5h1u - Revision history

OCA at 07:21, 9 August 2023

OCA — Wed, 09 Aug 2023 07:21:12 GMT

←Older revision		Revision as of 07:21, 9 August 2023
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	==Complex structure of TRIM24 PHD-bromodomain and inhibitor 2==		==Complex structure of TRIM24 PHD-bromodomain and inhibitor 2==
-	<StructureSection load='5h1u' size='340' side='right' caption='[[5h1u]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5h1u' size='340' side='right'caption='[[5h1u]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h1u]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h1u]] is a 4 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=5H1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H1U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6KT:2-AMINO-1,3-BENZOTHIAZOLE-6-CARBOXAMIDE'>6KT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.901Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h1t\|5h1t]], [[5h1v\|5h1v]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6KT:2-AMINO-1,3-BENZOTHIAZOLE-6-CARBOXAMIDE'>6KT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRIM24, RNF82, TIF1, TIF1A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5h1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1u OCA], [https://pdbe.org/5h1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h1u RCSB], [https://www.ebi.ac.uk/pdbsum/5h1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1u 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=5h1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1u OCA], [~~http~~://pdbe.org/5h1u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h1u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h1u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1u ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/TIF1A_HUMAN TIF1A_HUMAN]] Defects in TRIM24 are a cause of thyroid papillary carcinoma (TPC) [MIM:[~~http~~://omim.org/entry/188550 188550]]. TPC is a common tumor of the thyroid that typically arises as an irregular, solid or cystic mass from otherwise normal thyroid tissue. Papillary carcinomas are malignant neoplasm characterized by the formation of numerous, irregular, finger-like projections of fibrous stroma that is covered with a surface layer of neoplastic epithelial cells. Note=A chromosomal aberration involving TRIM24/TIF1 is found in thyroid papillary carcinomas. Translocation t(7;10)(q32;q11) with RET. The translocation generates the TRIM24/RET (PTC6) oncogene.	+	[https://www.uniprot.org/uniprot/TIF1A_HUMAN TIF1A_HUMAN] Defects in TRIM24 are a cause of thyroid papillary carcinoma (TPC) [MIM:[https://omim.org/entry/188550 188550]. TPC is a common tumor of the thyroid that typically arises as an irregular, solid or cystic mass from otherwise normal thyroid tissue. Papillary carcinomas are malignant neoplasm characterized by the formation of numerous, irregular, finger-like projections of fibrous stroma that is covered with a surface layer of neoplastic epithelial cells. Note=A chromosomal aberration involving TRIM24/TIF1 is found in thyroid papillary carcinomas. Translocation t(7;10)(q32;q11) with RET. The translocation generates the TRIM24/RET (PTC6) oncogene.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TIF1A_HUMAN TIF1A_HUMAN]] Transcriptional coactivator that interacts with numerous nuclear receptors and coactivators and modulates the transcription of target genes. Interacts with chromatin depending on histone H3 modifications, having the highest affinity for histone H3 that is both unmodified at 'Lys-4' (H3K4me0) and acetylated at 'Lys-23' (H3K23ac). Has E3 protein-ubiquitin ligase activity. Promotes ubiquitination and proteasomal degradation of p53/TP53. Plays a role in the regulation of cell proliferation and apoptosis, at least in part via its effects on p53/TP53 levels. Up-regulates ligand-dependent transcription activation by AR, GCR/NR3C1, thyroid hormone receptor (TR) and ESR1. Modulates transcription activation by retinoic acid (RA) receptors, including RARA. Plays a role in regulating retinoic acid-dependent proliferation of hepatocytes (By similarity).<ref>PMID:16322096</ref> <ref>PMID:19556538</ref> <ref>PMID:21164480</ref>	+	[https://www.uniprot.org/uniprot/TIF1A_HUMAN TIF1A_HUMAN] Transcriptional coactivator that interacts with numerous nuclear receptors and coactivators and modulates the transcription of target genes. Interacts with chromatin depending on histone H3 modifications, having the highest affinity for histone H3 that is both unmodified at 'Lys-4' (H3K4me0) and acetylated at 'Lys-23' (H3K23ac). Has E3 protein-ubiquitin ligase activity. Promotes ubiquitination and proteasomal degradation of p53/TP53. Plays a role in the regulation of cell proliferation and apoptosis, at least in part via its effects on p53/TP53 levels. Up-regulates ligand-dependent transcription activation by AR, GCR/NR3C1, thyroid hormone receptor (TR) and ESR1. Modulates transcription activation by retinoic acid (RA) receptors, including RARA. Plays a role in regulating retinoic acid-dependent proliferation of hepatocytes (By similarity).<ref>PMID:16322096</ref> <ref>PMID:19556538</ref> <ref>PMID:21164480</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Liu, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Transcription transcription inhibitor]]~~	+	[[Category: Liu J]]
-	~~[[Category: Transcription-transcription inhibitor complex~~]]	+

