6qgh - Revision history

OCA at 12:00, 24 January 2024

OCA — Wed, 24 Jan 2024 12:00:18 GMT

←Older revision		Revision as of 12:00, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6qgh' size='340' side='right'caption='[[6qgh]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6qgh' size='340' side='right'caption='[[6qgh]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qgh]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QGH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QGH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qgh]] 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=6QGH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QGH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1XJ:4-(4-{[2-(4-CHLOROPHENYL)-5,5-DIMETHYLCYCLOHEX-1-EN-1-YL]METHYL}PIPERAZIN-1-YL)-N-[(4-{[(2R)-4-(MORPHOLIN-4-YL)-1-(PHENYLSULFANYL)BUTAN-2-YL]AMINO}-3-[(TRIFLUOROMETHYL)SULFONYL]PHENYL)SULFONYL]BENZAMIDE'>1XJ</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">[[6qg8\|6qg8]], [[6qgg\|6qgg]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1XJ:4-(4-{[2-(4-CHLOROPHENYL)-5,5-DIMETHYLCYCLOHEX-1-EN-1-YL]METHYL}PIPERAZIN-1-YL)-N-[(4-{[(2R)-4-(MORPHOLIN-4-YL)-1-(PHENYLSULFANYL)BUTAN-2-YL]AMINO}-3-[(TRIFLUOROMETHYL)SULFONYL]PHENYL)SULFONYL]BENZAMIDE'>1XJ</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=6qgh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qgh OCA], [~~http~~://pdbe.org/6qgh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qgh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qgh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qgh 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=6qgh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qgh OCA], [https://pdbe.org/6qgh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qgh RCSB], [https://www.ebi.ac.uk/pdbsum/6qgh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qgh ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/BCL2_HUMAN BCL2_HUMAN]] Note=A chromosomal aberration involving BCL2 has been found in chronic lymphatic leukemia. Translocation t(14;18)(q32;q21) with immunoglobulin gene regions. BCL2 mutations found in non-Hodgkin lymphomas carrying the chromosomal translocation could be attributed to the Ig somatic hypermutation mechanism resulting in nucleotide transitions.	+	[https://www.uniprot.org/uniprot/BCL2_HUMAN BCL2_HUMAN] Note=A chromosomal aberration involving BCL2 has been found in chronic lymphatic leukemia. Translocation t(14;18)(q32;q21) with immunoglobulin gene regions. BCL2 mutations found in non-Hodgkin lymphomas carrying the chromosomal translocation could be attributed to the Ig somatic hypermutation mechanism resulting in nucleotide transitions.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BCL2_HUMAN BCL2_HUMAN]] Suppresses apoptosis in a variety of cell systems including factor-dependent lymphohematopoietic and neural cells. Regulates cell death by controlling the mitochondrial membrane permeability. Appears to function in a feedback loop system with caspases. Inhibits caspase activity either by preventing the release of cytochrome c from the mitochondria and/or by binding to the apoptosis-activating factor (APAF-1).<ref>PMID:18570871</ref>	+	[https://www.uniprot.org/uniprot/BCL2_HUMAN BCL2_HUMAN] Suppresses apoptosis in a variety of cell systems including factor-dependent lymphohematopoietic and neural cells. Regulates cell death by controlling the mitochondrial membrane permeability. Appears to function in a feedback loop system with caspases. Inhibits caspase activity either by preventing the release of cytochrome c from the mitochondria and/or by binding to the apoptosis-activating factor (APAF-1).<ref>PMID:18570871</ref> [https://www.uniprot.org/uniprot/B2CL1_HUMAN B2CL1_HUMAN] Potent inhibitor of cell death. Inhibits activation of caspases (By similarity). Appears to regulate cell death by blocking the voltage-dependent anion channel (VDAC) by binding to it and preventing the release of the caspase activator, CYC1, from the mitochondrial membrane. Also acts as a regulator of G2 checkpoint and progression to cytokinesis during mitosis.