6jok - Revision history

OCA at 10:17, 22 November 2023

2023-11-22T10:17:01Z

←Older revision		Revision as of 10:17, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6jok' size='340' side='right'caption='[[6jok]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='6jok' size='340' side='right'caption='[[6jok]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jok]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JOK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JOK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jok]] 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=6JOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JOK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B49:N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>B49</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 3.8Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B49:N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>B49</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=6jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jok OCA], [~~http~~://pdbe.org/6jok PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jok RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jok PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jok 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=6jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jok OCA], [https://pdbe.org/6jok PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jok RCSB], [https://www.ebi.ac.uk/pdbsum/6jok PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jok ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PGFRA_HUMAN PGFRA_HUMAN]] Myeloid neoplasm associated with PDGFRA rearrangement;Primary hypereosinophilic syndrome;Precursor B-cell acute lymphoblastic leukemia;Gastrointestinal stromal tumor. A chromosomal aberration involving PDGFRA is found in some cases of hypereosinophilic syndrome. Interstitial chromosomal deletion del(4)(q12q12) causes the fusion of FIP1L1 and PDGFRA (FIP1L1-PDGFRA). Mutations that cause overexpression and/or constitutive activation of PDGFRA may be a cause of hypereosinophilic syndrome.<ref>PMID:12808148</ref> The gene represented in this entry may be involved in disease pathogenesis. Mutations causing PDGFRA constitutive activation have been found in gastrointestinal stromal tumors lacking KIT mutations (PubMed:12522257).<ref>PMID:12522257</ref>	+	[https://www.uniprot.org/uniprot/PGFRA_HUMAN PGFRA_HUMAN] Myeloid neoplasm associated with PDGFRA rearrangement;Primary hypereosinophilic syndrome;Precursor B-cell acute lymphoblastic leukemia;Gastrointestinal stromal tumor. A chromosomal aberration involving PDGFRA is found in some cases of hypereosinophilic syndrome. Interstitial chromosomal deletion del(4)(q12q12) causes the fusion of FIP1L1 and PDGFRA (FIP1L1-PDGFRA). Mutations that cause overexpression and/or constitutive activation of PDGFRA may be a cause of hypereosinophilic syndrome.<ref>PMID:12808148</ref> The gene represented in this entry may be involved in disease pathogenesis. Mutations causing PDGFRA constitutive activation have been found in gastrointestinal stromal tumors lacking KIT mutations (PubMed:12522257).<ref>PMID:12522257</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PGFRA_HUMAN PGFRA_HUMAN]] Tyrosine-protein kinase that acts as a cell-surface receptor for PDGFA, PDGFB and PDGFC and plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemotaxis. Depending on the context, promotes or inhibits cell proliferation and cell migration. Plays an important role in the differentiation of bone marrow-derived mesenchymal stem cells. Required for normal skeleton development and cephalic closure during embryonic development. Required for normal development of the mucosa lining the gastrointestinal tract, and for recruitment of mesenchymal cells and normal development of intestinal villi. Plays a role in cell migration and chemotaxis in wound healing. Plays a role in platelet activation, secretion of agonists from platelet granules, and in thrombin-induced platelet aggregation. Binding of its cognate ligands - homodimeric PDGFA, homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFC -leads to the activation of several signaling cascades; the response depends on the nature of the bound ligand and is modulated by the formation of heterodimers between PDGFRA and PDGFRB. Phosphorylates PIK3R1, PLCG1, and PTPN11. