5ywx - Revision history

OCA at 08:39, 22 November 2023

OCA — Wed, 22 Nov 2023 08:39:35 GMT

←Older revision		Revision as of 08:39, 22 November 2023
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	==Crystal structure of hematopoietic prostaglandin D synthase in complex with F092==		==Crystal structure of hematopoietic prostaglandin D synthase in complex with F092==
-	<StructureSection load='5ywx' size='340' side='right' caption='[[5ywx]], [[Resolution\|resolution]] 1.74Å' scene=''>	+	<StructureSection load='5ywx' size='340' side='right'caption='[[5ywx]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ywx]] is a 4 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=5YWX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YWX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ywx]] is a 4 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=5YWX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YWX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=93C:N-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl)pyrimidine-5-carboxamide'>93C</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.74Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPGDS, GSTS, PGDS, PTGDS2 ([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=93C:N-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl)pyrimidine-5-carboxamide'>93C</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5ywx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ywx OCA], [~~http~~://pdbe.org/5ywx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ywx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ywx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ywx 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=5ywx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ywx OCA], [https://pdbe.org/5ywx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ywx RCSB], [https://www.ebi.ac.uk/pdbsum/5ywx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ywx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HPGDS_HUMAN HPGDS_HUMAN]] Bifunctional enzyme which catalyzes both the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation, and the conjugation of glutathione with a wide range of aryl halides and organic isothiocyanates. Also exhibits low glutathione-peroxidase activity towards cumene hydroperoxide.<ref>PMID:10824118</ref> <ref>PMID:11672424</ref> <ref>PMID:9425264</ref> <ref>PMID:9353279</ref> <ref>PMID:12627223</ref> <ref>PMID:15113825</ref> <ref>PMID:16547010</ref> <ref>PMID:19939518</ref>	+	[https://www.uniprot.org/uniprot/HPGDS_HUMAN HPGDS_HUMAN] Bifunctional enzyme which catalyzes both the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation, and the conjugation of glutathione with a wide range of aryl halides and organic isothiocyanates. Also exhibits low glutathione-peroxidase activity towards cumene hydroperoxide.<ref>PMID:10824118</ref> <ref>PMID:11672424</ref> <ref>PMID:9425264</ref> <ref>PMID:9353279</ref> <ref>PMID:12627223</ref> <ref>PMID:15113825</ref> <ref>PMID:16547010</ref> <ref>PMID:19939518</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5ywx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ywx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutathione S-transferase 3D structures\|Glutathione S-transferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Aritake, K]]	+	[[Category: Large Structures]]
-	[[Category: Furubayashi, N]]	+	[[Category: Aritake K]]
-	[[Category: Inaka, K]]	+	[[Category: Furubayashi N]]
-	[[Category: Kamo, M]]	+	[[Category: Inaka K]]
-	[[Category: Omura, A]]	+	[[Category: Kamo M]]
-	[[Category: Tanaka, A]]	+	[[Category: Omura A]]
-	~~[[Category: Inhibitor]]~~	+	[[Category: Tanaka A]]
-	~~[[Category: Prostaglandin]]~~	+
-	~~[[Category: Synthase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-transferase inhibitor complex~~]]	+

OCA at 07:47, 12 September 2018

OCA — Wed, 12 Sep 2018 07:47:52 GMT

←Older revision		Revision as of 07:47, 12 September 2018
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	<StructureSection load='5ywx' size='340' side='right' caption='[[5ywx]], [[Resolution\|resolution]] 1.74Å' scene=''>		<StructureSection load='5ywx' size='340' side='right' caption='[[5ywx]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ywx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YWX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YWX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ywx]] is a 4 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=5YWX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YWX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=93C:N-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl)pyrimidine-5-carboxamide'>93C</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=93C:N-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl)pyrimidine-5-carboxamide'>93C</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HPGDS, GSTS, PGDS, PTGDS2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5ywx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ywx OCA], [http://pdbe.org/5ywx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ywx RCSB], [http://www.ebi.ac.uk/pdbsum/5ywx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ywx 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=5ywx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ywx OCA], [http://pdbe.org/5ywx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ywx RCSB], [http://www.ebi.ac.uk/pdbsum/5ywx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ywx ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Aritake, K]]		[[Category: Aritake, K]]
	[[Category: Furubayashi, N]]		[[Category: Furubayashi, N]]

