5zwi - Revision history

OCA at 10:29, 27 March 2024

OCA — Wed, 27 Mar 2024 10:29:19 GMT

←Older revision		Revision as of 10:29, 27 March 2024
Line 1:		Line 1:

	==Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group==		==Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group==
-	<StructureSection load='5zwi' size='340' side='right' caption='[[5zwi]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5zwi' size='340' side='right'caption='[[5zwi]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zwi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZWI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZWI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zwi]] 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=5ZWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZWI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9KX:(2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one'>9KX</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]] 2.4Å</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=9KX:(2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one'>9KX</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=5zwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zwi OCA], [~~http~~://pdbe.org/5zwi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zwi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zwi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zwi 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=5zwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zwi OCA], [https://pdbe.org/5zwi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zwi RCSB], [https://www.ebi.ac.uk/pdbsum/5zwi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zwi 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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	We designed and synthesized vitamin D analogues with an electrophile as covalent modifiers for the vitamin D receptor (VDR). Novel vitamin D analogues 1-4 have an electrophilic enone group at the side chain for conjugate addition to His301 or His393 in the VDR. All compounds showed specific VDR-binding potency and agonistic activity. Covalent bond formations of 1-4 with the ligand-binding domain (LBD) of VDR were evaluated by electrospray ionization mass spectrometry. All compounds were shown to covalently bind to the VDR-LBD, and the abundance of VDR-LBD corresponding conjugate adducts of 1-4 increased with incubation time. Enone compounds 1 and 2 showed higher reactivity than the ene-ynone 3 and dienone 4 compounds. Furthermore, we successfully obtained cocrystals of VDR-LBD with analogues 1-4. X-ray crystallographic analysis showed a covalent bond with His301 in VDR-LBD. We successfully synthesized vitamin D analogues that form a covalent bond with VDR-LBD.	+

-	Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands.,Yoshizawa M, Itoh T, Hori T, Kato A, Anami Y, Yoshimoto N, Yamamoto K J Med Chem. 2018 Jul 11. doi: 10.1021/acs.jmedchem.8b00774. PMID:29936834<ref>PMID:29936834</ref>	+	==See Also==
-		+	*[[Vitamin D receptor 3D structures\|Vitamin D receptor 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 5zwi" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Anami, Y]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Itoh, T]]	+	[[Category: Anami Y]]
-	[[Category: Kato, A]]	+	[[Category: Itoh T]]
-	[[Category: Yamamoto, K]]	+	[[Category: Kato A]]
-	[[Category: Yoshimoto, N]]	+	[[Category: Yamamoto K]]
-	[[Category: Yoshizawa, M]]	+	[[Category: Yoshimoto N]]
-	~~[[Category: Hormone]]~~	+	[[Category: Yoshizawa M]]
-	~~[[Category: Hormone covalent modifier transcription factor vitamind3 enone michael addition electrophile~~]]	+

OCA at 22:06, 9 August 2018

OCA — Thu, 09 Aug 2018 22:06:02 GMT

←Older revision		Revision as of 22:06, 9 August 2018
Line 3:		Line 3:
	<StructureSection load='5zwi' size='340' side='right' caption='[[5zwi]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5zwi' size='340' side='right' caption='[[5zwi]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zwi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZWI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zwi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZWI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9KX:(2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one'>9KX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9KX:(2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one'>9KX</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=5zwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zwi OCA], [http://pdbe.org/5zwi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zwi RCSB], [http://www.ebi.ac.uk/pdbsum/5zwi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zwi 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=5zwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zwi OCA], [http://pdbe.org/5zwi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zwi RCSB], [http://www.ebi.ac.uk/pdbsum/5zwi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zwi ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
		+	[[Category: Human]]
	[[Category: Anami, Y]]		[[Category: Anami, Y]]
	[[Category: Itoh, T]]		[[Category: Itoh, T]]

