6oco - Revision history

OCA at 14:51, 13 March 2024

2024-03-13T14:51:28Z

← Older revision		Revision as of 14:51, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6oco' size='340' side='right'caption='[[6oco]], [[Resolution\|resolution]] 2.58Å' scene=''>		<StructureSection load='6oco' size='340' side='right'caption='[[6oco]], [[Resolution\|resolution]] 2.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6oco]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bovin Bovin~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OCO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OCO FirstGlance]. <br>		<table><tr><td colspan='2'>[[6oco]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OCO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OCO FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=M5V:4~~-[~~(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo~~[~~2.2.1~~]~~heptan-2-yl~~]-2~~-(pyridin-3-yl)pyrimidine-5-carbonitrile'>M5V</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]] 2.58Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">PIK3CD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), PIK3R1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M5V:4-[(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-(pyridin-3-yl)pyrimidine-5-carbonitrile'>M5V</scene></td></tr>
	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Phosphatidylinositol~~-4,5-~~bisphosphate_3~~-~~kinase Phosphatidylinositol~~-4,5-~~bisphosphate 3-kinase], with EC number~~ [~~http://www.brenda-enzymes~~.~~info/php/result_flat.php4?ecno=~~2.7.1~~.153~~ 2~~.7.1.153~~] </~~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=6oco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oco OCA], [https://pdbe.org/6oco PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oco RCSB], [https://www.ebi.ac.uk/pdbsum/6oco PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oco 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=6oco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oco OCA], [~~http~~://pdbe.org/6oco PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6oco RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6oco PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6oco ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[~~[http~~://www.uniprot.org/uniprot/PK3CD_HUMAN PK3CD_HUMAN]] Activated PIK3-delta syndrome. The disease is caused by mutations affecting the gene represented in this entry.		[https://www.uniprot.org/uniprot/PK3CD_HUMAN PK3CD_HUMAN] Activated PIK3-delta syndrome. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/PK3CD_HUMAN PK3CD_HUMAN]] Phosphoinositide-3-kinase (PI3K) that phosphorylates PftdIns(4,5)P2 (Phosphatidylinositol 4,5-bisphosphate) to generate phosphatidylinositol 3,4,5-trisphosphate (PIP3). PIP3 plays a key role by recruiting PH domain-containing proteins to the membrane, including AKT1 and PDPK1, activating signaling cascades involved in cell growth, survival, proliferation, motility and morphology. Mediates immune responses. Plays a role in B-cell development, proliferation, migration, and function. Required for B-cell receptor (BCR) signaling. Mediates B-cell proliferation response to anti-IgM, anti-CD40 and IL4 stimulation. Promotes cytokine production in response to TLR4 and TLR9. Required for antibody class switch mediated by TLR9. Involved in the antigen presentation function of B-cells. Involved in B-cell chemotaxis in response to CXCL13 and sphingosine 1-phosphate (S1P). Required for proliferation, signaling and cytokine production of naive, effector and memory T-cells. Required for T-cell receptor (TCR) signaling. Mediates TCR signaling events at the immune synapse. Activation by TCR leads to antigen-dependent memory T-cell migration and retention to antigenic tissues. Together with PIK3CG participates in T-cell development. Contributes to T-helper cell expansion and differentiation. Required for T-cell migration mediated by homing receptors SELL/CD62L, CCR7 and S1PR1 and antigen dependent recruitment of T-cells. Together with PIK3CG is involved in natural killer (NK) cell development and migration towards the sites of inflammation. Participates in NK cell receptor activation. Have a role in NK cell maturation and cytokine production. Together with PIK3CG is involved in neutrophil chemotaxis and extravasation. Together with PIK3CG participates in neutrophil respiratory burst. Have important roles in mast-cell development and mast cell mediated allergic response. Involved in stem cell factor (SCF)-mediated proliferation, adhesion and migration. Required for allergen-IgE-induced degranulation and cytokine release. The lipid kinase activity is required for its biological function. Isoform 2 may be involved in stabilizing total RAS levels, resulting in increased ERK phosphorylation and increased PI3K activity.<ref>PMID:20081091</ref> <ref>PMID:22020336</ref> [[http://www.uniprot.org/uniprot/P85A_BOVIN P85A_BOVIN]] Binds to activated (phosphorylated) protein-Tyr kinases, through its SH2 domain, and acts as an adapter, mediating the association of the p110 catalytic unit to the plasma membrane. Necessary for the insulin-stimulated increase in glucose uptake and glycogen synthesis in insulin-sensitive tissues. Plays an important role in signaling in response to FGFR1, FGFR2, FGFR3, FGFR4, KITLG/SCF, KIT, PDGFRA and PDGFRB. Likewise, plays a role in ITGB2 signaling (By similarity).		[https://www.uniprot.org/uniprot/PK3CD_HUMAN PK3CD_HUMAN] Phosphoinositide-3-kinase (PI3K) that phosphorylates PftdIns(4,5)P2 (Phosphatidylinositol 4,5-bisphosphate) to generate phosphatidylinositol 3,4,5-trisphosphate (PIP3). PIP3 plays a key role by recruiting PH domain-containing proteins to the membrane, including AKT1 and PDPK1, activating signaling cascades involved in cell growth, survival, proliferation, motility and morphology. Mediates immune responses. Plays a role in B-cell development, proliferation, migration, and function. Required for B-cell receptor (BCR) signaling. Mediates B-cell proliferation response to anti-IgM, anti-CD40 and IL4 stimulation. Promotes cytokine production in response to TLR4 and TLR9. Required for antibody class switch mediated by TLR9. Involved in the antigen presentation function of B-cells. Involved in B-cell chemotaxis in response to CXCL13 and sphingosine 1-phosphate (S1P). Required for proliferation, signaling and cytokine production of naive, effector and memory T-cells. Required for T-cell receptor (TCR) signaling. Mediates TCR signaling events at the immune synapse. Activation by TCR leads to antigen-dependent memory T-cell migration and retention to antigenic tissues. Together with PIK3CG participates in T-cell development. Contributes to T-helper cell expansion and differentiation. Required for T-cell migration mediated by homing receptors SELL/CD62L, CCR7 and S1PR1 and antigen dependent recruitment of T-cells. Together with PIK3CG is involved in natural killer (NK) cell development and migration towards the sites of inflammation. Participates in NK cell receptor activation. Have a role in NK cell maturation and cytokine production. Together with PIK3CG is involved in neutrophil chemotaxis and extravasation. Together with PIK3CG participates in neutrophil respiratory burst. Have important roles in mast-cell development and mast cell mediated allergic response. Involved in stem cell factor (SCF)-mediated proliferation, adhesion and migration. Required for allergen-IgE-induced degranulation and cytokine release. The lipid kinase activity is required for its biological function. Isoform 2 may be involved in stabilizing total RAS levels, resulting in increased ERK phosphorylation and increased PI3K activity.<ref>PMID:20081091</ref> <ref>PMID:22020336</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	A high-throughput screening (HTS) campaign identified a class of heteroaryl piperazines with excellent baseline affinity and selectivity for phosphoinositide 3-kinase delta (PI3Kdelta) over closely related isoforms. Rapid evaluation and optimization of structure-activity relationships (SAR) for this class, leveraging the modular nature of this scaffold, facilitated development of this hit class into a series of potent and selective inhibitors of PI3Kdelta. This effort culminated in the identification of 29, which displayed excellent potency in enzyme and cell-based assays, as well as favorable pharmacokinetic and off-target profiles.

