6k5o - Revision history

OCA at 10:26, 22 November 2023

OCA — Wed, 22 Nov 2023 10:26:59 GMT

←Older revision		Revision as of 10:26, 22 November 2023
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	<StructureSection load='6k5o' size='340' side='right'caption='[[6k5o]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6k5o' size='340' side='right'caption='[[6k5o]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k5o]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K5O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k5o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K5O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D0O:(4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic+acid'>D0O</scene>~~</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]] 1.8Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D0O:(4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic+acid'>D0O</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6k5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5o OCA], [~~http~~://pdbe.org/6k5o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k5o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k5o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5o ProSAT]</span></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=6k5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5o OCA], [https://pdbe.org/6k5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k5o RCSB], [https://www.ebi.ac.uk/pdbsum/6k5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref> [[http://www.uniprot.org/uniprot/MED1_HUMAN MED1_HUMAN]] Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.<ref>PMID:9653119</ref> <ref>PMID:10406464</ref> <ref>PMID:12218053</ref> <ref>PMID:12037571</ref> <ref>PMID:11867769</ref> <ref>PMID:12556447</ref> <ref>PMID:14636573</ref> <ref>PMID:15471764</ref> <ref>PMID:15340084</ref> <ref>PMID:15989967</ref> <ref>PMID:16574658</ref>	+	[https://www.uniprot.org/uniprot/VDR_RAT VDR_RAT] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6k5o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6k5o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Vitamin D receptor 3D structures\|Vitamin D receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ito, N~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Kagechika, H~~]]	+	[[Category: Ito N]]
-	[[Category: ~~Masuno,~~ H]]	+	[[Category: Kagechika H]]
-	[[Category: ~~Transcription]]~~	+	[[Category: Masuno H]]
-	~~[[Category: Vitamin d receptor~~]]	+

OCA at 17:23, 14 August 2019

OCA — Wed, 14 Aug 2019 17:23:21 GMT

←Older revision		Revision as of 17:23, 14 August 2019
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	<StructureSection load='6k5o' size='340' side='right'caption='[[6k5o]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6k5o' size='340' side='right'caption='[[6k5o]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k5o]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K5O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k5o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K5O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D0O:(4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic+acid'>D0O</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D0O:(4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic+acid'>D0O</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6k5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5o OCA], [http://pdbe.org/6k5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k5o RCSB], [http://www.ebi.ac.uk/pdbsum/6k5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5o ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6k5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5o OCA], [http://pdbe.org/6k5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k5o RCSB], [http://www.ebi.ac.uk/pdbsum/6k5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5o ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ito, N]]		[[Category: Ito, N]]

OCA at 06:14, 24 July 2019

OCA — Wed, 24 Jul 2019 06:14:10 GMT

←Older revision		Revision as of 06:14, 24 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6k5o is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Development of Novel Lithocholic Acid Derivatives as Vitamin D Receptor Agonists==
		+	<StructureSection load='6k5o' size='340' side='right'caption='[[6k5o]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6k5o]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K5O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K5O FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D0O:(4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic+acid'>D0O</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6k5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k5o OCA], [http://pdbe.org/6k5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k5o RCSB], [http://www.ebi.ac.uk/pdbsum/6k5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k5o ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref> [[http://www.uniprot.org/uniprot/MED1_HUMAN MED1_HUMAN]] Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.<ref>PMID:9653119</ref> <ref>PMID:10406464</ref> <ref>PMID:12218053</ref> <ref>PMID:12037571</ref> <ref>PMID:11867769</ref> <ref>PMID:12556447</ref> <ref>PMID:14636573</ref> <ref>PMID:15471764</ref> <ref>PMID:15340084</ref> <ref>PMID:15989967</ref> <ref>PMID:16574658</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lithocholic acid (2) was identified as the second endogenous ligand of vitamin D receptor (VDR), though its binding affinity to VDR and its vitamin D activity are very weak compared to those of the active metabolite of vitamin D3, 1alpha,25-dihydroxyvitamin D3 (1). 3-Acylated lithocholic acids were reported to be slightly more potent than lithocholic acid (2) as VDR agonists. Here, aiming to develop more potent lithocholic acid derivatives, we synthesized several derivatives bearing a 3-sulfonate/carbonate or 3-amino/amide substituent, and examined their differentiation-inducing activity toward human promyelocytic leukemia HL-60 cells. Introduction of a nitrogen atom at the 3-position of lithocholic acid (2) decreased the activity, but compound 6 bearing a 3-methylsulfonate group showed more potent activity than lithocholic acid (2) or its acylated derivatives. The binding of 6 to VDR was confirmed by competitive binding assay and X-ray crystallographic analysis of the complex of VDR ligand-binding domain (LBD) with 6.

-	~~Authors: Masuno~~, H., ~~Kagechika~~, H., ~~Ito~~, N.	+	Development of novel lithocholic acid derivatives as vitamin D receptor agonists.,Masuno H, Kazui Y, Tanatani A, Fujii S, Kawachi E, Ikura T, Ito N, Yamamoto K, Kagechika H Bioorg Med Chem. 2019 Jul 3. pii: S0968-0896(19)30931-9. doi:, 10.1016/j.bmc.2019.07.003. PMID:31300316<ref>PMID:31300316</ref>

-	~~Description: Development~~ of ~~Novel Lithocholic Acid Derivatives as Vitamin D Receptor Agonists~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6k5o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ito, N]]		[[Category: Ito, N]]
	[[Category: Kagechika, H]]		[[Category: Kagechika, H]]
	[[Category: Masuno, H]]		[[Category: Masuno, H]]
		+	[[Category: Transcription]]
		+	[[Category: Vitamin d receptor]]

OCA at 05:03, 26 June 2019

OCA — Wed, 26 Jun 2019 05:03:53 GMT

←Older revision		Revision as of 05:03, 26 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k5o is ON HOLD	+	The entry 6k5o is ON HOLD until Paper Publication

	Authors: Masuno, H., Kagechika, H., Ito, N.		Authors: Masuno, H., Kagechika, H., Ito, N.
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	Description: Development of Novel Lithocholic Acid Derivatives as Vitamin D Receptor Agonists		Description: Development of Novel Lithocholic Acid Derivatives as Vitamin D Receptor Agonists
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Masuno, H]]
	[[Category: Ito, N]]		[[Category: Ito, N]]
	[[Category: Kagechika, H]]		[[Category: Kagechika, H]]
		+	[[Category: Masuno, H]]

OCA: Protected "6k5o" [edit=sysop:move=sysop]

OCA — Wed, 05 Jun 2019 21:02:23 GMT

Protected "6k5o" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:02, 5 June 2019

OCA: New page: '''Unreleased structure''' The entry 6k5o is ON HOLD Authors: Masuno, H., Kagechika, H., Ito, N. Description: Development of Novel Lithocholic Acid Derivatives as Vitamin D Receptor Ag...

OCA — Wed, 05 Jun 2019 21:02:21 GMT

New page: '''Unreleased structure''' The entry 6k5o is ON HOLD Authors: Masuno, H., Kagechika, H., Ito, N. Description: Development of Novel Lithocholic Acid Derivatives as Vitamin D Receptor Ag...

New page

'''Unreleased structure'''

The entry 6k5o is ON HOLD

Authors: Masuno, H., Kagechika, H., Ito, N.

Description: Development of Novel Lithocholic Acid Derivatives as Vitamin D Receptor Agonists
[[Category: Unreleased Structures]]
[[Category: Masuno, H]]
[[Category: Ito, N]]
[[Category: Kagechika, H]]