3vtd - Revision history

OCA at 12:37, 8 November 2023

OCA — Wed, 08 Nov 2023 12:37:13 GMT

←Older revision		Revision as of 12:37, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='3vtd' size='340' side='right'caption='[[3vtd]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3vtd' size='340' side='right'caption='[[3vtd]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vtd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VTD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vtd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VTD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TKD:(1R,3R,7E,17BETA)-17-{(2R,6S)-6-HYDROXY-7-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEPT-4-YN-2-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>TKD</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]] 2.7Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zlc\|2zlc]], [[3vtb\|3vtb]], [[3vtc\|3vtc]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TKD:(1R,3R,7E,17BETA)-17-{(2R,6S)-6-HYDROXY-7-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEPT-4-YN-2-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>TKD</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3vtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtd OCA], [https://pdbe.org/3vtd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vtd RCSB], [https://www.ebi.ac.uk/pdbsum/3vtd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vtd 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=3vtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtd OCA], [https://pdbe.org/3vtd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vtd RCSB], [https://www.ebi.ac.uk/pdbsum/3vtd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vtd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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>	+	[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 ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ikura, T]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Ito, N]]	+	[[Category: Ikura T]]
-	[[Category: Kudo, T]]	+	[[Category: Ito N]]
-	[[Category: Makishima, M]]	+	[[Category: Kudo T]]
-	[[Category: Nakabayashi, M]]	+	[[Category: Makishima M]]
-	[[Category: Tokiwa, H]]	+	[[Category: Nakabayashi M]]
-	[[Category: Yamada, S]]	+	[[Category: Tokiwa H]]
-	~~[[Category: Hormone receptor]]~~	+	[[Category: Yamada S]]
-	~~[[Category: Transcription~~]]	+

OCA at 19:03, 27 July 2022

OCA — Wed, 27 Jul 2022 19:03:14 GMT

←Older revision		Revision as of 19:03, 27 July 2022
Line 1:		Line 1:

	==Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4==		==Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4==
-	<StructureSection load='3vtd' size='340' side='right' caption='[[3vtd]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='3vtd' size='340' side='right'caption='[[3vtd]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vtd]] 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=3VTD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VTD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vtd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VTD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TKD:(1R,3R,7E,17BETA)-17-{(2R,6S)-6-HYDROXY-7-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEPT-4-YN-2-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>TKD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TKD:(1R,3R,7E,17BETA)-17-{(2R,6S)-6-HYDROXY-7-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEPT-4-YN-2-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>TKD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zlc\|2zlc]], [[3vtb\|3vtb]], [[3vtc\|3vtc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zlc\|2zlc]], [[3vtb\|3vtb]], [[3vtc\|3vtc]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([https://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=3vtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtd OCA], [~~http~~://pdbe.org/3vtd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vtd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vtd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vtd 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=3vtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtd OCA], [https://pdbe.org/3vtd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vtd RCSB], [https://www.ebi.ac.uk/pdbsum/3vtd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vtd 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>	+	[[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 ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Ikura, T]]		[[Category: Ikura, T]]
	[[Category: Ito, N]]		[[Category: Ito, N]]

OCA at 12:03, 5 August 2016

OCA — Fri, 05 Aug 2016 12:03:01 GMT

←Older revision		Revision as of 12:03, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4==		==Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4==
	<StructureSection load='3vtd' size='340' side='right' caption='[[3vtd]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3vtd' size='340' side='right' caption='[[3vtd]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zlc\|2zlc]], [[3vtb\|3vtb]], [[3vtc\|3vtc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zlc\|2zlc]], [[3vtb\|3vtb]], [[3vtc\|3vtc]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([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=3vtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vtd RCSB], [http://www.ebi.ac.uk/pdbsum/3vtd PDBsum]</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=3vtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtd OCA], [http://pdbe.org/3vtd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vtd RCSB], [http://www.ebi.ac.uk/pdbsum/3vtd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vtd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3vtd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:40, 25 December 2014

