5x4q - Revision history

OCA at 07:53, 22 November 2023

OCA — Wed, 22 Nov 2023 07:53:54 GMT

←Older revision		Revision as of 07:53, 22 November 2023
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	==Crystal structure of the BCL6 BTB domain in complex with Compound 7==		==Crystal structure of the BCL6 BTB domain in complex with Compound 7==
-	<StructureSection load='5x4q' size='340' side='right' caption='[[5x4q]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5x4q' size='340' side='right'caption='[[5x4q]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x4q]] 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=5X4Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X4Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x4q]] 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=5X4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X4Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7Z6:5-[[5-CHLORANYL-2-(PYRIDIN-3-YLMETHYLAMINO)PYRIMIDIN-4-YL]AMINO]-1,3-DIHYDROINDOL-2-ONE'>7Z6</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x4m\|5x4m]], [[5x4n\|5x4n]], [[5x4o\|5x4o]], [[5x4p\|5x4p]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7Z6:5-[[5-CHLORANYL-2-(PYRIDIN-3-YLMETHYLAMINO)PYRIMIDIN-4-YL]AMINO]-1,3-DIHYDROINDOL-2-ONE'>7Z6</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BCL6, BCL5, LAZ3, ZBTB27, ZNF51 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5x4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4q OCA], [https://pdbe.org/5x4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x4q RCSB], [https://www.ebi.ac.uk/pdbsum/5x4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4q 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=5x4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4q OCA], [~~http~~://pdbe.org/5x4q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x4q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x4q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4q ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN]] Note=Chromosomal aberrations involving BCL6 may be a cause of B-cell non-Hodgkin lymphoma. Translocation t(3;14)(q27;q32); translocation t(3;22)(q27;q11) with immunoglobulin gene regions. Note=A chromosomal aberration involving BCL6 may be a cause of a form of B-cell leukemia. Translocation t(3;11)(q27;q23) with POU2AF1/OBF1. Note=A chromosomal aberration involving BCL6 may be a cause of lymphoma. Translocation t(3;4)(q27;p11) with ARHH/TTF.	+	[https://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN] Note=Chromosomal aberrations involving BCL6 may be a cause of B-cell non-Hodgkin lymphoma. Translocation t(3;14)(q27;q32); translocation t(3;22)(q27;q11) with immunoglobulin gene regions. Note=A chromosomal aberration involving BCL6 may be a cause of a form of B-cell leukemia. Translocation t(3;11)(q27;q23) with POU2AF1/OBF1. Note=A chromosomal aberration involving BCL6 may be a cause of lymphoma. Translocation t(3;4)(q27;p11) with ARHH/TTF.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN]] Transcriptional repressor which is required for germinal center formation and antibody affinity maturation. Probably plays an important role in lymphomagenesis.<ref>PMID:9649500</ref> <ref>PMID:18280243</ref>	+	[https://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN] Transcriptional repressor which is required for germinal center formation and antibody affinity maturation. Probably plays an important role in lymphomagenesis.<ref>PMID:9649500</ref> <ref>PMID:18280243</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5x4q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x4q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[B-cell lymphoma proteins 3D structures\|B-cell lymphoma proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Ida, K]]	+	[[Category: Large Structures]]
-	[[Category: Lane, W]]	+	[[Category: Ida K]]
-	[[Category: Snell, G]]	+	[[Category: Lane W]]
-	[[Category: Sogabe, S]]	+	[[Category: Snell G]]
-	~~[[Category: Transcription repressor]]~~	+	[[Category: Sogabe S]]
-	~~[[Category: Transcription-inhibitor complex~~]]	+

OCA at 20:51, 24 January 2018

OCA — Wed, 24 Jan 2018 20:51:09 GMT

←Older revision		Revision as of 20:51, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5x4q' size='340' side='right' caption='[[5x4q]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5x4q' size='340' side='right' caption='[[5x4q]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x4q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X4Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x4q]] 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=5X4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X4Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7Z6:5-[[5-CHLORANYL-2-(PYRIDIN-3-YLMETHYLAMINO)PYRIMIDIN-4-YL]AMINO]-1,3-DIHYDROINDOL-2-ONE'>7Z6</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7Z6:5-[[5-CHLORANYL-2-(PYRIDIN-3-YLMETHYLAMINO)PYRIMIDIN-4-YL]AMINO]-1,3-DIHYDROINDOL-2-ONE'>7Z6</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x4m\|5x4m]], [[5x4n\|5x4n]], [[5x4o\|5x4o]], [[5x4p\|5x4p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x4m\|5x4m]], [[5x4n\|5x4n]], [[5x4o\|5x4o]], [[5x4p\|5x4p]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BCL6, BCL5, LAZ3, ZBTB27, ZNF51 ([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=5x4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4q OCA], [http://pdbe.org/5x4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x4q RCSB], [http://www.ebi.ac.uk/pdbsum/5x4q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4q 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=5x4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4q OCA], [http://pdbe.org/5x4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x4q RCSB], [http://www.ebi.ac.uk/pdbsum/5x4q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4q ProSAT]</span></td></tr>
	</table>		</table>
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Ida, K]]		[[Category: Ida, K]]
	[[Category: Lane, W]]		[[Category: Lane, W]]

