5x9o - Revision history

OCA at 07:56, 22 November 2023

OCA — Wed, 22 Nov 2023 07:56:38 GMT

←Older revision		Revision as of 07:56, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of the BCL6 BTB domain in complex with Compound 1a==		==Crystal structure of the BCL6 BTB domain in complex with Compound 1a==
-	<StructureSection load='5x9o' size='340' side='right' caption='[[5x9o]], [[Resolution\|resolution]] 1.58Å' scene=''>	+	<StructureSection load='5x9o' size='340' side='right'caption='[[5x9o]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x9o]] 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=5X9O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X9O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x9o]] 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=5X9O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X9O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=80R:5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one'>80R</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]] 1.58Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x9p\|5x9p]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=80R:5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one'>80R</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=5x9o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9o OCA], [https://pdbe.org/5x9o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x9o RCSB], [https://www.ebi.ac.uk/pdbsum/5x9o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9o 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=5x9o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9o OCA], [~~http~~://pdbe.org/5x9o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x9o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x9o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9o 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 5x9o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x9o" 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 00:21, 16 November 2017

OCA — Thu, 16 Nov 2017 00:21:54 GMT

←Older revision		Revision as of 00:21, 16 November 2017
Line 3:		Line 3:
	<StructureSection load='5x9o' size='340' side='right' caption='[[5x9o]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='5x9o' size='340' side='right' caption='[[5x9o]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x9o]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X9O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X9O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x9o]] 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=5X9O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X9O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=80R:5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one'>80R</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=80R:5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one'>80R</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">[[5x9p\|5x9p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x9p\|5x9p]]</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=5x9o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9o OCA], [http://pdbe.org/5x9o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x9o RCSB], [http://www.ebi.ac.uk/pdbsum/5x9o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9o 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=5x9o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9o OCA], [http://pdbe.org/5x9o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x9o RCSB], [http://www.ebi.ac.uk/pdbsum/5x9o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9o 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 05:55, 17 August 2017

OCA — Thu, 17 Aug 2017 05:55:57 GMT

←Older revision		Revision as of 05:55, 17 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x9o is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the BCL6 BTB domain in complex with Compound 1a==
		+	<StructureSection load='5x9o' size='340' side='right' caption='[[5x9o]], [[Resolution\|resolution]] 1.58Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x9o]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X9O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X9O FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=80R:5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one'>80R</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">[[5x9p\|5x9p]]</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=5x9o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9o OCA], [http://pdbe.org/5x9o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x9o RCSB], [http://www.ebi.ac.uk/pdbsum/5x9o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9o 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 repressor that can form complexes with corepressors via protein-protein interactions (PPIs). The complexes of BCL6 and corepressors play an important role in the formation of germinal centers (GCs), and differentiation and proliferation of lymphocytes. Therefore, BCL6-corepressor interaction inhibitors would be drug candidates for managing autoimmune diseases and cancer. Starting from high-throughput screening hits 1a and 2a, we identified a novel BCL6-corepressor interaction inhibitor 8c (cell-free enzyme-linked immunosorbent assay [ELISA] IC50=0.10microM, cell-based mammalian two-hybrid [M2H] assay IC50=0.72microM) by utilizing structure-based drug design (SBDD) based on an X-ray crystal structure of 1a bound to BCL6. Compound 8c also showed a good pharmacokinetic profile, which was acceptable for both in vitro and in vivo studies.

-	~~Authors: Sogabe, S~~., ~~Ida~~, K., ~~Lane~~, W., Snell, G.	+	Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design.,Yasui T, Yamamoto T, Sakai N, Asano K, Takai T, Yoshitomi Y, Davis M, Takagi T, Sakamoto K, Sogabe S, Kamada Y, Lane W, Snell G, Iwata M, Goto M, Inooka H, Sakamoto JI, Nakada Y, Imaeda Y Bioorg Med Chem. 2017 Sep 1;25(17):4876-4886. doi: 10.1016/j.bmc.2017.07.037., Epub 2017 Jul 20. PMID:28760529<ref>PMID:28760529</ref>

-	~~Description: Crystal structure~~ of the ~~BCL6 BTB domain in complex with Compound 1a~~	+	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 5x9o" 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 at 12:23, 5 April 2017

OCA — Wed, 05 Apr 2017 12:23:31 GMT

←Older revision		Revision as of 12:23, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x9o is ON HOLD	+	The entry 5x9o is ON HOLD until Paper Publication

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

OCA: Protected "5x9o" [edit=sysop:move=sysop]

OCA — Wed, 15 Mar 2017 20:20:53 GMT

Protected "5x9o" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:20, 15 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x9o is ON HOLD Authors: Sogabe, S., Ida, K., Lane, W., Snell, G. Description: Crystal structure of the BCL6 BTB domain in complex with Compound 1a...

OCA — Wed, 15 Mar 2017 20:20:51 GMT

New page: '''Unreleased structure''' The entry 5x9o is ON HOLD Authors: Sogabe, S., Ida, K., Lane, W., Snell, G. Description: Crystal structure of the BCL6 BTB domain in complex with Compound 1a...

New page

'''Unreleased structure'''

The entry 5x9o is ON HOLD

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

Description: Crystal structure of the BCL6 BTB domain in complex with Compound 1a
[[Category: Unreleased Structures]]
[[Category: Snell, G]]
[[Category: Lane, W]]
[[Category: Ida, K]]
[[Category: Sogabe, S]]