5khm - Revision history

OCA at 10:01, 27 September 2023

2023-09-27T10:01:09Z

←Older revision		Revision as of 10:01, 27 September 2023
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	<StructureSection load='5khm' size='340' side='right'caption='[[5khm]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='5khm' size='340' side='right'caption='[[5khm]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5khm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KHM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KHM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5khm]] is a 2 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=5KHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KHM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=XNH:(3~{R})-4-[2-[4-[1-(3-METHOXY-[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-6-YL)PIPERIDIN-4-YL]PHENOXY]ETHYL]-1,3-DIMETHYL-PIPERAZIN-2-ONE'>XNH</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]] 1.48Å</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=5khm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5khm OCA], [~~http~~://pdbe.org/5khm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5khm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5khm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5khm ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=XNH:(3~{R})-4-[2-[4-[1-(3-METHOXY-[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-6-YL)PIPERIDIN-4-YL]PHENOXY]ETHYL]-1,3-DIMETHYL-PIPERAZIN-2-ONE'>XNH</scene></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=5khm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5khm OCA], [https://pdbe.org/5khm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5khm RCSB], [https://www.ebi.ac.uk/pdbsum/5khm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5khm 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Patel, J]]	+	[[Category: Patel J]]
-	~~[[Category: Bromodomain]]~~	+
-	~~[[Category: Transcription factor~~]]	+

OCA at 15:25, 8 July 2020

2020-07-08T15:25:40Z

←Older revision		Revision as of 15:25, 8 July 2020
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	==The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner==		==The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner==
-	<StructureSection load='5khm' size='340' side='right' caption='[[5khm]], [[Resolution\|resolution]] 1.48Å' scene=''>	+	<StructureSection load='5khm' size='340' side='right'caption='[[5khm]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5khm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KHM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KHM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5khm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KHM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KHM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=XNH:(3~{R})-4-[2-[4-[1-(3-METHOXY-[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-6-YL)PIPERIDIN-4-YL]PHENOXY]ETHYL]-1,3-DIMETHYL-PIPERAZIN-2-ONE'>XNH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=XNH:(3~{R})-4-[2-[4-[1-(3-METHOXY-[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-6-YL)PIPERIDIN-4-YL]PHENOXY]ETHYL]-1,3-DIMETHYL-PIPERAZIN-2-ONE'>XNH</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=5khm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5khm OCA], [http://pdbe.org/5khm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5khm RCSB], [http://www.ebi.ac.uk/pdbsum/5khm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5khm 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=5khm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5khm OCA], [http://pdbe.org/5khm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5khm RCSB], [http://www.ebi.ac.uk/pdbsum/5khm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5khm ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 22:		Line 22:

	==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: Large Structures]]
	[[Category: Patel, J]]		[[Category: Patel, J]]
	[[Category: Bromodomain]]		[[Category: Bromodomain]]
	[[Category: Transcription factor]]		[[Category: Transcription factor]]

OCA at 09:13, 9 August 2017

2017-08-09T09:13:14Z

←Older revision		Revision as of 09:13, 9 August 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5khm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5khm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bromodomain-containing protein\|Bromodomain-containing protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:55, 21 September 2016

2016-09-21T13:55:34Z

←Older revision		Revision as of 13:55, 21 September 2016
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-	'''Unreleased structure'''

-	The ~~entry~~ 5khm is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner==
		+	<StructureSection load='5khm' size='340' side='right' caption='[[5khm]], [[Resolution\|resolution]] 1.48Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5khm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KHM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=XNH:(3~{R})-4-[2-[4-[1-(3-METHOXY-[1,2,4]TRIAZOLO[4,3-B]PYRIDAZIN-6-YL)PIPERIDIN-4-YL]PHENOXY]ETHYL]-1,3-DIMETHYL-PIPERAZIN-2-ONE'>XNH</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=5khm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5khm OCA], [http://pdbe.org/5khm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5khm RCSB], [http://www.ebi.ac.uk/pdbsum/5khm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5khm 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 ==
		+	Here we report the discovery and optimization of a series of bivalent bromodomain and extraterminal inhibitors. Starting with the observation of BRD4 activity of compounds from a previous program, the compounds were optimized for BRD4 potency and physical properties. The optimized compound from this campaign exhibited excellent pharmacokinetic profile and exhibited high potency in vitro and in vivo effecting c-Myc downregulation and tumor growth inhibition in xenograft studies. This compound was selected as the development candidate, AZD5153. The series showed enhanced potency as a result of bivalent binding and a clear correlation between BRD4 activity and cellular potency.

-	~~Authors~~: Patel, J.	+	Optimization of a Series of Bivalent Triazolopyridazine Based Bromodomain and Extraterminal Inhibitors: The Discovery of (3R)-4-[2-[4-[1-(3-Methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-4-piperidyl]phen oxy]ethyl]-1,3-dimethyl-piperazin-2-one (AZD5153).,Bradbury RH, Callis R, Carr GR, Chen H, Clark E, Feron L, Glossop S, Graham MA, Hattersley M, Jones C, Lamont SG, Ouvry G, Patel A, Patel J, Rabow AA, Roberts CA, Stokes S, Stratton N, Walker GE, Ward L, Whalley D, Whittaker D, Wrigley G, Waring MJ J Med Chem. 2016 Sep 8;59(17):7801-17. doi: 10.1021/acs.jmedchem.6b00070. Epub, 2016 Aug 24. PMID:27528113<ref>PMID:27528113</ref>

-	~~Description: The first BET bromodomain of BRD4 bound to compound 13 in~~ a ~~bivalent manner~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5khm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Patel, J]]		[[Category: Patel, J]]
		+	[[Category: Bromodomain]]
		+	[[Category: Transcription factor]]

OCA at 00:21, 13 July 2016

2016-07-13T00:21:56Z

←Older revision		Revision as of 00:21, 13 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: Patel, J	+	Authors: Patel, J.

	Description: The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner		Description: The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Patel, J]]		[[Category: Patel, J]]

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

2016-06-23T21:37:52Z

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

←Older revision

Revision as of 21:37, 23 June 2016

OCA: New page: '''Unreleased structure''' The entry 5khm is ON HOLD Authors: Patel, J Description: The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner [[Category: Unreleased S...

2016-06-23T21:37:50Z

New page: '''Unreleased structure''' The entry 5khm is ON HOLD Authors: Patel, J Description: The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner [[Category: Unreleased S...

New page

'''Unreleased structure'''

The entry 5khm is ON HOLD

Authors: Patel, J

Description: The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner
[[Category: Unreleased Structures]]
[[Category: Patel, J]]