OCA — Thu, 25 Dec 2014 18:40:13 GMT

←Older revision		Revision as of 18:40, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='3vtd' size='340' side='right' caption='[[3vtd]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3vtd' size='340' side='right' caption='[[3vtd]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vtd]] 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=3VTD OCA]. <br>	+	<table><tr><td colspan='2'>[[3vtd]] 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=3VTD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VTD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TKD:(1R,3R,7E,17BETA)-17-{(2R,6S)-6-HYDROXY-7-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEPT-4-YN-2-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>TKD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TKD:(1R,3R,7E,17BETA)-17-{(2R,6S)-6-HYDROXY-7-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEPT-4-YN-2-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>TKD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zlc\|2zlc]], [[3vtb\|3vtb]], [[3vtc\|3vtc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zlc\|2zlc]], [[3vtb\|3vtb]], [[3vtc\|3vtc]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=3vtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vtd RCSB], [http://www.ebi.ac.uk/pdbsum/3vtd PDBsum]</span></td></tr>
-	~~<tr~~><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vtd RCSB], [http://www.ebi.ac.uk/pdbsum/3vtd PDBsum]</span></td></tr>	+	</table>
-	<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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 16:
	Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.,Kudo T, Ishizawa M, Maekawa K, Nakabayashi M, Watarai Y, Uchida H, Tokiwa H, Ikura T, Ito N, Makishima M, Yamada S J Med Chem. 2014 May 7. PMID:24773565<ref>PMID:24773565</ref>		Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.,Kudo T, Ishizawa M, Maekawa K, Nakabayashi M, Watarai Y, Uchida H, Tokiwa H, Ikura T, Ito N, Makishima M, Yamada S J Med Chem. 2014 May 7. PMID:24773565<ref>PMID:24773565</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 22:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
-	[[Category: Ikura, T.]]	+	[[Category: Ikura, T]]
-	[[Category: Ito, N.]]	+	[[Category: Ito, N]]
-	[[Category: Kudo, T.]]	+	[[Category: Kudo, T]]
-	[[Category: Makishima, M.]]	+	[[Category: Makishima, M]]
-	[[Category: Nakabayashi, M.]]	+	[[Category: Nakabayashi, M]]
-	[[Category: Tokiwa, H.]]	+	[[Category: Tokiwa, H]]
-	[[Category: Yamada, S.]]	+	[[Category: Yamada, S]]
	[[Category: Hormone receptor]]		[[Category: Hormone receptor]]
	[[Category: Transcription]]		[[Category: Transcription]]

OCA at 06:37, 14 May 2014

OCA — Wed, 14 May 2014 06:37:28 GMT

←Older revision		Revision as of 06:37, 14 May 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3vtd\| PDB=3vtd \| SCENE= }}~~	+	==Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4==
-	===Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4===	+	<StructureSection load='3vtd' size='340' side='right' caption='[[3vtd]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3vtd]] 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=3VTD OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TKD:(1R,3R,7E,17BETA)-17-{(2R,6S)-6-HYDROXY-7-[(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]HEPT-4-YN-2-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>TKD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zlc\|2zlc]], [[3vtb\|3vtb]], [[3vtc\|3vtc]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nr1i1, Vdr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vtd RCSB], [http://www.ebi.ac.uk/pdbsum/3vtd PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Vitamin D receptor (VDR) ligands are therapeutic agents that are used for the treatment of psoriasis, osteoporosis, and secondary hyperparathyroidism and have immense potential as therapeutic agents for autoimmune diseases, cancers, and cardiovascular diseases. However, the major side effect of VDR ligands, the development of hypercalcemia, limits their expanded use. To develop tissue-selective VDR modulators, we have designed vitamin D analogues with an adamantane ring at the side chain terminal, which would interfere with helix 12, the activation function 2, and modulate the VDR potency. Here we report 25- or 26-adamantyl-23,23,24,24-tetradehydro-19-norvitamin D derivatives (ADTK1-4, 4b,a and 5a,b). These compounds showed high VDR affinities (90% at maximum), partial agonistic activities (EC50 10-9-10-8 M with 40-80% efficacy) in transactivation, and tissue-selective activity in target gene expressions. We investigate the structure-activity relationships of these compounds on the basis of their X-ray crystal structures.