	Discovery and optimization of heteroaryl piperazines as potent and selective PI3Kdelta inhibitors.,Zhou H, McGowan MA, Lipford K, Christopher M, Fradera X, Witter D, Lesburg CA, Li C, Methot JL, Lampe J, Achab A, Shaffer L, Goldenblatt P, Shah S, Bass A, Schroeder G, Chen D, Zeng H, Augustin MA, Katz JD Bioorg Med Chem Lett. 2020 Jan 1;30(1):126715. doi: 10.1016/j.bmcl.2019.126715., Epub 2019 Oct 18. PMID:31757666<ref>PMID:31757666</ref>		==See Also==
			*[[Phosphoinositide 3-kinase 3D structures\|Phosphoinositide 3-kinase 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe~~-~~citations 6oco" style="background~~-~~color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bovin~~]]		[[Category: Bos taurus]]
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Phosphatidylinositol-4,5-bisphosphate 3-kinase]]~~		[[Category: Augustin MA]]
	[[Category: Augustin~~, M A~~]]		[[Category: Lesburg CA]]
	[[Category: Lesburg~~, C A]]~~
	~~[[Category: Pi3kdelta kinase]]~~
	~~[[Category: Transferase]]~~
	~~[[Category: Transferase-transferase inhibitor complex~~]]

