5dlz - Revision history

OCA at 21:48, 28 June 2023

2023-06-28T21:48:39Z

←Older revision		Revision as of 21:48, 28 June 2023
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	==FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide==		==FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide==
-	<StructureSection load='5dlz' size='340' side='right' caption='[[5dlz]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5dlz' size='340' side='right'caption='[[5dlz]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dlz]] 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=5DLZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DLZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dlz]] 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=5DLZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DLZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5D1:N-{[1-(3-METHYLBENZYL)PIPERIDIN-4-YL]METHYL}-4-[(1-METHYL-2-OXO-1,2-DIHYDROQUINOLIN-4-YL)OXY]BUTANAMIDE'>5D1</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]] 1.7Å</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=5D1:N-{[1-(3-METHYLBENZYL)PIPERIDIN-4-YL]METHYL}-4-[(1-METHYL-2-OXO-1,2-DIHYDROQUINOLIN-4-YL)OXY]BUTANAMIDE'>5D1</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=5dlz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dlz OCA], [~~http~~://pdbe.org/5dlz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dlz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dlz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dlz 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=5dlz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dlz OCA], [https://pdbe.org/5dlz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dlz RCSB], [https://www.ebi.ac.uk/pdbsum/5dlz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dlz 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 23:		Line 23:

	==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: Betzi, S]]	+	[[Category: Large Structures]]
-	[[Category: Morelli, X]]	+	[[Category: Betzi S]]
-	[[Category: Raux, B]]	+	[[Category: Morelli X]]
-	[[Category: Rebuffet, E]]	+	[[Category: Raux B]]
-	~~[[Category: Brd4]]~~	+	[[Category: Rebuffet E]]
-	~~[[Category: Brd4_bd1]]~~	+
-	~~[[Category: Bromodomain]]~~	+
-	~~[[Category: Epigenetic reader]]~~	+
-	~~[[Category: Histone]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 08:14, 6 March 2019

2019-03-06T08:14:38Z

←Older revision		Revision as of 08:14, 6 March 2019
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	==FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide==		==FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide==
-	<StructureSection load='5dlz' size='340' side='right' caption='[[5dlz]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5dlz' size='340' side='right' caption='[[5dlz]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dlz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DLZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DLZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dlz]] 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=5DLZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DLZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5D1:N-{[1-(3-METHYLBENZYL)PIPERIDIN-4-YL]METHYL}-4-[(1-METHYL-2-OXO-1,2-DIHYDROQUINOLIN-4-YL)OXY]BUTANAMIDE'>5D1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5D1:N-{[1-(3-METHYLBENZYL)PIPERIDIN-4-YL]METHYL}-4-[(1-METHYL-2-OXO-1,2-DIHYDROQUINOLIN-4-YL)OXY]BUTANAMIDE'>5D1</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=5dlz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dlz OCA], [http://pdbe.org/5dlz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dlz RCSB], [http://www.ebi.ac.uk/pdbsum/5dlz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dlz 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=5dlz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dlz OCA], [http://pdbe.org/5dlz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dlz RCSB], [http://www.ebi.ac.uk/pdbsum/5dlz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dlz ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5dlz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dlz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bromodomain-containing protein\|Bromodomain-containing protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Betzi, S]]		[[Category: Betzi, S]]
	[[Category: Morelli, X]]		[[Category: Morelli, X]]

OCA at 04:38, 9 September 2016

2016-09-09T04:38:15Z

←Older revision		Revision as of 04:38, 9 September 2016
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5dlz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DLZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DLZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dlz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DLZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DLZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5D1:N-{[1-(3-METHYLBENZYL)PIPERIDIN-4-YL]METHYL}-4-[(1-METHYL-2-OXO-1,2-DIHYDROQUINOLIN-4-YL)OXY]BUTANAMIDE'>5D1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5D1:N-{[1-(3-METHYLBENZYL)PIPERIDIN-4-YL]METHYL}-4-[(1-METHYL-2-OXO-1,2-DIHYDROQUINOLIN-4-YL)OXY]BUTANAMIDE'>5D1</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=5dlz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dlz OCA], [http://pdbe.org/5dlz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dlz RCSB], [http://www.ebi.ac.uk/pdbsum/5dlz PDBsum]</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=5dlz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dlz OCA], [http://pdbe.org/5dlz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dlz RCSB], [http://www.ebi.ac.uk/pdbsum/5dlz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dlz ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 15:35, 1 June 2016