-	~~==Function==~~	+	Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.,Kudo T, Ishizawa M, Maekawa K, Nakabayashi M, Watarai Y, Uchida H, Tokiwa H, Ikura T, Ito N, Makishima M, Yamada S J Med Chem. 2014 May 7. PMID:24773565<ref>PMID:24773565</ref>
-	~~[[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>	+

-	~~==About this Structure==~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3vtd]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3VTD OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
-	[[Category: ~~Rattus norvegicus~~]]	+	</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Ikura, T.]]		[[Category: Ikura, T.]]
	[[Category: Ito, N.]]		[[Category: Ito, N.]]

OCA at 21:01, 19 June 2013

OCA — Wed, 19 Jun 2013 21:01:31 GMT

←Older revision		Revision as of 21:01, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3vtd\| PDB=3vtd \| SCENE= }}
		+	===Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4===

-	~~The entry 3vtd is ON HOLD~~ ~~until Paper Publication~~	+	==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>

-	~~Authors~~: ~~Nakabayashi, M~~.~~, Kudo, T~~.~~, Tokiwa, H~~.~~, Makishima, M~~.~~, Yamada, S~~.~~, Ikura, T~~.~~, Ito, N~~.	+	==About this Structure==
		+	[[3vtd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTD OCA].

-	~~Description~~: ~~Crystal structure of rat vitamin D~~ receptor ~~bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Rattus norvegicus]]
		+	[[Category: Ikura, T.]]
		+	[[Category: Ito, N.]]
		+	[[Category: Kudo, T.]]
		+	[[Category: Makishima, M.]]
		+	[[Category: Nakabayashi, M.]]
		+	[[Category: Tokiwa, H.]]
		+	[[Category: Yamada, S.]]
		+	[[Category: Hormone receptor]]
		+	[[Category: Transcription]]

OCA at 04:40, 5 September 2012

OCA — Wed, 05 Sep 2012 04:40:52 GMT

←Older revision		Revision as of 04:40, 5 September 2012
Line 3:		Line 3:
	The entry 3vtd is ON HOLD until Paper Publication		The entry 3vtd is ON HOLD until Paper Publication

-	Authors: Nakabayashi, M., Kudo, T., Tokiwa, H., Makishima, M., Yamada, T., Ikura, T., Ito, N.	+	Authors: Nakabayashi, M., Kudo, T., Tokiwa, H., Makishima, M., Yamada, S., Ikura, T., Ito, N.

	Description: Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4		Description: Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4

OCA at 04:51, 18 July 2012

OCA — Wed, 18 Jul 2012 04:51:19 GMT

←Older revision		Revision as of 04:51, 18 July 2012
Line 3:		Line 3:
	The entry 3vtd is ON HOLD until Paper Publication		The entry 3vtd is ON HOLD until Paper Publication

-	Authors: Nakabayashi, M., ~~Shimizu~~, M., Ikura, T., Ito, N.	+	Authors: Nakabayashi, M., Kudo, T., Tokiwa, H., Makishima, M., Yamada, T., Ikura, T., Ito, N.

	Description: Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4		Description: Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4

OCA at 05:12, 27 June 2012

OCA — Wed, 27 Jun 2012 05:12:44 GMT

←Older revision		Revision as of 05:12, 27 June 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3vtd is ON HOLD	+	The entry 3vtd is ON HOLD until Paper Publication

	Authors: Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.		Authors: Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

	Description: Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4		Description: Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4

OCA at 05:36, 13 June 2012

OCA — Wed, 13 Jun 2012 05:36:43 GMT

←Older revision		Revision as of 05:36, 13 June 2012
Line 3:		Line 3:
	The entry 3vtd is ON HOLD		The entry 3vtd is ON HOLD

-	Authors: Nakabayashi M., ~~Kudoh T., Tokiwa H.~~, ~~Makishima~~ M., ~~Yamada S.~~, ~~Ikura~~ T., Ito N.	+	Authors: Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

	Description: Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4		Description: Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4