<ref>PMID:19917720</ref> <ref>PMID:21840391</ref> Isoform Bcl-X(S) promotes apoptosis.<ref>PMID:19917720</ref> <ref>PMID:21840391</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We describe our work to establish structure- and fragment-based drug discovery to identify small molecules that inhibit the anti-apoptotic activity of the proteins Mcl-1 and Bcl-2. This identified hit series of compounds, some of which were subsequently optimized to clinical candidates in trials for treating various cancers. Many protein constructs were designed to identify protein with suitable properties for different biophysical assays and structural methods. Fragment screening using ligand-observed NMR experiments identified several series of compounds for each protein. The series were assessed for their potential for subsequent optimization using (1)H and (15)N heteronuclear single-quantum correlation NMR, surface plasmon resonance, and isothermal titration calorimetry measurements to characterize and validate binding. Crystal structures could not be determined for the early hits, so NMR methods were developed to provide models of compound binding to guide compound optimization. For Mcl-1, a benzodioxane/benzoxazine series was optimized to a K (d) of 40 muM before a thienopyrimidine hit series was identified which subsequently led to the lead series from which the clinical candidate S 64315 (MIK 665) was identified. For Bcl-2, the fragment-derived series were difficult to progress, and a compound derived from a published tetrahydroquinone compound was taken forward as the hit from which the clinical candidate (S 55746) was obtained. For both the proteins, the work to establish a portfolio of assays gave confidence for identification of compounds suitable for optimization.
		+
		+	Establishing Drug Discovery and Identification of Hit Series for the Anti-apoptotic Proteins, Bcl-2 and Mcl-1.,Murray JB, Davidson J, Chen I, Davis B, Dokurno P, Graham CJ, Harris R, Jordan A, Matassova N, Pedder C, Ray S, Roughley SD, Smith J, Walmsley C, Wang Y, Whitehead N, Williamson DS, Casara P, Le Diguarher T, Hickman J, Stark J, Kotschy A, Geneste O, Hubbard RE ACS Omega. 2019 May 23;4(5):8892-8906. doi: 10.1021/acsomega.9b00611. eCollection , 2019 May 31. PMID:31459977<ref>PMID:31459977</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6qgh" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Casara, P]]	+	[[Category: Casara P]]
-	[[Category: Chen, I]]	+	[[Category: Chen I]]
-	[[Category: Davidson, J]]	+	[[Category: Davidson J]]
-	[[Category: Davis, B]]	+	[[Category: Davis B]]
-	~~[[Category: Diguarher, T Le~~]]	+	[[Category: Dokurno P]]
-	[[Category: Dokurno, P]]	+	[[Category: Geneste O]]
-	[[Category: Geneste, O]]	+	[[Category: Graham CJ]]
-	[[Category: Graham~~, C J~~]]	+	[[Category: Harris R]]
-	[[Category: Harris, R]]	+	[[Category: Hickman J]]
-	[[Category: Hickman, J]]	+	[[Category: Hubbard RE]]
-	[[Category: Hubbard~~, R E~~]]	+	[[Category: Jordan AM]]
-	[[Category: Jordan~~, A M~~]]	+	[[Category: Kotschy A]]
-	[[Category: Kotschy, A]]	+	[[Category: Le Diguarher T]]
-	[[Category: Matassova, N]]	+	[[Category: Matassova N]]
-	[[Category: Murray, J]]	+	[[Category: Murray J]]
-	[[Category: Pedder, C]]	+	[[Category: Pedder C]]
-	[[Category: Ray, S]]	+	[[Category: Ray S]]
-	[[Category: Roughley, S]]	+	[[Category: Roughley S]]
-	[[Category: Smith, J]]	+	[[Category: Smith J]]
-	[[Category: Stark, J]]	+	[[Category: Stark J]]
-	[[Category: Walmsley, C]]	+	[[Category: Walmsley C]]
-	[[Category: Wang, Y]]	+	[[Category: Wang Y]]
-	[[Category: Whitehead, N]]	+	[[Category: Whitehead N]]
-	[[Category: Williamson~~, D S]]~~	+	[[Category: Williamson DS]]
-	~~[[Category: Abt-263]]~~	+
-	~~[[Category: Apoptosis]]~~	+
-	~~[[Category: Bcl2]]~~	+
-	~~[[Category: Drug design~~]]	+