OCA at 13:36, 24 May 2017

OCA — Wed, 24 May 2017 13:36:02 GMT

←Older revision		Revision as of 13:36, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x4q is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the BCL6 BTB domain in complex with Compound 7==
		+	<StructureSection load='5x4q' size='340' side='right' caption='[[5x4q]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x4q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X4Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X4Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7Z6:5-[[5-CHLORANYL-2-(PYRIDIN-3-YLMETHYLAMINO)PYRIMIDIN-4-YL]AMINO]-1,3-DIHYDROINDOL-2-ONE'>7Z6</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x4m\|5x4m]], [[5x4n\|5x4n]], [[5x4o\|5x4o]], [[5x4p\|5x4p]]</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=5x4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4q OCA], [http://pdbe.org/5x4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x4q RCSB], [http://www.ebi.ac.uk/pdbsum/5x4q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4q ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN]] Note=Chromosomal aberrations involving BCL6 may be a cause of B-cell non-Hodgkin lymphoma. Translocation t(3;14)(q27;q32); translocation t(3;22)(q27;q11) with immunoglobulin gene regions. Note=A chromosomal aberration involving BCL6 may be a cause of a form of B-cell leukemia. Translocation t(3;11)(q27;q23) with POU2AF1/OBF1. Note=A chromosomal aberration involving BCL6 may be a cause of lymphoma. Translocation t(3;4)(q27;p11) with ARHH/TTF.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN]] Transcriptional repressor which is required for germinal center formation and antibody affinity maturation. Probably plays an important role in lymphomagenesis.<ref>PMID:9649500</ref> <ref>PMID:18280243</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	B-cell lymphoma 6 (BCL6) is a transcriptional factor that expresses in lymphocytes and regulates the differentiation and proliferation of lymphocytes. Therefore, BCL6 is a therapeutic target for autoimmune diseases and cancer treatment. This report presents the discovery of BCL6-corepressor interaction inhibitors by using a biophysics-driven fragment-based approach. Using the surface plasmon resonance (SPR)-based fragment screening, we successfully identified fragment 1 (SPR KD = 1200 muM, ligand efficiency (LE) = 0.28), a competitive binder to the natural ligand BCoR peptide. Moreover, we elaborated 1 into the more potent compound 7 (SPR KD = 0.078 muM, LE = 0.37, cell-free protein-protein interaction (PPI) IC50 = 0.48 muM (ELISA), cellular PPI IC50 = 8.6 muM (M2H)) by a structure-based design and structural integration with a second high-throughput screening hit.

-	~~Authors: Sogabe~~, S., Ida, K., Lane, W., Snell, G.	+	Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach.,Kamada Y, Sakai N, Sogabe S, Ida K, Oki H, Sakamoto K, Lane W, Snell G, Iida M, Imaeda Y, Sakamoto J, Matsui J J Med Chem. 2017 May 11. doi: 10.1021/acs.jmedchem.7b00313. PMID:28471657<ref>PMID:28471657</ref>

-	~~Description: Crystal structure~~ of the ~~BCL6 BTB domain in complex with Compound 7~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Snell, G]]~~	+	<div class="pdbe-citations 5x4q" style="background-color:#fffaf0;"></div>
-	~~[[Category: Lane, W]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Ida, K]]		[[Category: Ida, K]]
		+	[[Category: Lane, W]]
		+	[[Category: Snell, G]]
	[[Category: Sogabe, S]]		[[Category: Sogabe, S]]
		+	[[Category: Transcription repressor]]
		+	[[Category: Transcription-inhibitor complex]]

OCA: Protected "5x4q" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:45:02 GMT

Protected "5x4q" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:45, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x4q is ON HOLD until Paper Publication Authors: Sogabe, S., Ida, K., Lane, W., Snell, G. Description: Crystal structure of the BCL6 BTB domain in ...

OCA — Thu, 09 Mar 2017 15:45:01 GMT

New page: '''Unreleased structure''' The entry 5x4q is ON HOLD until Paper Publication Authors: Sogabe, S., Ida, K., Lane, W., Snell, G. Description: Crystal structure of the BCL6 BTB domain in ...

New page

'''Unreleased structure'''

The entry 5x4q is ON HOLD until Paper Publication

Authors: Sogabe, S., Ida, K., Lane, W., Snell, G.

Description: Crystal structure of the BCL6 BTB domain in complex with Compound 7
[[Category: Unreleased Structures]]
[[Category: Snell, G]]
[[Category: Lane, W]]
[[Category: Ida, K]]
[[Category: Sogabe, S]]