6kei - Revision history

OCA at 10:31, 22 November 2023

OCA — Wed, 22 Nov 2023 10:31:50 GMT

←Older revision		Revision as of 10:31, 22 November 2023
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	<StructureSection load='6kei' size='340' side='right'caption='[[6kei]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='6kei' size='340' side='right'caption='[[6kei]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kei]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KEI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kei]] 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=6KEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KEI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D6U:16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one'>D6U</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 1.451Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD4, HUNK1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D6U:16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one'>D6U</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=6kei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kei OCA], [https://pdbe.org/6kei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kei RCSB], [https://www.ebi.ac.uk/pdbsum/6kei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kei 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=6kei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kei OCA], [https://pdbe.org/6kei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kei RCSB], [https://www.ebi.ac.uk/pdbsum/6kei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kei ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[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>	+	[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 ==
-	[[https://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 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6kei" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kei" 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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lee~~, B I~~]]	+	[[Category: Lee BI]]
-	[[Category: Park~~, T H]]~~	+	[[Category: Park TH]]
-	~~[[Category: Brd4]]~~	+
-	~~[[Category: Bromodomain 1]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 08:27, 21 April 2021

OCA — Wed, 21 Apr 2021 08:27:17 GMT

←Older revision		Revision as of 08:27, 21 April 2021
Line 12:		Line 12:
	== Function ==		== Function ==
	[[https://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;">
		+	== Publication Abstract from PubMed ==
		+	Epigenetic regulation is known to play a key role in progression of anti-cancer therapeutics. Lysine acetylation is an important mechanism in controlling gene expression. There has been increasing interest in bromodomain owing to its ability to modulate transcription of various genes as an epigenetic 'reader.' Herein, we report the design, synthesis, and X-ray studies of novel aristoyagonine (benzo[6,7]oxepino[4,3,2-cd]isoindol-2(1H)-one) derivatives and investigate their inhibitory effect against Brd4 bromodomain. Five compounds 8ab, 8bc, 8bd, 8be, and 8bf have been discovered with high binding affinity over the Brd4 protein. Co-crystal structures of these five inhibitors with human Brd4 bromodomain demonstrated that it has a key binding mode occupying the hydrophobic pocket, which is known to be the acetylated lysine binding site. These novel Brd4 bromodomain inhibitors demonstrated impressive inhibitory activity and mode of action for the treatment of cancer diseases.
		+
		+	Synthesis and Structure-Activity Relationships of Aristoyagonine Derivatives as Brd4 Bromodomain Inhibitors with X-ray Co-Crystal Research.,Yoo M, Park TH, Yoo M, Kim Y, Lee JY, Lee KM, Ryu SE, Lee BI, Jung KY, Park CH Molecules. 2021 Mar 17;26(6). pii: molecules26061686. doi:, 10.3390/molecules26061686. PMID:33802888<ref>PMID:33802888</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kei" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:39, 31 March 2021

OCA — Wed, 31 Mar 2021 10:39:26 GMT

←Older revision		Revision as of 10:39, 31 March 2021
Line 1:		Line 1:

	==Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one==		==Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one==
-	<StructureSection load='6kei' size='340' side='right'caption='[[6kei]]' scene=''>	+	<StructureSection load='6kei' size='340' side='right'caption='[[6kei]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KEI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KEI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kei]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KEI FirstGlance]. <br>
-	</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=6kei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kei OCA], [~~http~~://pdbe.org/6kei PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kei RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kei PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kei ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D6U:16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one'>D6U</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD4, HUNK1 ([https://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=6kei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kei OCA], [https://pdbe.org/6kei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kei RCSB], [https://www.ebi.ac.uk/pdbsum/6kei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kei ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[[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 ==
		+	[[https://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lee BI]]	+	[[Category: Lee, B I]]
-	[[Category: Park TH]]	+	[[Category: Park, T H]]
		+	[[Category: Brd4]]
		+	[[Category: Bromodomain 1]]
		+	[[Category: Transcription]]

OCA at 13:58, 8 July 2020

OCA — Wed, 08 Jul 2020 13:58:42 GMT

←Older revision		Revision as of 13:58, 8 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6kei is ON HOLD until Paper Publication~~	+	==Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one==
-		+	<StructureSection load='6kei' size='340' side='right'caption='[[6kei]]' scene=''>
-	~~Authors: Lee, B.I., Park, T.H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KEI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KEI FirstGlance]. <br>
-	~~Description:~~ Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one	+	</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=6kei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kei OCA], [http://pdbe.org/6kei PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kei RCSB], [http://www.ebi.ac.uk/pdbsum/6kei PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kei ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Park~~, T.H]]	+	__TOC__
-	[[Category: Lee~~, B.I~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lee BI]]
		+	[[Category: Park TH]]

OCA at 04:34, 31 July 2019

OCA — Wed, 31 Jul 2019 04:34:16 GMT

←Older revision		Revision as of 04:34, 31 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kei is ON HOLD	+	The entry 6kei is ON HOLD until Paper Publication

	Authors: Lee, B.I., Park, T.H.		Authors: Lee, B.I., Park, T.H.

OCA: Protected "6kei" [edit=sysop:move=sysop]

OCA — Wed, 10 Jul 2019 04:03:12 GMT

Protected "6kei" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:03, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kei is ON HOLD Authors: Lee, B.I., Park, T.H. Description: Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 16-methoxy-11-methyl-6-[(...

OCA — Wed, 10 Jul 2019 04:03:11 GMT

New page: '''Unreleased structure''' The entry 6kei is ON HOLD Authors: Lee, B.I., Park, T.H. Description: Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 16-methoxy-11-methyl-6-[(...

New page

'''Unreleased structure'''

The entry 6kei is ON HOLD

Authors: Lee, B.I., Park, T.H.

Description: Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one
[[Category: Unreleased Structures]]
[[Category: Park, T.H]]
[[Category: Lee, B.I]]