OCA at 11:00, 22 November 2023

2023-11-22T11:00:52Z

←Older revision		Revision as of 11:00, 22 November 2023
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	==Crystal structure of human PDK2 complexed with GM67520==		==Crystal structure of human PDK2 complexed with GM67520==
-	<StructureSection load='6lio' size='340' side='right'caption='[[6lio]]' scene=''>	+	<StructureSection load='6lio' size='340' side='right'caption='[[6lio]], [[Resolution\|resolution]] 1.76Å' 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=6LIO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lio]] is a 2 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=6LIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LIO 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=6lio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lio OCA], [~~http~~://pdbe.org/6lio PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6lio RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6lio PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6lio ProSAT]</span></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]] 1.76Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EH3:4-[[[5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-4-[4-(1-methylsulfonylpiperidin-4-yl)oxyphenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]cyclohexane-1-carboxylic+acid'>EH3</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6lio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lio OCA], [https://pdbe.org/6lio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lio RCSB], [https://www.ebi.ac.uk/pdbsum/6lio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lio ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PDK2_HUMAN PDK2_HUMAN] Serine/threonine kinase that plays a key role in the regulation of glucose and fatty acid metabolism and homeostasis via phosphorylation of the pyruvate dehydrogenase subunits PDHA1 and PDHA2. This inhibits pyruvate dehydrogenase activity, and thereby regulates metabolite flux through the tricarboxylic acid cycle, down-regulates aerobic respiration and inhibits the formation of acetyl-coenzyme A from pyruvate. Inhibition of pyruvate dehydrogenase decreases glucose utilization and increases fat metabolism. Mediates cellular responses to insulin. Plays an important role in maintaining normal blood glucose levels and in metabolic adaptation to nutrient availability. Via its regulation of pyruvate dehydrogenase activity, plays an important role in maintaining normal blood pH and in preventing the accumulation of ketone bodies under starvation. Plays a role in the regulation of cell proliferation and in resistance to apoptosis under oxidative stress. Plays a role in p53/TP53-mediated apoptosis.<ref>PMID:7499431</ref> <ref>PMID:9787110</ref> <ref>PMID:17222789</ref> <ref>PMID:19833728</ref> <ref>PMID:21283817</ref> <ref>PMID:22123926</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyruvate dehydrogenase kinase (PDK) controls the activity of pyruvate decarboxylase complex (PDC) by phosphorylating key serine residues on the E1 subunit, which leads to a decreased oxidative phosphorylation in mitochondria. Inhibition of PDK activity by natural/synthetic compounds has been shown to reverse the Warburg effect, a characteristic metabolism in cancer cells. PDK-PDC axis also has been associated with diabetes and heart disease. Therefore, regulation of PDK activity has been considered as a promising strategy to treat related diseases. Here we present the X-ray crystal structure of PDK2 complexed with a recently identified PDK4 inhibitor, compound 8c, which has been predicted to bind at the lipoyl-binding site and interrupt intermolecular interactions with the E2-E3bp subunits of PDC. The co-crystal structure confirmed the specific binding location of compound 8c and revealed the remote conformational change in the ATP-binding pocket. In addition, two novel 4,5-diarylisoxazole derivatives, GM10030 and GM67520, were synthesized and used for structural studies, which target the ATP-binding site of PDK2. These compounds bind to PDK2 with a sub-100nM affinity as determined by isothermal titration calorimetry experiments. Notably, the crystal structure of the PDK2-GM10030 complex displays unprecedented asymmetric conformation of human PDK2 dimer, especially in the ATP-lids and C-terminal tails.
		+
		+	Structural basis for the inhibition of PDK2 by novel ATP- and lipoyl-binding site targeting compounds.,Kang J, Pagire HS, Kang D, Song YH, Lee IK, Lee KT, Park CJ, Ahn JH, Kim J Biochem Biophys Res Commun. 2020 Jun 30;527(3):778-784. doi:, 10.1016/j.bbrc.2020.04.102. Epub 2020 May 20. PMID:32444142<ref>PMID:32444142</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6lio" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pyruvate dehydrogenase kinase\|Pyruvate dehydrogenase kinase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kang J]]		[[Category: Kang J]]
	[[Category: Kim J]]		[[Category: Kim J]]

OCA at 07:04, 30 September 2020

2020-09-30T07:04:30Z

←Older revision		Revision as of 07:04, 30 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6lio ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of human PDK2 complexed with GM67520==
-		+	<StructureSection load='6lio' size='340' side='right'caption='[[6lio]]' scene=''>
-	~~Authors~~: ~~Kang~~, J., ~~Kim~~, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LIO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LIO FirstGlance]. <br>
-	~~Description: Crystal structure of human PDK2 complexed with GM67520~~	+	</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=6lio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lio OCA], [http://pdbe.org/6lio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lio RCSB], [http://www.ebi.ac.uk/pdbsum/6lio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lio ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kang, J]]	+	__TOC__
-	[[Category: Kim, J]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kang J]]
		+	[[Category: Kim J]]

OCA at 06:33, 1 January 2020

2020-01-01T06:33:30Z

←Older revision		Revision as of 06:33, 1 January 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kang, J., Kim, J.		Authors: Kang, J., Kim, J.

-	Description: Crystal structure of human PDK2 complexed with ~~an allosteric inhibitor GM10123~~	+	Description: Crystal structure of human PDK2 complexed with GM67520
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kang, J]]		[[Category: Kang, J]]
	[[Category: Kim, J]]		[[Category: Kim, J]]

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

2019-12-18T05:44:33Z

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

←Older revision

Revision as of 05:44, 18 December 2019

OCA: New page: '''Unreleased structure''' The entry 6lio is ON HOLD Authors: Kang, J., Kim, J. Description: Crystal structure of human PDK2 complexed with an allosteric inhibitor GM10123 [[Category: ...

2019-12-18T05:44:31Z

New page: '''Unreleased structure''' The entry 6lio is ON HOLD Authors: Kang, J., Kim, J. Description: Crystal structure of human PDK2 complexed with an allosteric inhibitor GM10123 [[Category: ...

New page

'''Unreleased structure'''

The entry 6lio is ON HOLD

Authors: Kang, J., Kim, J.

Description: Crystal structure of human PDK2 complexed with an allosteric inhibitor GM10123
[[Category: Unreleased Structures]]
[[Category: Kang, J]]
[[Category: Kim, J]]

6lio - Revision history

OCA at 11:00, 22 November 2023

OCA at 07:04, 30 September 2020

OCA at 06:33, 1 January 2020

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

OCA: New page: '''Unreleased structure''' The entry 6lio is ON HOLD Authors: Kang, J., Kim, J. Description: Crystal structure of human PDK2 complexed with an allosteric inhibitor GM10123 [[Category: ...