8bdx - Revision history

OCA at 08:17, 7 February 2024

2024-02-07T08:17:51Z

←Older revision		Revision as of 08:17, 7 February 2024
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	== 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 ==
-	Herein, we describe a systematic SAR- and SPR-investigation of the peptidomimetic hydroxy-proline based VHL-ligand VH032, from which most to-date published VHL-targeting PROTACs have been derived. This study provides for the first time a consistent data set which allows for direct comparison of structural variations including those which were so far hidden in patent literature. The gained knowledge about improved VHL binders was used to design a small library of highly potent BRD4-degraders comprising different VHL exit vectors. Newly designed degraders showed favorable molecular properties and significantly improved degradation potency compared to MZ1.
-
-	Systematic Potency & Property Assessment of VHL Ligands and Implications on PROTAC Design.,Krieger J, Sorell FJ, Wegener AA, Leuthner B, Machrouhi-Porcher F, Hecht M, Leibrock EM, Mueller JE, Eisert J, Hartung IV, Schlesiger S ChemMedChem. 2023 Feb 7. doi: 10.1002/cmdc.202200615. PMID:36749883<ref>PMID:36749883</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8bdx" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:50, 24 January 2024

2024-01-24T13:50:45Z

←Older revision		Revision as of 13:50, 24 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8bdx]] is a 8 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=8BDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BDX FirstGlance]. <br>		<table><tr><td colspan='2'>[[8bdx]] is a 8 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=8BDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BDX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QIY:(2~{S},4~{R})-~{N}-[(1~{S})-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide'>QIY</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]] 2.93Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QIY:(2~{S},4~{R})-~{N}-[(1~{S})-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide'>QIY</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=8bdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bdx OCA], [https://pdbe.org/8bdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bdx RCSB], [https://www.ebi.ac.uk/pdbsum/8bdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bdx 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=8bdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bdx OCA], [https://pdbe.org/8bdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bdx RCSB], [https://www.ebi.ac.uk/pdbsum/8bdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bdx ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:26, 15 February 2023

2023-02-15T10:26:44Z

←Older revision		Revision as of 10:26, 15 February 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8bdx is ~~ON HOLD until Paper~~ Publication	+	==Ternary complex between VCB, BRD4-BD2 and PROTAC 48==
		+	<StructureSection load='8bdx' size='340' side='right'caption='[[8bdx]], [[Resolution\|resolution]] 2.93Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8bdx]] is a 8 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=8BDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BDX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QIY:(2~{S},4~{R})-~{N}-[(1~{S})-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide'>QIY</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=8bdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bdx OCA], [https://pdbe.org/8bdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bdx RCSB], [https://www.ebi.ac.uk/pdbsum/8bdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bdx ProSAT]</span></td></tr>
		+	</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).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Herein, we describe a systematic SAR- and SPR-investigation of the peptidomimetic hydroxy-proline based VHL-ligand VH032, from which most to-date published VHL-targeting PROTACs have been derived. This study provides for the first time a consistent data set which allows for direct comparison of structural variations including those which were so far hidden in patent literature. The gained knowledge about improved VHL binders was used to design a small library of highly potent BRD4-degraders comprising different VHL exit vectors. Newly designed degraders showed favorable molecular properties and significantly improved degradation potency compared to MZ1.

-	~~Authors~~:	+	Systematic Potency & Property Assessment of VHL Ligands and Implications on PROTAC Design.,Krieger J, Sorell FJ, Wegener AA, Leuthner B, Machrouhi-Porcher F, Hecht M, Leibrock EM, Mueller JE, Eisert J, Hartung IV, Schlesiger S ChemMedChem. 2023 Feb 7. doi: 10.1002/cmdc.202200615. PMID:36749883<ref>PMID:36749883</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8bdx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Lehmann M]]
		+	[[Category: Mueller JE]]
		+	[[Category: Sorrell FJ]]
		+	[[Category: Wegener A]]

OCA at 17:51, 16 November 2022

2022-11-16T17:51:59Z

←Older revision		Revision as of 17:51, 16 November 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8bdx is ON HOLD	+	The entry 8bdx is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8bdx" [edit=sysop:move=sysop]

2022-10-26T03:55:41Z

Protected "8bdx" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:55, 26 October 2022

OCA: New page: '''Unreleased structure''' The entry 8bdx is ON HOLD Authors: Description: Category: Unreleased Structures

2022-10-26T03:55:40Z

New page: '''Unreleased structure''' The entry 8bdx is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8bdx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]