5yg2 - Revision history

OCA at 08:29, 22 November 2023

2023-11-22T08:29:12Z

←Older revision		Revision as of 08:29, 22 November 2023
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	<StructureSection load='5yg2' size='340' side='right'caption='[[5yg2]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5yg2' size='340' side='right'caption='[[5yg2]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yg2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YG2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yg2]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YG2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=N05:3-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidin-4-yl]propanoic+acid'>N05</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</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]] 2.2Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=N05:3-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidin-4-yl]propanoic+acid'>N05</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene></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=5yg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg2 OCA], [~~http~~://pdbe.org/5yg2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yg2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yg2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg2 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=5yg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg2 OCA], [https://pdbe.org/5yg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yg2 RCSB], [https://www.ebi.ac.uk/pdbsum/5yg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1G4H5I1_PLAVI A0A1G4H5I1_PLAVI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:

	==See Also==		==See Also==
-	*[[Serine hydroxymethyltransferase\|Serine hydroxymethyltransferase]]	+	*[[Serine hydroxymethyltransferase 3D structures\|Serine hydroxymethyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Glycine hydroxymethyltransferase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chitnumsub, P]]	+	[[Category: Plasmodium vivax]]
-	[[Category: Diederich, F]]	+	[[Category: Chitnumsub P]]
-	[[Category: Jaruwat, A]]	+	[[Category: Diederich F]]
-	[[Category: Leartsakulpanich, U]]	+	[[Category: Jaruwat A]]
-	[[Category: Schwertz, G]]	+	[[Category: Leartsakulpanich U]]
-	~~[[Category: Alpha and beta protein]]~~	+	[[Category: Schwertz G]]
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Methyltransferase activity]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-inhibitor complex~~]]	+

OCA at 09:18, 21 October 2020

2020-10-21T09:18:31Z

←Older revision		Revision as of 09:18, 21 October 2020
Line 1:		Line 1:

	==Plasmodium vivax SHMT bound with PLP-glycine and GS705==		==Plasmodium vivax SHMT bound with PLP-glycine and GS705==
-	<StructureSection load='5yg2' size='340' side='right' caption='[[5yg2]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5yg2' size='340' side='right'caption='[[5yg2]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yg2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YG2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yg2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YG2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=N05:3-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidin-4-yl]propanoic+acid'>N05</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=N05:3-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidin-4-yl]propanoic+acid'>N05</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </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=5yg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg2 OCA], [http://pdbe.org/5yg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yg2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg2 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=5yg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg2 OCA], [http://pdbe.org/5yg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yg2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5yg2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yg2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Serine hydroxymethyltransferase\|Serine hydroxymethyltransferase]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Glycine hydroxymethyltransferase]]		[[Category: Glycine hydroxymethyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Chitnumsub, P]]		[[Category: Chitnumsub, P]]
	[[Category: Diederich, F]]		[[Category: Diederich, F]]

OCA at 05:53, 6 June 2018

2018-06-06T05:53:04Z

←Older revision		Revision as of 05:53, 6 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yg2 is ~~ON HOLD until Paper~~ Publication	+	==Plasmodium vivax SHMT bound with PLP-glycine and GS705==
		+	<StructureSection load='5yg2' size='340' side='right' caption='[[5yg2]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yg2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YG2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=N05:3-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidin-4-yl]propanoic+acid'>N05</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </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=5yg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg2 OCA], [http://pdbe.org/5yg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yg2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg2 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	With the discovery that serine hydroxymethyltransferase (SHMT) is a druggable target for antimalarials, the aim of this study was to design novel inhibitors of this key enzyme in the folate biosynthesis cycle. Herein, 19 novel spirocyclic ligands based on either 2-indolinone or dihydroindene scaffolds and featuring a pyrazolopyran core are reported. Strong target affinities for Plasmodium falciparum (Pf) SHMT (14-76 nm) and cellular potencies in the low nanomolar range (165-334 nm) were measured together with interesting selectivity against human cytosolic SHMT1 (hSHMT1). Four co-crystal structures with Plasmodium vivax (Pv) SHMT solved at 2.2-2.4 A resolution revealed the key role of the vinylogous cyanamide for anchoring ligands within the active site. The spirocyclic motif in the molecules enforces the pyrazolopyran core to adopt a substantially more curved conformation than that of previous non-spirocyclic analogues. Finally, solvation of the spirocyclic lactam ring of the receptor-bound ligands is discussed.