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate, mobilization of cytosolic Ca(2+) and the activation of protein kinase C. Phosphorylates PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, and thereby mediates activation of the AKT1 signaling pathway. Mediates activation of HRAS and of the MAP kinases MAPK1/ERK2 and/or MAPK3/ERK1. Promotes activation of STAT family members STAT1, STAT3 and STAT5A and/or STAT5B. Receptor signaling is down-regulated by protein phosphatases that dephosphorylate the receptor and its down-stream effectors, and by rapid internalization of the activated receptor.<ref>PMID:10734113</ref> <ref>PMID:10947961</ref> <ref>PMID:11297552</ref> <ref>PMID:12522257</ref> <ref>PMID:1646396</ref> <ref>PMID:1709159</ref> <ref>PMID:17141222</ref> <ref>PMID:20972453</ref> <ref>PMID:21224473</ref> <ref>PMID:21596750</ref> <ref>PMID:2554309</ref> <ref>PMID:8188664</ref> <ref>PMID:8760137</ref> <ref>PMID:8943348</ref>	+	[https://www.uniprot.org/uniprot/PGFRA_HUMAN PGFRA_HUMAN] Tyrosine-protein kinase that acts as a cell-surface receptor for PDGFA, PDGFB and PDGFC and plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemotaxis. Depending on the context, promotes or inhibits cell proliferation and cell migration. Plays an important role in the differentiation of bone marrow-derived mesenchymal stem cells. Required for normal skeleton development and cephalic closure during embryonic development. Required for normal development of the mucosa lining the gastrointestinal tract, and for recruitment of mesenchymal cells and normal development of intestinal villi. Plays a role in cell migration and chemotaxis in wound healing. Plays a role in platelet activation, secretion of agonists from platelet granules, and in thrombin-induced platelet aggregation. Binding of its cognate ligands - homodimeric PDGFA, homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFC -leads to the activation of several signaling cascades; the response depends on the nature of the bound ligand and is modulated by the formation of heterodimers between PDGFRA and PDGFRB. Phosphorylates PIK3R1, PLCG1, and PTPN11. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate, mobilization of cytosolic Ca(2+) and the activation of protein kinase C. Phosphorylates PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, and thereby mediates activation of the AKT1 signaling pathway. Mediates activation of HRAS and of the MAP kinases MAPK1/ERK2 and/or MAPK3/ERK1. Promotes activation of STAT family members STAT1, STAT3 and STAT5A and/or STAT5B. Receptor signaling is down-regulated by protein phosphatases that dephosphorylate the receptor and its down-stream effectors, and by rapid internalization of the activated receptor.<ref>PMID:10734113</ref> <ref>PMID:10947961</ref> <ref>PMID:11297552</ref> <ref>PMID:12522257</ref> <ref>PMID:1646396</ref> <ref>PMID:1709159</ref> <ref>PMID:17141222</ref> <ref>PMID:20972453</ref> <ref>PMID:21224473</ref> <ref>PMID:21596750</ref> <ref>PMID:2554309</ref> <ref>PMID:8188664</ref> <ref>PMID:8760137</ref> <ref>PMID:8943348</ref>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Receptor protein-tyrosine kinase]]~~	+	[[Category: Liang L]]
-	[[Category: Liang, L]]	+	[[Category: Yan XE]]
-	[[Category: Yan~~, X E~~]]	+	[[Category: Yun CH]]
-	[[Category: Yun~~, C H]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Oncoprotein]]~~	+
-	~~[[Category: Pdgfra]]~~	+
-	~~[[Category: Sunitinib~~]]	+