OCA at 07:33, 18 July 2018

OCA — Wed, 18 Jul 2018 07:33:07 GMT

←Older revision		Revision as of 07:33, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zwi is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group==
		+	<StructureSection load='5zwi' size='340' side='right' caption='[[5zwi]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zwi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZWI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9KX:(2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one'>9KX</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=5zwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zwi OCA], [http://pdbe.org/5zwi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zwi RCSB], [http://www.ebi.ac.uk/pdbsum/5zwi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zwi 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We designed and synthesized vitamin D analogues with an electrophile as covalent modifiers for the vitamin D receptor (VDR). Novel vitamin D analogues 1-4 have an electrophilic enone group at the side chain for conjugate addition to His301 or His393 in the VDR. All compounds showed specific VDR-binding potency and agonistic activity. Covalent bond formations of 1-4 with the ligand-binding domain (LBD) of VDR were evaluated by electrospray ionization mass spectrometry. All compounds were shown to covalently bind to the VDR-LBD, and the abundance of VDR-LBD corresponding conjugate adducts of 1-4 increased with incubation time. Enone compounds 1 and 2 showed higher reactivity than the ene-ynone 3 and dienone 4 compounds. Furthermore, we successfully obtained cocrystals of VDR-LBD with analogues 1-4. X-ray crystallographic analysis showed a covalent bond with His301 in VDR-LBD. We successfully synthesized vitamin D analogues that form a covalent bond with VDR-LBD.

-	~~Authors: Yoshizawa~~, M., Itoh, T~~., Anami, Y.~~, Kato, A., ~~Yoshimoto~~, N., Yamamoto, K.	+	Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands.,Yoshizawa M, Itoh T, Hori T, Kato A, Anami Y, Yoshimoto N, Yamamoto K J Med Chem. 2018 Jul 11. doi: 10.1021/acs.jmedchem.8b00774. PMID:29936834<ref>PMID:29936834</ref>

-	~~Description: Interaction between Vitamin D receptor (VDR) and~~ a ~~ligand having a dienone group~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Yamamoto, K]]~~	+	<div class="pdbe-citations 5zwi" style="background-color:#fffaf0;"></div>
-	~~[[Category: Itoh, T]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Anami, Y]]		[[Category: Anami, Y]]
		+	[[Category: Itoh, T]]
	[[Category: Kato, A]]		[[Category: Kato, A]]
		+	[[Category: Yamamoto, K]]
	[[Category: Yoshimoto, N]]		[[Category: Yoshimoto, N]]
	[[Category: Yoshizawa, M]]		[[Category: Yoshizawa, M]]
		+	[[Category: Hormone]]
		+	[[Category: Hormone covalent modifier transcription factor vitamind3 enone michael addition electrophile]]

OCA at 03:52, 11 July 2018

OCA — Wed, 11 Jul 2018 03:52:54 GMT

←Older revision		Revision as of 03:52, 11 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zwi is ON HOLD	+	The entry 5zwi is ON HOLD until Paper Publication

	Authors: Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K.		Authors: Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K.

OCA at 03:52, 30 May 2018

OCA — Wed, 30 May 2018 03:52:51 GMT

←Older revision		Revision as of 03:52, 30 May 2018
Line 5:		Line 5:
	Authors: Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K.		Authors: Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K.

-	Description: Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group.	+	Description: Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yamamoto, K]]		[[Category: Yamamoto, K]]
-	[[Category: Anami, Y]]
	[[Category: Itoh, T]]		[[Category: Itoh, T]]
		+	[[Category: Anami, Y]]
	[[Category: Kato, A]]		[[Category: Kato, A]]
	[[Category: Yoshimoto, N]]		[[Category: Yoshimoto, N]]
	[[Category: Yoshizawa, M]]		[[Category: Yoshizawa, M]]

OCA: Protected "5zwi" [edit=sysop:move=sysop]

OCA — Wed, 23 May 2018 05:52:55 GMT

Protected "5zwi" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:52, 23 May 2018

OCA: New page: '''Unreleased structure''' The entry 5zwi is ON HOLD Authors: Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K. Description: Interaction between Vitamin D recep...

OCA — Wed, 23 May 2018 05:52:54 GMT

New page: '''Unreleased structure''' The entry 5zwi is ON HOLD Authors: Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K. Description: Interaction between Vitamin D recep...

New page

'''Unreleased structure'''

The entry 5zwi is ON HOLD

Authors: Yoshizawa, M., Itoh, T., Anami, Y., Kato, A., Yoshimoto, N., Yamamoto, K.

Description: Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group.
[[Category: Unreleased Structures]]
[[Category: Yamamoto, K]]
[[Category: Anami, Y]]
[[Category: Itoh, T]]
[[Category: Kato, A]]
[[Category: Yoshimoto, N]]
[[Category: Yoshizawa, M]]