OCA at 05:46, 12 June 2019

OCA — Wed, 12 Jun 2019 05:46:39 GMT

←Older revision		Revision as of 05:46, 12 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qgh ~~is ON HOLD until Paper Publication~~	+	==Structure of human Bcl-2 in complex with ABT-263==
-		+	<StructureSection load='6qgh' size='340' side='right'caption='[[6qgh]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Dokurno, P~~.~~, Murray, J~~.~~, Davidson, J~~.~~, Chen, I~~.~~, Davis, B~~.~~, Graham, C~~.J.~~, Harris, R~~., ~~Jordan~~, A.M.~~, Matassova, N~~.~~, Pedder, C~~., ~~Ray, S~~.~~, Roughley, S~~.~~, Smith, J~~., ~~Walmsley, C~~., ~~Wang, Y~~.~~, Whitehead, N~~., ~~Williamson, D~~.S.~~, Casara, P~~., ~~Le Diguarher, T~~.~~, Hickman, J~~.~~, Stark, J~~.~~, Kotschy,~~ A.~~, Geneste, O~~.~~, Hubbard, R.E~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6qgh]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QGH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QGH FirstGlance]. <br>
-	~~Description~~: ~~Structure~~ of ~~human Bcl~~-2 in ~~complex~~ with ~~ABT~~-~~263~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1XJ:4-(4-{[2-(4-CHLOROPHENYL)-5,5-DIMETHYLCYCLOHEX-1-EN-1-YL]METHYL}PIPERAZIN-1-YL)-N-[(4-{[(2R)-4-(MORPHOLIN-4-YL)-1-(PHENYLSULFANYL)BUTAN-2-YL]AMINO}-3-[(TRIFLUOROMETHYL)SULFONYL]PHENYL)SULFONYL]BENZAMIDE'>1XJ</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6qg8\|6qg8]], [[6qgg\|6qgg]]</td></tr>
-	[[Category: ~~Pedder~~, C]]	+	<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=6qgh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qgh OCA], [http://pdbe.org/6qgh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qgh RCSB], [http://www.ebi.ac.uk/pdbsum/6qgh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qgh ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/BCL2_HUMAN BCL2_HUMAN]] Note=A chromosomal aberration involving BCL2 has been found in chronic lymphatic leukemia. Translocation t(14;18)(q32;q21) with immunoglobulin gene regions. BCL2 mutations found in non-Hodgkin lymphomas carrying the chromosomal translocation could be attributed to the Ig somatic hypermutation mechanism resulting in nucleotide transitions.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BCL2_HUMAN BCL2_HUMAN]] Suppresses apoptosis in a variety of cell systems including factor-dependent lymphohematopoietic and neural cells. Regulates cell death by controlling the mitochondrial membrane permeability. Appears to function in a feedback loop system with caspases. Inhibits caspase activity either by preventing the release of cytochrome c from the mitochondria and/or by binding to the apoptosis-activating factor (APAF-1).<ref>PMID:18570871</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Casara, P]]
	[[Category: Chen, I]]		[[Category: Chen, I]]
-	[[Category: Williamson, D.S]]
-	[[Category: Smith, J]]
-	[[Category: Le Diguarher, T]]
-	[[Category: Matassova, N]]
	[[Category: Davidson, J]]		[[Category: Davidson, J]]
-	[[Category: Wang, Y]]
-	[[Category: Roughley, S]]
-	[[Category: Walmsley, C]]
-	[[Category: Graham, C.J]]
-	[[Category: Hubbard, R.E]]
	[[Category: Davis, B]]		[[Category: Davis, B]]
		+	[[Category: Diguarher, T Le]]
		+	[[Category: Dokurno, P]]
		+	[[Category: Geneste, O]]
		+	[[Category: Graham, C J]]
		+	[[Category: Harris, R]]
	[[Category: Hickman, J]]		[[Category: Hickman, J]]
		+	[[Category: Hubbard, R E]]
		+	[[Category: Jordan, A M]]
		+	[[Category: Kotschy, A]]
		+	[[Category: Matassova, N]]
		+	[[Category: Murray, J]]
		+	[[Category: Pedder, C]]
		+	[[Category: Ray, S]]
		+	[[Category: Roughley, S]]
		+	[[Category: Smith, J]]
	[[Category: Stark, J]]		[[Category: Stark, J]]
		+	[[Category: Walmsley, C]]
		+	[[Category: Wang, Y]]
	[[Category: Whitehead, N]]		[[Category: Whitehead, N]]
-	[[Category: ~~Jordan~~, ~~A.M~~]]	+	[[Category: Williamson, D S]]
-	[[Category: ~~Harris, R~~]]	+	[[Category: Abt-263]]
-	[[Category: ~~Murray, J~~]]	+	[[Category: Apoptosis]]
-	[[Category: ~~Dokurno, P~~]]	+	[[Category: Bcl2]]
-	[[Category: ~~Kotschy, A]]~~	+	[[Category: Drug design]]
-	~~[[Category: Casara, P]]~~	+
-	~~[[Category: Geneste, O]]~~	+
-	~~[[Category: Ray, S~~]]	+

