OCA at 17:40, 29 November 2023

OCA — Wed, 29 Nov 2023 17:40:38 GMT

←Older revision		Revision as of 17:40, 29 November 2023
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	==X-ray structure of human PPAR delta ligand binding domain-pemafibrate co-crystals obtained by co-crystallization==		==X-ray structure of human PPAR delta ligand binding domain-pemafibrate co-crystals obtained by co-crystallization==
-	<StructureSection load='7wgn' size='340' side='right'caption='[[7wgn]]' scene=''>	+	<StructureSection load='7wgn' size='340' side='right'caption='[[7wgn]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WGN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7wgn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WGN FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7wgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wgn OCA], [https://pdbe.org/7wgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wgn RCSB], [https://www.ebi.ac.uk/pdbsum/7wgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wgn ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.813Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=P7F:(2~{R})-2-[3-[[1,3-benzoxazol-2-yl-[3-(4-methoxyphenoxy)propyl]amino]methyl]phenoxy]butanoic+acid'>P7F</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7wgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wgn OCA], [https://pdbe.org/7wgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wgn RCSB], [https://www.ebi.ac.uk/pdbsum/7wgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wgn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PPARD_HUMAN PPARD_HUMAN] Ligand-activated transcription factor. Receptor that binds peroxisome proliferators such as hypolipidemic drugs and fatty acids. Has a preference for poly-unsaturated fatty acids, such as gamma-linoleic acid and eicosapentanoic acid. Once activated by a ligand, the receptor binds to promoter elements of target genes. Regulates the peroxisomal beta-oxidation pathway of fatty acids. Functions as transcription activator for the acyl-CoA oxidase gene. Decreases expression of NPC1L1 once activated by a ligand.<ref>PMID:1333051</ref> <ref>PMID:15604518</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Among the agonists against three peroxisome proliferator-activated receptor (PPAR) subtypes, those against PPARalpha (fibrates) and PPARgamma (glitazones) are currently used to treat dyslipidemia and type 2 diabetes, respectively, whereas PPARdelta agonists are expected to be the next-generation metabolic disease drug. In addition, some dual/pan PPAR agonists are currently being investigated via clinical trials as one of the first curative drugs against nonalcoholic fatty liver disease (NAFLD). Because PPARalpha/delta/gamma share considerable amino acid identity and three-dimensional structures, especially in ligand-binding domains (LBDs), clinically approved fibrates, such as bezafibrate, fenofibric acid, and pemafibrate, could also act on PPARdelta/gamma when used as anti-NAFLD drugs. Therefore, this study examined their PPARalpha/delta/gamma selectivity using three independent assays-a dual luciferase-based GAL4 transactivation assay for COS-7 cells, time-resolved fluorescence resonance energy transfer-based coactivator recruitment assay, and circular dichroism spectroscopy-based thermostability assay. Although the efficacy and efficiency highly varied between agonists, assay types, and PPAR subtypes, the three fibrates, except fenofibric acid that did not affect PPARdelta-mediated transactivation and coactivator recruitment, activated all PPAR subtypes in those assays. Furthermore, we aimed to obtain cocrystal structures of PPARdelta/gamma-LBD and the three fibrates via X-ray diffraction and versatile crystallization methods, which we recently used to obtain 34 structures of PPARalpha-LBD cocrystallized with 17 ligands, including the fibrates. We herein reveal five novel high-resolution structures of PPARdelta/gamma-bezafibrate, PPARgamma-fenofibric acid, and PPARdelta/gamma-pemafibrate, thereby providing the molecular basis for their application beyond dyslipidemia treatment.
		+
		+	Functional and Structural Insights into Human PPARalpha/delta/gamma Subtype Selectivity of Bezafibrate, Fenofibric Acid, and Pemafibrate.,Honda A, Kamata S, Akahane M, Machida Y, Uchii K, Shiiyama Y, Habu Y, Miyawaki S, Kaneko C, Oyama T, Ishii I Int J Mol Sci. 2022 Apr 25;23(9). pii: ijms23094726. doi: 10.3390/ijms23094726. PMID:35563117<ref>PMID:35563117</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7wgn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Peroxisome proliferator-activated receptor 3D structures\|Peroxisome proliferator-activated receptor 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Akahane M]]		[[Category: Akahane M]]

OCA at 08:00, 25 May 2022

OCA — Wed, 25 May 2022 08:00:19 GMT

←Older revision		Revision as of 08:00, 25 May 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7wgn is ~~ON HOLD until Paper Publication~~	+	==X-ray structure of human PPAR delta ligand binding domain-pemafibrate co-crystals obtained by co-crystallization==
-		+	<StructureSection load='7wgn' size='340' side='right'caption='[[7wgn]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WGN FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7wgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wgn OCA], [https://pdbe.org/7wgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wgn RCSB], [https://www.ebi.ac.uk/pdbsum/7wgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wgn ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Akahane M]]
		+	[[Category: Honda A]]
		+	[[Category: Ishii I]]
		+	[[Category: Kamata S]]
		+	[[Category: Machida Y]]
		+	[[Category: Masuda R]]
		+	[[Category: Oyama T]]
		+	[[Category: Shiiyama Y]]
		+	[[Category: Uchii K]]

OCA at 06:25, 9 February 2022

OCA — Wed, 09 Feb 2022 06:25:35 GMT

←Older revision		Revision as of 06:25, 9 February 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7wgn is ON HOLD	+	The entry 7wgn is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7wgn" [edit=sysop:move=sysop]

OCA — Wed, 05 Jan 2022 09:28:35 GMT

Protected "7wgn" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:28, 5 January 2022

OCA: New page: '''Unreleased structure''' The entry 7wgn is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Jan 2022 09:28:34 GMT

New page: '''Unreleased structure''' The entry 7wgn is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7wgn is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7wgn - Revision history

OCA at 17:40, 29 November 2023

OCA at 08:00, 25 May 2022

OCA at 06:25, 9 February 2022

OCA: Protected "7wgn" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7wgn is ON HOLD Authors: Description: Category: Unreleased Structures