5ovb - Revision history

OCA at 01:25, 28 December 2023

OCA — Thu, 28 Dec 2023 01:25:22 GMT

←Older revision		Revision as of 01:25, 28 December 2023
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	<StructureSection load='5ovb' size='340' side='right'caption='[[5ovb]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5ovb' size='340' side='right'caption='[[5ovb]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ovb]] is a 2 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=5OVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OVB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ovb]] 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=5OVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OVB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AY2:~{N}-[3-(5-ethanoyl-2-ethoxy-phenyl)-5-(1-methylpyrazol-3-yl)phenyl]furan-2-carboxamide'>AY2</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]] 1.95Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD4, HUNK1 ([http://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=AY2:~{N}-[3-(5-ethanoyl-2-ethoxy-phenyl)-5-(1-methylpyrazol-3-yl)phenyl]furan-2-carboxamide'>AY2</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=5ovb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovb OCA], [~~http~~://pdbe.org/5ovb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ovb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ovb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovb 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=5ovb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovb OCA], [https://pdbe.org/5ovb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ovb RCSB], [https://www.ebi.ac.uk/pdbsum/5ovb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovb 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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Caflisch, A]]	+	[[Category: Caflisch A]]
-	[[Category: Zhu, J]]	+	[[Category: Zhu J]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Inhibitor~~]]	+

OCA at 07:45, 23 October 2019

OCA — Wed, 23 Oct 2019 07:45:08 GMT

←Older revision		Revision as of 07:45, 23 October 2019
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	==Crystal structure of human BRD4(1) bromodomain in complex with DR46==		==Crystal structure of human BRD4(1) bromodomain in complex with DR46==
-	<StructureSection load='5ovb' size='340' side='right' caption='[[5ovb]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5ovb' size='340' side='right'caption='[[5ovb]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ovb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OVB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ovb]] is a 2 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=5OVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OVB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AY2:~{N}-[3-(5-ethanoyl-2-ethoxy-phenyl)-5-(1-methylpyrazol-3-yl)phenyl]furan-2-carboxamide'>AY2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AY2:~{N}-[3-(5-ethanoyl-2-ethoxy-phenyl)-5-(1-methylpyrazol-3-yl)phenyl]furan-2-carboxamide'>AY2</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD4, HUNK1 ([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=5ovb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovb OCA], [http://pdbe.org/5ovb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ovb RCSB], [http://www.ebi.ac.uk/pdbsum/5ovb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovb 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=5ovb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovb OCA], [http://pdbe.org/5ovb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ovb RCSB], [http://www.ebi.ac.uk/pdbsum/5ovb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovb ProSAT]</span></td></tr>
	</table>		</table>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).		[[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 ==
		+	Expanding the chemical space and simultaneously ensuring synthetic accessibility is of upmost importance, not only for the discovery of effective binders for novel protein classes but, more importantly, for the development of compounds against hard-to-drug proteins. Here, we present AutoCouple, a de novo approach to computational ligand design focused on the diversity-oriented generation of chemical entities via virtual couplings. In a benchmark application, chemically diverse compounds with low-nanomolar potency for the CBP bromodomain and high selectivity against the BRD4(1) bromodomain were achieved by the synthesis of about 50 derivatives of the original fragment. The binding mode was confirmed by X-ray crystallography, target engagement in cells was demonstrated, and antiproliferative activity was showcased in three cancer cell lines. These results reveal AutoCouple as a useful in silico coupling method to expand the chemical space in hit optimization campaigns resulting in potent, selective, and cell permeable bromodomain ligands.
		+
		+	Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple).,Batiste L, Unzue A, Dolbois A, Hassler F, Wang X, Deerain N, Zhu J, Spiliotopoulos D, Nevado C, Caflisch A ACS Cent Sci. 2018 Feb 28;4(2):180-188. doi: 10.1021/acscentsci.7b00401. Epub, 2018 Feb 7. PMID:29532017<ref>PMID:29532017</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ovb" 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: Large Structures]]
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]
	[[Category: Zhu, J]]		[[Category: Zhu, J]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Inhibitor]]		[[Category: Inhibitor]]

OCA at 07:46, 10 October 2018

OCA — Wed, 10 Oct 2018 07:46:13 GMT

←Older revision		Revision as of 07:46, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ovb is ~~ON HOLD~~	+	==Crystal structure of human BRD4(1) bromodomain in complex with DR46==
-		+	<StructureSection load='5ovb' size='340' side='right' caption='[[5ovb]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~Authors~~: ~~Zhu~~, J., ~~Caflisch~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ovb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OVB FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of human~~ BRD4(1) ~~bromodomain in complex~~ with ~~DR46~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AY2:~{N}-[3-(5-ethanoyl-2-ethoxy-phenyl)-5-(1-methylpyrazol-3-yl)phenyl]furan-2-carboxamide'>AY2</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5ovb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ovb OCA], [http://pdbe.org/5ovb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ovb RCSB], [http://www.ebi.ac.uk/pdbsum/5ovb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ovb 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).
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]
	[[Category: Zhu, J]]		[[Category: Zhu, J]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Inhibitor]]

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

OCA — Wed, 27 Sep 2017 12:53:29 GMT

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

←Older revision

Revision as of 12:53, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ovb is ON HOLD Authors: Zhu, J., Caflisch, A. Description: Crystal structure of human BRD4(1) bromodomain in complex with DR46 [[Category: Unrelea...

OCA — Wed, 27 Sep 2017 12:53:28 GMT

New page: '''Unreleased structure''' The entry 5ovb is ON HOLD Authors: Zhu, J., Caflisch, A. Description: Crystal structure of human BRD4(1) bromodomain in complex with DR46 [[Category: Unrelea...

New page

'''Unreleased structure'''

The entry 5ovb is ON HOLD

Authors: Zhu, J., Caflisch, A.

Description: Crystal structure of human BRD4(1) bromodomain in complex with DR46
[[Category: Unreleased Structures]]
[[Category: Caflisch, A]]
[[Category: Zhu, J]]