5xhk - Revision history

OCA at 08:02, 22 November 2023

OCA — Wed, 22 Nov 2023 08:02:19 GMT

←Older revision		Revision as of 08:02, 22 November 2023
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	==Crystal structure of the BRD2-BD2 in complex with phenanthridinone==		==Crystal structure of the BRD2-BD2 in complex with phenanthridinone==
-	<StructureSection load='5xhk' size='340' side='right' caption='[[5xhk]], [[Resolution\|resolution]] 1.28Å' scene=''>	+	<StructureSection load='5xhk' size='340' side='right'caption='[[5xhk]], [[Resolution\|resolution]] 1.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xhk]] is a 1 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=5XHK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XHK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xhk]] 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=5XHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XHK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=2ME:METHOXYETHANE'>2ME</scene~~>, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LDR:PHENANTHRIDIN-6(5H)-ONE'>LDR</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]] 1.28Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5xhe\|5xhe]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2ME:METHOXYETHANE'>2ME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LDR:PHENANTHRIDIN-6(5H)-ONE'>LDR</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BRD2, KIAA9001, RING3 ([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=5xhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xhk OCA], [https://pdbe.org/5xhk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xhk RCSB], [https://www.ebi.ac.uk/pdbsum/5xhk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xhk 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=5xhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xhk OCA], [~~http~~://pdbe.org/5xhk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xhk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xhk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xhk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN]] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>	+	[https://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:

	==See Also==		==See Also==
-	*[[Bromodomain-containing protein\|Bromodomain-containing protein]]	+	*[[Bromodomain-containing protein 3D structures\|Bromodomain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Deshmukh, P]]	+	[[Category: Large Structures]]
-	[[Category: Mathur, S]]	+	[[Category: Deshmukh P]]
-	[[Category: Padmanabhan, B]]	+	[[Category: Mathur S]]
-	[[Category: Tripathi, S]]	+	[[Category: Padmanabhan B]]
-	~~[[Category: Bet family]]~~	+	[[Category: Tripathi S]]
-	~~[[Category: Brd2]]~~	+
-	~~[[Category: Bromodomain]]~~	+
-	~~[[Category: Phenanthridinone]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 19:03, 1 August 2018

OCA — Wed, 01 Aug 2018 19:03:03 GMT

←Older revision		Revision as of 19:03, 1 August 2018
Line 3:		Line 3:
	<StructureSection load='5xhk' size='340' side='right' caption='[[5xhk]], [[Resolution\|resolution]] 1.28Å' scene=''>		<StructureSection load='5xhk' size='340' side='right' caption='[[5xhk]], [[Resolution\|resolution]] 1.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xhk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XHK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xhk]] is a 1 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=5XHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XHK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2ME:METHOXYETHANE'>2ME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LDR:PHENANTHRIDIN-6(5H)-ONE'>LDR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2ME:METHOXYETHANE'>2ME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LDR:PHENANTHRIDIN-6(5H)-ONE'>LDR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xhe\|5xhe]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xhe\|5xhe]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD2, KIAA9001, RING3 ([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=5xhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xhk OCA], [http://pdbe.org/5xhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xhk RCSB], [http://www.ebi.ac.uk/pdbsum/5xhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xhk 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=5xhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xhk OCA], [http://pdbe.org/5xhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xhk RCSB], [http://www.ebi.ac.uk/pdbsum/5xhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xhk ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5xhk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xhk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bromodomain-containing protein\|Bromodomain-containing protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Deshmukh, P]]		[[Category: Deshmukh, P]]
	[[Category: Mathur, S]]		[[Category: Mathur, S]]

OCA at 03:49, 6 September 2017

OCA — Wed, 06 Sep 2017 03:49:49 GMT

←Older revision		Revision as of 03:49, 6 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~5xhk~~ is ~~ON HOLD~~	+	==Crystal structure of the BRD2-BD2 in complex with phenanthridinone==
		+	<StructureSection load='5xhk' size='340' side='right' caption='[[5xhk]], [[Resolution\|resolution]] 1.28Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xhk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XHK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2ME:METHOXYETHANE'>2ME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LDR:PHENANTHRIDIN-6(5H)-ONE'>LDR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xhe\|5xhe]]</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=5xhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xhk OCA], [http://pdbe.org/5xhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xhk RCSB], [http://www.ebi.ac.uk/pdbsum/5xhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xhk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN]] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bromodomain and extra-terminal family proteins recognize the acetylated histone code on chromatin and participate in downstream processes like DNA replication, modification, and repair. As part of epigenetic approaches, BRD2 and BRD4 were identified as putative targets, for the management of chronic diseases. We have recently reported the discovery of a new scaffold of the phenanthridinone-based inhibitor (L10) of the second bromodomain of BRD2 (BRD2-BD2). Here, we present the crystal structure of the BRD2-BD2, refined to 1.4 A resolution, in complex with beta-mercaptoethanol (a component of the protein buffer). The beta-mercaptoethanol covalently links to C425 of BD2 in the acetyl-lysine binding pocket, to form a modified cysteine mercaptoethanol (CME). The CME modification significantly hinders the entry of ligands into the BD2 binding pocket, suggesting that beta-mercaptoethanol should be removed during protein production process. Next, to confirm whether phenanthridionone scaffold is a new inhibitor family of BRD2-BD2, we have determined the crystal structure of BD2 in complex with 6(5H)-Phenanthridinone (a core moiety of L10), refined to 1.28 A resolution. It confirmed that the phenanthridinone molecule, unambiguously, binds to BD2. Moreover, we performed molecular docking and molecular dynamic studies on selected phenanthridinone analogs. The predicted L10 analogs are stable with essential hydrophobic and hydrophilic interactions with BD2 during molecular dynamic simulations. We propose that the predicted phenanthridinone analogs may be potential molecules for inhibiting the BD2 function of acetylated histone recognition.

-	~~Authors~~:	+	Insights into the crystal structure of BRD2-BD2 - phenanthridinone complex and theoretical studies on phenanthridinone analogs.,Mathur S, Deshmukh P, Tripathi S, Marimuthu P, Padmanabhan B J Biomol Struct Dyn. 2017 Jul 31:1-19. doi: 10.1080/07391102.2017.1353441. PMID:28696179<ref>PMID:28696179</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xhk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Deshmukh, P]]
		+	[[Category: Mathur, S]]
		+	[[Category: Padmanabhan, B]]
		+	[[Category: Tripathi, S]]
		+	[[Category: Bet family]]
		+	[[Category: Brd2]]
		+	[[Category: Bromodomain]]
		+	[[Category: Phenanthridinone]]
		+	[[Category: Transcription]]

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

OCA — Thu, 04 May 2017 12:12:28 GMT

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

←Older revision

Revision as of 12:12, 4 May 2017

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

OCA — Thu, 04 May 2017 12:12:27 GMT

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

New page

'''Unreleased structure'''

The entry 5xhk is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]