OCA: Protected "6qgh" [edit=sysop:move=sysop]

OCA — Wed, 30 Jan 2019 06:54:31 GMT

Protected "6qgh" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:54, 30 January 2019

OCA: New page: '''Unreleased structure''' The entry 6qgh is ON HOLD until Paper Publication Authors: Dokurno, P., Murray, J., Davidson, J., Chen, I., Davis, B., Graham, C.J., Harris, R., Jordan, A.M.,...

OCA — Wed, 30 Jan 2019 06:54:30 GMT

New page: '''Unreleased structure''' The entry 6qgh is ON HOLD until Paper Publication Authors: Dokurno, P., Murray, J., Davidson, J., Chen, I., Davis, B., Graham, C.J., Harris, R., Jordan, A.M.,...

New page

'''Unreleased structure'''

The entry 6qgh is ON HOLD until Paper Publication

Authors: Dokurno, P., Murray, J., Davidson, J., Chen, I., Davis, B., Graham, C.J., Harris, R., Jordan, A.M., Matassova, N., Pedder, C., Ray, S., Roughley, S., Smith, J., Walmsley, C., Wang, Y., Whitehead, N., Williamson, D.S., Casara, P., Le Diguarher, T., Hickman, J., Stark, J., Kotschy, A., Geneste, O., Hubbard, R.E.

Description: Structure of human Bcl-2 in complex with ABT-263
[[Category: Unreleased Structures]]
[[Category: Pedder, C]]
[[Category: Chen, I]]
[[Category: Williamson, D.S]]
[[Category: Smith, J]]
[[Category: Le Diguarher, T]]
[[Category: Matassova, N]]
[[Category: Davidson, J]]
[[Category: Wang, Y]]
[[Category: Roughley, S]]
[[Category: Walmsley, C]]
[[Category: Graham, C.J]]
[[Category: Hubbard, R.E]]
[[Category: Davis, B]]
[[Category: Hickman, J]]
[[Category: Stark, J]]
[[Category: Whitehead, N]]
[[Category: Jordan, A.M]]
[[Category: Harris, R]]
[[Category: Murray, J]]
[[Category: Dokurno, P]]
[[Category: Kotschy, A]]
[[Category: Casara, P]]
[[Category: Geneste, O]]
[[Category: Ray, S]]