7akg - Revision history

OCA at 12:11, 1 February 2024

2024-02-01T12:11:03Z

←Older revision		Revision as of 12:11, 1 February 2024
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	<StructureSection load='7akg' size='340' side='right'caption='[[7akg]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='7akg' size='340' side='right'caption='[[7akg]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7akg]] 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=7AKG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7AKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7akg]] 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=7AKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AKG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=38O:4-AMINO-5-FLUORO-3-[5-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]QUINOLIN-2(1H)-ONE'>38O</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 2.08Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STK17B, DRAK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=38O:4-AMINO-5-FLUORO-3-[5-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]QUINOLIN-2(1H)-ONE'>38O</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=7akg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7akg OCA], [https://pdbe.org/7akg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7akg RCSB], [https://www.ebi.ac.uk/pdbsum/7akg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7akg ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7akg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7akg OCA], [~~http~~://pdbe.org/7akg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7akg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7akg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7akg ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ST17B_HUMAN ST17B_HUMAN]] Phosphorylates myosin light chains (By similarity). Acts as a positive regulator of apoptosis.<ref>PMID:9786912</ref>	+	[https://www.uniprot.org/uniprot/ST17B_HUMAN ST17B_HUMAN] Phosphorylates myosin light chains (By similarity). Acts as a positive regulator of apoptosis.<ref>PMID:9786912</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7akg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7akg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Serine/threonine protein kinase 3D structures\|Serine/threonine protein kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Non-specific serine/threonine protein kinase]]~~	+	[[Category: Chaikuad A]]
-	[[Category: Chaikuad, A]]	+	[[Category: Knapp S]]
-	[[Category: Knapp, S]]	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Sgc]]~~	+
-	~~[[Category: Stk17b]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:03, 20 January 2021

2021-01-20T06:03:51Z

←Older revision		Revision as of 06:03, 20 January 2021
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	==Crystal structure of STK17B with bound dovitinib==		==Crystal structure of STK17B with bound dovitinib==
-	<StructureSection load='7akg' size='340' side='right'caption='[[7akg]]' scene=''>	+	<StructureSection load='7akg' size='340' side='right'caption='[[7akg]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AKG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7AKG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7akg]] 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=7AKG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7AKG FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7akg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7akg OCA], [http://pdbe.org/7akg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7akg RCSB], [http://www.ebi.ac.uk/pdbsum/7akg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7akg ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=38O:4-AMINO-5-FLUORO-3-[5-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]QUINOLIN-2(1H)-ONE'>38O</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STK17B, DRAK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7akg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7akg OCA], [http://pdbe.org/7akg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7akg RCSB], [http://www.ebi.ac.uk/pdbsum/7akg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7akg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ST17B_HUMAN ST17B_HUMAN]] Phosphorylates myosin light chains (By similarity). Acts as a positive regulator of apoptosis.<ref>PMID:9786912</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	STK17B is a member of the death-associated protein kinase family and has been genetically linked to the development of diverse diseases. However, the role of STK17B in normal and disease pathology is poorly defined. Here, we present the discovery of thieno[3,2-d] pyrimidine SGC-STK17B-1 (11s), a high-quality chemical probe for this understudied "dark" kinase. 11s is an ATP-competitive inhibitor that showed remarkable selectivity over other kinases including the closely related STK17A. X-ray crystallography of 11s and related thieno[3,2-d]pyrimidines bound to STK17B revealed a unique P-loop conformation characterized by a salt bridge between R41 and the carboxylic acid of the inhibitor. Molecular dynamic simulations of STK17B revealed the flexibility of the P-loop and a wide range of R41 conformations available to the apo-protein. The isomeric thieno[2,3-d]pyrimidine SGC-STK17B-1N (19g) was identified as a negative control compound. The >100-fold lower activity of 19g on STK17B was attributed to the reduced basicity of its pyrimidine N1.
		+
		+	A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation.,Picado A, Chaikuad A, Wells CI, Shrestha S, Zuercher WJ, Pickett JE, Kwarcinski FE, Sinha P, de Silva CS, Zutshi R, Liu S, Kannan N, Knapp S, Drewry DH, Willson TM J Med Chem. 2020 Dec 10;63(23):14626-14646. doi: 10.1021/acs.jmedchem.0c01174., Epub 2020 Nov 20. PMID:33215924<ref>PMID:33215924</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7akg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chaikuad A]]	+	[[Category: Non-specific serine/threonine protein kinase]]
-	[[Category: Knapp S]]	+	[[Category: Chaikuad, A]]
		+	[[Category: Knapp, S]]
		+	[[Category: Structural genomic]]
		+	[[Category: Inhibitor]]
		+	[[Category: Kinase]]
		+	[[Category: Sgc]]
		+	[[Category: Stk17b]]
		+	[[Category: Transferase]]

OCA at 07:50, 2 December 2020

2020-12-02T07:50:15Z

←Older revision		Revision as of 07:50, 2 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7akg ~~is ON HOLD~~	+	==Crystal structure of STK17B with bound dovitinib==
-		+	<StructureSection load='7akg' size='340' side='right'caption='[[7akg]]' scene=''>
-	~~Authors~~: ~~Chaikuad~~, A., ~~Knapp~~, S., ~~Structural Genomics Consortium (SGC)~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AKG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7AKG FirstGlance]. <br>
-	~~Description: Crystal structure of STK17B with bound dovitinib~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7akg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7akg OCA], [http://pdbe.org/7akg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7akg RCSB], [http://www.ebi.ac.uk/pdbsum/7akg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7akg ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Chaikuad, A]]	+	__TOC__
-	[[Category: Knapp, S]]	+	</StructureSection>
-	~~[[Category: Structural Genomics Consortium (Sgc)~~]]	+	[[Category: Large Structures]]
		+	[[Category: Chaikuad A]]
		+	[[Category: Knapp S]]

OCA: Protected "7akg" [edit=sysop:move=sysop]

2020-10-07T04:31:06Z

Protected "7akg" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:31, 7 October 2020

OCA: New page: '''Unreleased structure''' The entry 7akg is ON HOLD Authors: Chaikuad, A., Knapp, S., Structural Genomics Consortium (SGC) Description: Crystal structure of STK17B with bound dovitini...

2020-10-07T04:31:04Z

New page: '''Unreleased structure''' The entry 7akg is ON HOLD Authors: Chaikuad, A., Knapp, S., Structural Genomics Consortium (SGC) Description: Crystal structure of STK17B with bound dovitini...

New page

'''Unreleased structure'''

The entry 7akg is ON HOLD

Authors: Chaikuad, A., Knapp, S., Structural Genomics Consortium (SGC)

Description: Crystal structure of STK17B with bound dovitinib
[[Category: Unreleased Structures]]
[[Category: Chaikuad, A]]
[[Category: Knapp, S]]
[[Category: Structural Genomics Consortium (Sgc)]]