OCA at 12:44, 6 November 2017

OCA — Mon, 06 Nov 2017 12:44:16 GMT

←Older revision		Revision as of 12:44, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5h1u' size='340' side='right' caption='[[5h1u]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5h1u' size='340' side='right' caption='[[5h1u]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h1u]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H1U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h1u]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H1U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6KT:2-AMINO-1,3-BENZOTHIAZOLE-6-CARBOXAMIDE'>6KT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6KT:2-AMINO-1,3-BENZOTHIAZOLE-6-CARBOXAMIDE'>6KT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h1t\|5h1t]], [[5h1v\|5h1v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h1t\|5h1t]], [[5h1v\|5h1v]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRIM24, RNF82, TIF1, TIF1A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5h1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1u OCA], [http://pdbe.org/5h1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h1u RCSB], [http://www.ebi.ac.uk/pdbsum/5h1u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1u 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=5h1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1u OCA], [http://pdbe.org/5h1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h1u RCSB], [http://www.ebi.ac.uk/pdbsum/5h1u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1u ProSAT]</span></td></tr>
	</table>		</table>
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Liu, J]]		[[Category: Liu, J]]
	[[Category: Transcription transcription inhibitor]]		[[Category: Transcription transcription inhibitor]]
	[[Category: Transcription-transcription inhibitor complex]]		[[Category: Transcription-transcription inhibitor complex]]

OCA at 08:20, 9 March 2017

OCA — Thu, 09 Mar 2017 08:20:36 GMT

←Older revision		Revision as of 08:20, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5h1u is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Complex structure of TRIM24 PHD-bromodomain and inhibitor 2==
		+	<StructureSection load='5h1u' size='340' side='right' caption='[[5h1u]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5h1u]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H1U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6KT:2-AMINO-1,3-BENZOTHIAZOLE-6-CARBOXAMIDE'>6KT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h1t\|5h1t]], [[5h1v\|5h1v]]</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=5h1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1u OCA], [http://pdbe.org/5h1u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h1u RCSB], [http://www.ebi.ac.uk/pdbsum/5h1u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1u ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/TIF1A_HUMAN TIF1A_HUMAN]] Defects in TRIM24 are a cause of thyroid papillary carcinoma (TPC) [MIM:[http://omim.org/entry/188550 188550]]. TPC is a common tumor of the thyroid that typically arises as an irregular, solid or cystic mass from otherwise normal thyroid tissue. Papillary carcinomas are malignant neoplasm characterized by the formation of numerous, irregular, finger-like projections of fibrous stroma that is covered with a surface layer of neoplastic epithelial cells. Note=A chromosomal aberration involving TRIM24/TIF1 is found in thyroid papillary carcinomas. Translocation t(7;10)(q32;q11) with RET. The translocation generates the TRIM24/RET (PTC6) oncogene.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TIF1A_HUMAN TIF1A_HUMAN]] Transcriptional coactivator that interacts with numerous nuclear receptors and coactivators and modulates the transcription of target genes. Interacts with chromatin depending on histone H3 modifications, having the highest affinity for histone H3 that is both unmodified at 'Lys-4' (H3K4me0) and acetylated at 'Lys-23' (H3K23ac). Has E3 protein-ubiquitin ligase activity. Promotes ubiquitination and proteasomal degradation of p53/TP53. Plays a role in the regulation of cell proliferation and apoptosis, at least in part via its effects on p53/TP53 levels. Up-regulates ligand-dependent transcription activation by AR, GCR/NR3C1, thyroid hormone receptor (TR) and ESR1. Modulates transcription activation by retinoic acid (RA) receptors, including RARA. Plays a role in regulating retinoic acid-dependent proliferation of hepatocytes (By similarity).<ref>PMID:16322096</ref> <ref>PMID:19556538</ref> <ref>PMID:21164480</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tripartite motif-containing protein 24 (TRIM24) is closely correlated with multiple cancers, and a recent study demonstrated that the bromodomain of TRIM24 is essential for the proliferation of lethal castration-resistant prostate cancer. Here, we identify three new inhibitors of the TRIM24 bromodomain using NMR fragment-based screening. The crystal structures of two new inhibitors in complex with the TRIM24 bromodomain reveal that the water-bridged interaction network is conserved in the same fashion as those for known benzoimidazolone inhibitors. Interestingly, the polar substitution on the warhead of one new inhibitor pulls the whole ligand approximately 2 A into the inner side pocket of the TRIM24 bromodomain, and thus exhibits a binding mode significantly different from other known bromodomain ligands. This mode provides a useful handle for further hit-to-lead evolution towards novel inhibitors of the TRIM24 bromodomain. This article is protected by copyright. All rights reserved.

-	~~Authors~~:	+	The Polar Warhead of a TRIM24 Bromodomain Inhibitor Rearranges a Water-Mediated Interaction Network.,Liu J, Li F, Bao H, Jiang Y, Zhang S, Ma R, Gao J, Wu J, Ruan K FEBS J. 2017 Feb 16. doi: 10.1111/febs.14041. PMID:28207202<ref>PMID:28207202</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5h1u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Liu, J]]
		+	[[Category: Transcription transcription inhibitor]]
		+	[[Category: Transcription-transcription inhibitor complex]]

OCA at 12:52, 2 November 2016

OCA — Wed, 02 Nov 2016 12:52:33 GMT

←Older revision		Revision as of 12:52, 2 November 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h1u is ON HOLD	+	The entry 5h1u is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5h1u" [edit=sysop:move=sysop]

OCA — Wed, 19 Oct 2016 12:03:12 GMT

Protected "5h1u" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:03, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5h1u is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Oct 2016 12:03:11 GMT

New page: '''Unreleased structure''' The entry 5h1u is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5h1u is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]