OCA at 11:57, 18 December 2019

2019-12-18T11:57:34Z

← Older revision		Revision as of 11:57, 18 December 2019
Line 3:		Line 3:
	<StructureSection load='6oco' size='340' side='right'caption='[[6oco]], [[Resolution\|resolution]] 2.58Å' scene=''>		<StructureSection load='6oco' size='340' side='right'caption='[[6oco]], [[Resolution\|resolution]] 2.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6oco]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OCO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OCO FirstGlance]. <br>		<table><tr><td colspan='2'>[[6oco]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OCO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OCO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M5V:4-[(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-(pyridin-3-yl)pyrimidine-5-carbonitrile'>M5V</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M5V:4-[(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-(pyridin-3-yl)pyrimidine-5-carbonitrile'>M5V</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PIK3CD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), PIK3R1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphatidylinositol-4,5-bisphosphate_3-kinase Phosphatidylinositol-4,5-bisphosphate 3-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.153 2.7.1.153] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphatidylinositol-4,5-bisphosphate_3-kinase Phosphatidylinositol-4,5-bisphosphate 3-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.153 2.7.1.153] </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=6oco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oco OCA], [http://pdbe.org/6oco PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oco RCSB], [http://www.ebi.ac.uk/pdbsum/6oco PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oco 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=6oco FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oco OCA], [http://pdbe.org/6oco PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oco RCSB], [http://www.ebi.ac.uk/pdbsum/6oco PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oco ProSAT]</span></td></tr>
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bovin]]
			[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Phosphatidylinositol-4,5-bisphosphate 3-kinase]]		[[Category: Phosphatidylinositol-4,5-bisphosphate 3-kinase]]

OCA at 15:09, 11 December 2019

2019-12-11T15:09:16Z

@@ Line 1: / Line 1: @@
-The entry 6oco is ON HOLD  until Paper Publication
+==HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 6==
-Authors: Lesburg, C.A., Augustin, M.A.
+Discovery and optimization of heteroaryl piperazines as potent and selective PI3Kdelta inhibitors.,Zhou H, McGowan MA, Lipford K, Christopher M, Fradera X, Witter D, Lesburg CA, Li C, Methot JL, Lampe J, Achab A, Shaffer L, Goldenblatt P, Shah S, Bass A, Schroeder G, Chen D, Zeng H, Augustin MA, Katz JD Bioorg Med Chem Lett. 2020 Jan 1;30(1):126715. doi: 10.1016/j.bmcl.2019.126715., Epub 2019 Oct 18. PMID:31757666<ref>PMID:31757666</ref>
-Description: HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 6
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Augustin, M.A]]
+<div class="pdbe-citations 6oco" style="background-color:#fffaf0;"></div>
-[[Category: Lesburg, C.A]]
+== References ==

OCA at 04:40, 31 July 2019

2019-07-31T04:40:36Z

← Older revision		Revision as of 04:40, 31 July 2019
Line 5:		Line 5:
	Authors: Lesburg, C.A., Augustin, M.A.		Authors: Lesburg, C.A., Augustin, M.A.

	Description: HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 5		Description: HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 6
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Augustin, M.A]]		[[Category: Augustin, M.A]]
	[[Category: Lesburg, C.A]]		[[Category: Lesburg, C.A]]

OCA at 04:07, 17 April 2019

2019-04-17T04:07:11Z

← Older revision		Revision as of 04:07, 17 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6oco is ON HOLD		The entry 6oco is ON HOLD until Paper Publication

	Authors: Lesburg, C.A., Augustin, M.A.		Authors: Lesburg, C.A., Augustin, M.A.

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

2019-04-03T04:39:47Z

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

← Older revision	Revision as of 04:39, 3 April 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6oco is ON HOLD Authors: Lesburg, C.A., Augustin, M.A. Description: HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 5 Category: Unreleased Structures ...

2019-04-03T04:39:46Z

New page: '''Unreleased structure''' The entry 6oco is ON HOLD Authors: Lesburg, C.A., Augustin, M.A. Description: HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 5 Category: Unreleased Structures ...

New page

'''Unreleased structure'''

The entry 6oco is ON HOLD

Authors: Lesburg, C.A., Augustin, M.A.

Description: HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 5
[[Category: Unreleased Structures]]
[[Category: Augustin, M.A]]
[[Category: Lesburg, C.A]]