OCA at 10:03, 27 March 2020

2020-03-27T10:03:03Z

←Older revision		Revision as of 10:03, 27 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jok is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of PDGFRA in complex with sunitinib by soaking==
-		+	<StructureSection load='6jok' size='340' side='right'caption='[[6jok]], [[Resolution\|resolution]] 3.80Å' scene=''>
-	~~Authors~~: ~~Liang~~, L., ~~Yan~~, X.E., ~~Yun~~, C.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jok]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JOK FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of PDGFRA in ~~complex with sunitinib~~ by ~~soaking~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B49:N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>B49</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </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=6jok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jok OCA], [http://pdbe.org/6jok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jok RCSB], [http://www.ebi.ac.uk/pdbsum/6jok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jok ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PGFRA_HUMAN PGFRA_HUMAN]] Myeloid neoplasm associated with PDGFRA rearrangement;Primary hypereosinophilic syndrome;Precursor B-cell acute lymphoblastic leukemia;Gastrointestinal stromal tumor. A chromosomal aberration involving PDGFRA is found in some cases of hypereosinophilic syndrome. Interstitial chromosomal deletion del(4)(q12q12) causes the fusion of FIP1L1 and PDGFRA (FIP1L1-PDGFRA). Mutations that cause overexpression and/or constitutive activation of PDGFRA may be a cause of hypereosinophilic syndrome.<ref>PMID:12808148</ref> The gene represented in this entry may be involved in disease pathogenesis. Mutations causing PDGFRA constitutive activation have been found in gastrointestinal stromal tumors lacking KIT mutations (PubMed:12522257).<ref>PMID:12522257</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PGFRA_HUMAN PGFRA_HUMAN]] Tyrosine-protein kinase that acts as a cell-surface receptor for PDGFA, PDGFB and PDGFC and plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemotaxis. Depending on the context, promotes or inhibits cell proliferation and cell migration. Plays an important role in the differentiation of bone marrow-derived mesenchymal stem cells. Required for normal skeleton development and cephalic closure during embryonic development. Required for normal development of the mucosa lining the gastrointestinal tract, and for recruitment of mesenchymal cells and normal development of intestinal villi. Plays a role in cell migration and chemotaxis in wound healing. Plays a role in platelet activation, secretion of agonists from platelet granules, and in thrombin-induced platelet aggregation. Binding of its cognate ligands - homodimeric PDGFA, homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFC -leads to the activation of several signaling cascades; the response depends on the nature of the bound ligand and is modulated by the formation of heterodimers between PDGFRA and PDGFRB. Phosphorylates PIK3R1, PLCG1, and PTPN11. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate, mobilization of cytosolic Ca(2+) and the activation of protein kinase C. Phosphorylates PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, and thereby mediates activation of the AKT1 signaling pathway. Mediates activation of HRAS and of the MAP kinases MAPK1/ERK2 and/or MAPK3/ERK1. Promotes activation of STAT family members STAT1, STAT3 and STAT5A and/or STAT5B. Receptor signaling is down-regulated by protein phosphatases that dephosphorylate the receptor and its down-stream effectors, and by rapid internalization of the activated receptor.<ref>PMID:10734113</ref> <ref>PMID:10947961</ref> <ref>PMID:11297552</ref> <ref>PMID:12522257</ref> <ref>PMID:1646396</ref> <ref>PMID:1709159</ref> <ref>PMID:17141222</ref> <ref>PMID:20972453</ref> <ref>PMID:21224473</ref> <ref>PMID:21596750</ref> <ref>PMID:2554309</ref> <ref>PMID:8188664</ref> <ref>PMID:8760137</ref> <ref>PMID:8943348</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Receptor protein-tyrosine kinase]]
	[[Category: Liang, L]]		[[Category: Liang, L]]
-	[[Category: Yan, X.E]]	+	[[Category: Yan, X E]]
-	[[Category: Yun, C.H]]	+	[[Category: Yun, C H]]
		+	[[Category: Inhibitor]]
		+	[[Category: Oncoprotein]]
		+	[[Category: Pdgfra]]
		+	[[Category: Sunitinib]]

OCA at 06:27, 2 October 2019

2019-10-02T06:27:42Z

←Older revision		Revision as of 06:27, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jok is ON HOLD	+	The entry 6jok is ON HOLD until Paper Publication

	Authors: Liang, L., Yan, X.E., Yun, C.H.		Authors: Liang, L., Yan, X.E., Yun, C.H.

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

2019-03-27T04:54:35Z

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

←Older revision

Revision as of 04:54, 27 March 2019

OCA: New page: '''Unreleased structure''' The entry 6jok is ON HOLD Authors: Liang, L., Yan, X.E., Yun, C.H. Description: Crystal structure of PDGFRA in complex with sunitinib by soaking [[Category: ...

2019-03-27T04:54:34Z

New page: '''Unreleased structure''' The entry 6jok is ON HOLD Authors: Liang, L., Yan, X.E., Yun, C.H. Description: Crystal structure of PDGFRA in complex with sunitinib by soaking [[Category: ...

New page

'''Unreleased structure'''

The entry 6jok is ON HOLD

Authors: Liang, L., Yan, X.E., Yun, C.H.

Description: Crystal structure of PDGFRA in complex with sunitinib by soaking
[[Category: Unreleased Structures]]
[[Category: Liang, L]]
[[Category: Yan, X.E]]
[[Category: Yun, C.H]]