2016-06-01T15:35:46Z

←Older revision		Revision as of 15:35, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5dlz is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide==
		+	<StructureSection load='5dlz' size='340' side='right' caption='[[5dlz]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dlz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DLZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DLZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5D1:N-{[1-(3-METHYLBENZYL)PIPERIDIN-4-YL]METHYL}-4-[(1-METHYL-2-OXO-1,2-DIHYDROQUINOLIN-4-YL)OXY]BUTANAMIDE'>5D1</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=5dlz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dlz OCA], [http://pdbe.org/5dlz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dlz RCSB], [http://www.ebi.ac.uk/pdbsum/5dlz PDBsum]</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 ==
		+	Protein-protein interactions (PPIs) represent an enormous source of opportunity for therapeutic intervention. We and others have recently pinpointed key rules that will help in identifying the next generation of innovative drugs to tackle this challenging class of targets within the next decade. We used these rules to design an oriented chemical library corresponding to a set of diverse 'PPI-like' modulators with cores identified as privileged structures in therapeutics. In this work, we purchased the resulting 1664 structurally diverse compounds and evaluated them on a series of representative protein-protein interfaces with distinct "druggability" potential using Homogeneous Time-Resolved Fluorescence (HTRF(R)) technology. For certain PPI classes, analysis of the hit rates revealed up to 100 enrichment factors compared with non-oriented chemical libraries. This observation correlates with the predicted "druggability" of the targets. A specific focus on selectivity profiles, the three-dimensional (3D) molecular modes of action resolved by X-ray crystallography, and the biological activities of identified hits targeting the well-defined "druggable" bromodomains of the bromo and extraterminal (BET) family are presented as a proof-of-concept. Overall, our present study illustrates the potency of machine learning-based oriented chemical libraries to accelerate the identification of hits targeting PPIs. A generalization of this method to a larger set of compounds will accelerate the discovery of original and potent probes for this challenging class of targets.

-	~~Authors: Raux~~, B., ~~Rebuffet~~, E., ~~Betzi~~, S., ~~Morelli~~, X.	+	Protein-protein interaction inhibition (2P2I)-oriented chemical library accelerates hit discovery.,Milhas S, Raux B, Betzi S, Derviaux C, Roche P, Restouin A, Basse MJ, Rebuffet E, Lugari A, Badol M, Kashyap R, Lissitzky JC, Eydoux C, Hamon V, Gourdel ME, Combes S, Zimmermann P, Aurrand-Lions M, Roux T, Rogers C, Muller S, Knapp S, Trinquet E, Collette Y, Guillemot JC, Morelli X ACS Chem Biol. 2016 May 24. PMID:27219844<ref>PMID:27219844</ref>

-	~~Description: FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1~~,2-~~dihydroquinolin-4-yl)oxy]-N-({1~~-[~~(3-methylphe methyl~~]~~piperidin-4-yl}methyl)butanamide~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5dlz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Betzi, S]]
		+	[[Category: Morelli, X]]
	[[Category: Raux, B]]		[[Category: Raux, B]]
	[[Category: Rebuffet, E]]		[[Category: Rebuffet, E]]
-	[[Category: ~~Morelli, X~~]]	+	[[Category: Brd4]]
-	[[Category: ~~Betzi, S~~]]	+	[[Category: Brd4_bd1]]
		+	[[Category: Bromodomain]]
		+	[[Category: Epigenetic reader]]
		+	[[Category: Histone]]
		+	[[Category: Inhibitor]]
		+	[[Category: Transcription]]

OCA at 11:14, 16 December 2015

2015-12-16T11:14:37Z

←Older revision		Revision as of 11:14, 16 December 2015
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Raux, B]]		[[Category: Raux, B]]
		+	[[Category: Rebuffet, E]]
	[[Category: Morelli, X]]		[[Category: Morelli, X]]
	[[Category: Betzi, S]]		[[Category: Betzi, S]]
-	[[Category: Rebuffet, E]]

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

2015-09-30T13:09:18Z

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

←Older revision

Revision as of 13:09, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dlz is ON HOLD until Paper Publication Authors: Raux, B., Rebuffet, E., Betzi, S., Morelli, X. Description: FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4...

2015-09-30T13:09:17Z

New page: '''Unreleased structure''' The entry 5dlz is ON HOLD until Paper Publication Authors: Raux, B., Rebuffet, E., Betzi, S., Morelli, X. Description: FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4...

New page

'''Unreleased structure'''

The entry 5dlz is ON HOLD until Paper Publication

Authors: Raux, B., Rebuffet, E., Betzi, S., Morelli, X.

Description: FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide
[[Category: Unreleased Structures]]
[[Category: Raux, B]]
[[Category: Morelli, X]]
[[Category: Betzi, S]]
[[Category: Rebuffet, E]]