-	~~Authors: Chitnumsub~~, P., Jaruwat, A., ~~Leartsakulpanich~~, U., ~~Schwertz~~, G., ~~Diederich~~, F.	+	Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold.,Schwertz G, Witschel MC, Rottmann M, Leartsakulpanich U, Chitnumsub P, Jaruwat A, Amornwatcharapong W, Ittarat W, Schafer A, Aponte RA, Trapp N, Chaiyen P, Diederich F ChemMedChem. 2018 May 8;13(9):931-943. doi: 10.1002/cmdc.201800053. Epub 2018 Apr, 14. PMID:29655285<ref>PMID:29655285</ref>

-	~~Description: Plasmodium vivax SHMT bound with PLP-glycine and GS705~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Jaruwat, A~~]]	+	<div class="pdbe-citations 5yg2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glycine hydroxymethyltransferase]]
	[[Category: Chitnumsub, P]]		[[Category: Chitnumsub, P]]
	[[Category: Diederich, F]]		[[Category: Diederich, F]]
-	[[Category: ~~Schwertz~~, G]]	+	[[Category: Jaruwat, A]]
	[[Category: Leartsakulpanich, U]]		[[Category: Leartsakulpanich, U]]
		+	[[Category: Schwertz, G]]
		+	[[Category: Alpha and beta protein]]
		+	[[Category: Inhibitor]]
		+	[[Category: Methyltransferase activity]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-inhibitor complex]]

OCA at 05:34, 25 October 2017

2017-10-25T05:34:57Z

←Older revision		Revision as of 05:34, 25 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yg2 is ON HOLD	+	The entry 5yg2 is ON HOLD until Paper Publication

	Authors: Chitnumsub, P., Jaruwat, A., Leartsakulpanich, U., Schwertz, G., Diederich, F.		Authors: Chitnumsub, P., Jaruwat, A., Leartsakulpanich, U., Schwertz, G., Diederich, F.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Jaruwat, A]]		[[Category: Jaruwat, A]]
-	[[Category: Leartsakulpanich, U]]
-	[[Category: Schwertz, G]]
	[[Category: Chitnumsub, P]]		[[Category: Chitnumsub, P]]
	[[Category: Diederich, F]]		[[Category: Diederich, F]]
		+	[[Category: Schwertz, G]]
		+	[[Category: Leartsakulpanich, U]]

OCA: Protected "5yg2" [edit=sysop:move=sysop]

2017-09-27T16:31:42Z

Protected "5yg2" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:31, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5yg2 is ON HOLD Authors: Chitnumsub, P., Jaruwat, A., Leartsakulpanich, U., Schwertz, G., Diederich, F. Description: Plasmodium vivax SHMT bound wi...

2017-09-27T16:31:41Z

New page: '''Unreleased structure''' The entry 5yg2 is ON HOLD Authors: Chitnumsub, P., Jaruwat, A., Leartsakulpanich, U., Schwertz, G., Diederich, F. Description: Plasmodium vivax SHMT bound wi...

New page

'''Unreleased structure'''

The entry 5yg2 is ON HOLD

Authors: Chitnumsub, P., Jaruwat, A., Leartsakulpanich, U., Schwertz, G., Diederich, F.

Description: Plasmodium vivax SHMT bound with PLP-glycine and GS705
[[Category: Unreleased Structures]]
[[Category: Jaruwat, A]]
[[Category: Leartsakulpanich, U]]
[[Category: Schwertz, G]]
[[Category: Chitnumsub, P]]
[[Category: Diederich, F]]