OCA at 10:01, 5 September 2018

OCA — Wed, 05 Sep 2018 10:01:37 GMT

←Older revision		Revision as of 10:01, 5 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ywx is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of hematopoietic prostaglandin D synthase in complex with F092==
		+	<StructureSection load='5ywx' size='340' side='right' caption='[[5ywx]], [[Resolution\|resolution]] 1.74Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ywx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YWX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YWX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=93C:N-[4-(2-oxopyrrolidin-1-yl)phenyl]-2-(pyridin-2-yl)pyrimidine-5-carboxamide'>93C</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5ywx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ywx OCA], [http://pdbe.org/5ywx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ywx RCSB], [http://www.ebi.ac.uk/pdbsum/5ywx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ywx ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HPGDS_HUMAN HPGDS_HUMAN]] Bifunctional enzyme which catalyzes both the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation, and the conjugation of glutathione with a wide range of aryl halides and organic isothiocyanates. Also exhibits low glutathione-peroxidase activity towards cumene hydroperoxide.<ref>PMID:10824118</ref> <ref>PMID:11672424</ref> <ref>PMID:9425264</ref> <ref>PMID:9353279</ref> <ref>PMID:12627223</ref> <ref>PMID:15113825</ref> <ref>PMID:16547010</ref> <ref>PMID:19939518</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hematopoietic prostaglandin D synthase (H-PGDS) is one of the two enzymes that catalyze prostaglandin D2 synthesis and a potential therapeutic target of allergic and inflammatory responses. To reveal key molecular interactions between a high-affinity ligand and H-PGDS, we designed and synthesized a potent new inhibitor (KD: 0.14nM), determined the crystal structure in complex with human H-PGDS, and quantitatively analyzed the ligand-protein interactions by the fragment molecular orbital calculation method. In the cavity, 10 water molecules were identified, and the interaction energy calculation indicated their stable binding to the surface amino acids in the cavity. Among them, 6 water molecules locating from the deep inner cavity to the peripheral part of the cavity contributed directly to the ligand binding by forming hydrogen bonding interactions. Arg12, Gly13, Gln36, Asp96, Trp104, Lys112 and an essential co-factor glutathione also had strong interactions with the ligand. A strong repulsive interaction between Leu199 and the ligand was canceled out by forming a hydrogen bonding network with the adjacent conserved water molecule. Our quantitative studies including crystal water molecules explained that compounds with an elongated backbone structure to fit from the deep inner cavity to the peripheral part of the cavity would have strong affinity to human H-PGDS.

-	~~Authors~~:	+	Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies.,Takaya D, Inaka K, Omura A, Takenuki K, Kawanishi M, Yabuki Y, Nakagawa Y, Tsuganezawa K, Ogawa N, Watanabe C, Honma T, Aritake K, Urade Y, Shirouzu M, Tanaka A Bioorg Med Chem. 2018 Sep 1;26(16):4726-4734. doi: 10.1016/j.bmc.2018.08.014., Epub 2018 Aug 11. PMID:30121213<ref>PMID:30121213</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ywx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aritake, K]]
		+	[[Category: Furubayashi, N]]
		+	[[Category: Inaka, K]]
		+	[[Category: Kamo, M]]
		+	[[Category: Omura, A]]
		+	[[Category: Tanaka, A]]
		+	[[Category: Inhibitor]]
		+	[[Category: Prostaglandin]]
		+	[[Category: Synthase]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-transferase inhibitor complex]]

OCA at 04:49, 20 December 2017

OCA — Wed, 20 Dec 2017 04:49:36 GMT

←Older revision		Revision as of 04:49, 20 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ywx is ON HOLD	+	The entry 5ywx is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5ywx" [edit=sysop:move=sysop]

OCA — Wed, 06 Dec 2017 06:01:37 GMT

Protected "5ywx" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:01, 6 December 2017

OCA: New page: '''Unreleased structure''' The entry 5ywx is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 06 Dec 2017 06:01:36 GMT

New page: '''Unreleased structure''' The entry 5ywx is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ywx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]