazone.
(2014) Drug Des Devel Ther 8
PubMed: 25422585 | PubMedCentral: PMC4232041 | DOI: 10.2147/DDDT.S70383
These compounds were docked into PPARα (pdb 1I7G), PPARγ (pdb 2PRG), and PPARδ (pdb 2ZNP), respectively, screening out 23 compounds with higher docking scores and better bindin... poses than the original ligands.
Materials and methods Preparation of PPAR receptors structures The crystal structures of PPARα, PPARγ, and PPARδ receptors were downloaded from the Protein Data Bank (PDB) with PDB identification numbers 1I7G, 2PRG, and 2ZNP, respectively.
Structural basis for PPAR? transactivation by endocrine-disrupting organotin compounds.
(2015) Sci Rep 5
PubMed: 25687586 | PubMedCentral: PMC4330522 | DOI: 10.1038/srep08520
The structure of chain A assumed an “active” conformation that was found in the PPARγ-LBD/agonist/co-activator peptide complex (PDB No. 2PRG) 16 , where helix 12 (H12) of LBD e... ists in a position suitable to interact with the agonist and to form the binding site of the co-activator.
Publication Year: 2015
PubMed ID is not available.
Published in 2015
Figure 2 PPARγ FragMaps overlaid on the LBP of PPARγ (PDB 3U9Q) with ligands A) decanoic acid, B) Rosiglitazone (PDB: 2PRG,) C) GW409544 (PDB: 1K74), and D) Cerco-A (PDB: 3B1M) in thei... crystallographic orientations; receptor atoms occluding the view of the binding pocket were removed to facilitate visualization.
The predicted binding mode included two hydrogen bonds, a π-π stacking interaction, and several van der Waals forces with the surrounding amino acids such as Cys285, Met364, Ile326, Le... 330, Met329, and Ile281 ( Figure 7a and 7b ), which varied widely from that of rosiglitazone ( Figure 7c and 7d , PDB code 2PRG 37 ).
Molecular modeling studies using nuclear PPAR-γ as molecular target available on the PDB database as 2PRG, suggested that LPSF/GQ-02 is a PPARγligand [ 25 ].
Asterisks denote residues in contact with TBBPA and/or rosiglitazone (PDB code 2PRG).
(B) TBBPA (carbon atoms colored in green) and rosiglitazone (magenta, PDB code 2PRG) as they are positioned in the human PPARγ.
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