5ti3 - Revision history

OCA at 13:01, 4 October 2023

OCA — Wed, 04 Oct 2023 13:01:41 GMT

←Older revision		Revision as of 13:01, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5ti3' size='340' side='right'caption='[[5ti3]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5ti3' size='340' side='right'caption='[[5ti3]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ti3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TI3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5TI3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ti3]] 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=5TI3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TI3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7CG:2,5-dibromo-N-[3-(2-oxopyrrolidin-1-yl)phenyl]benzene-1-sulfonamide'>7CG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.703Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ti2\|5ti2]], [[5ti4\|5ti4]], [[5ti5\|5ti5]], [[5ti6\|5ti6]], [[5ti7\|5ti7]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7CG:2,5-dibromo-N-[3-(2-oxopyrrolidin-1-yl)phenyl]benzene-1-sulfonamide'>7CG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ti3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ti3 OCA], [~~http~~://pdbe.org/5ti3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ti3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ti3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ti3 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=5ti3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ti3 OCA], [https://pdbe.org/5ti3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ti3 RCSB], [https://www.ebi.ac.uk/pdbsum/5ti3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ti3 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein.<ref>PMID:12543779</ref> <ref>PMID:11733348</ref>	+	[https://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN] Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein.<ref>PMID:12543779</ref> <ref>PMID:11733348</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).	+	[https://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ember~~, S W.J~~]]	+	[[Category: Ember SWJ]]
-	[[Category: SCHONBRUNN, E]]	+	[[Category: SCHONBRUNN E]]
-	[[Category: Zhu, J Y]]	+	[[Category: Zhu J-Y]]
-	~~[[Category: Bromodomain]]~~	+
-	~~[[Category: Cap]]~~	+
-	~~[[Category: Cell cycle]]~~	+
-	~~[[Category: Hunk1]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Mcap]]~~	+
-	~~[[Category: Mitotic chromosome associated protein]]~~	+
-	~~[[Category: Protein binding-inhibitor complex]]~~	+
-	~~[[Category: Transcription-inhibitor complex~~]]	+

OCA at 12:11, 23 September 2020

OCA — Wed, 23 Sep 2020 12:11:27 GMT

←Older revision		Revision as of 12:11, 23 September 2020
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR 17503468==		==CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR 17503468==
-	<StructureSection load='5ti3' size='340' side='right' caption='[[5ti3]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5ti3' size='340' side='right'caption='[[5ti3]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ti3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TI3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TI3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ti3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TI3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5TI3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7CG:2,5-dibromo-N-[3-(2-oxopyrrolidin-1-yl)phenyl]benzene-1-sulfonamide'>7CG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7CG:2,5-dibromo-N-[3-(2-oxopyrrolidin-1-yl)phenyl]benzene-1-sulfonamide'>7CG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ti2\|5ti2]], [[5ti4\|5ti4]], [[5ti5\|5ti5]], [[5ti6\|5ti6]], [[5ti7\|5ti7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ti2\|5ti2]], [[5ti4\|5ti4]], [[5ti5\|5ti5]], [[5ti6\|5ti6]], [[5ti7\|5ti7]]</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=5ti3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ti3 OCA], [http://pdbe.org/5ti3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ti3 RCSB], [http://www.ebi.ac.uk/pdbsum/5ti3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ti3 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ti3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ti3 OCA], [http://pdbe.org/5ti3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ti3 RCSB], [http://www.ebi.ac.uk/pdbsum/5ti3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ti3 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5ti3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ti3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bromodomain-containing protein 3D structures\|Bromodomain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ember, S W.J]]		[[Category: Ember, S W.J]]
	[[Category: SCHONBRUNN, E]]		[[Category: SCHONBRUNN, E]]

OCA at 04:24, 21 September 2017

OCA — Thu, 21 Sep 2017 04:24:57 GMT

←Older revision		Revision as of 04:24, 21 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ti3 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR 17503468==
		+	<StructureSection load='5ti3' size='340' side='right' caption='[[5ti3]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ti3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TI3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TI3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7CG:2,5-dibromo-N-[3-(2-oxopyrrolidin-1-yl)phenyl]benzene-1-sulfonamide'>7CG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ti2\|5ti2]], [[5ti4\|5ti4]], [[5ti5\|5ti5]], [[5ti6\|5ti6]], [[5ti7\|5ti7]]</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=5ti3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ti3 OCA], [http://pdbe.org/5ti3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ti3 RCSB], [http://www.ebi.ac.uk/pdbsum/5ti3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ti3 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein.<ref>PMID:12543779</ref> <ref>PMID:11733348</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Computational screening is a method to prioritize small-molecule compounds based on the structural and biochemical attributes built from ligand and target information. Previously, we have developed a scalable virtual screening workflow to identify novel multitarget kinase/bromodomain inhibitors. In the current study, we identified several novel N-[3-(2-oxo-pyrrolidinyl)phenyl]-benzenesulfonamide derivatives that scored highly in our ensemble docking protocol. We quantified the binding affinity of these compounds for BRD4(BD1) biochemically and generated cocrystal structures, which were deposited in the Protein Data Bank. As the docking poses obtained in the virtual screening pipeline did not align with the experimental cocrystal structures, we evaluated the predictions of their precise binding modes by performing molecular dynamics (MD) simulations. The MD simulations closely reproduced the experimentally observed protein-ligand cocrystal binding conformations and interactions for all compounds. These results suggest a computational workflow to generate experimental-quality protein-ligand binding models, overcoming limitations of docking results due to receptor flexibility and incomplete sampling, as a useful starting point for the structure-based lead optimization of novel BRD4(BD1) inhibitors.

-	~~Authors~~:	+	Identification of a Novel Class of BRD4 Inhibitors by Computational Screening and Binding Simulations.,Allen BK, Mehta S, Ember SWJ, Zhu JY, Schonbrunn E, Ayad NG, Schurer SC ACS Omega. 2017 Aug 31;2(8):4760-4771. doi: 10.1021/acsomega.7b00553. Epub 2017, Aug 21. PMID:28884163<ref>PMID:28884163</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ti3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ember, S W.J]]
		+	[[Category: SCHONBRUNN, E]]
		+	[[Category: Zhu, J Y]]
		+	[[Category: Bromodomain]]
		+	[[Category: Cap]]
		+	[[Category: Cell cycle]]
		+	[[Category: Hunk1]]
		+	[[Category: Inhibitor]]
		+	[[Category: Mcap]]
		+	[[Category: Mitotic chromosome associated protein]]
		+	[[Category: Protein binding-inhibitor complex]]
		+	[[Category: Transcription-inhibitor complex]]

OCA at 17:02, 15 December 2016

OCA — Thu, 15 Dec 2016 17:02:28 GMT

←Older revision		Revision as of 17:02, 15 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ti3 is ON HOLD	+	The entry 5ti3 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5ti3" [edit=sysop:move=sysop]

OCA — Wed, 19 Oct 2016 15:50:24 GMT

Protected "5ti3" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:50, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5ti3 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Oct 2016 15:50:22 GMT

New page: '''Unreleased structure''' The entry 5ti3 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ti3 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]