5b1s - Revision history

OCA at 15:55, 8 November 2023

OCA — Wed, 08 Nov 2023 15:55:45 GMT

←Older revision		Revision as of 15:55, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b1s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_cruzi_strain_CL_Brener Trypanosoma cruzi strain CL Brener]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B1S FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b1s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_cruzi_strain_CL_Brener Trypanosoma cruzi strain CL Brener]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B1S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BSX:2-(2-FLUOROPHENYL)ETHANAMINE'>BSX</scene>, <scene name='pdbligand=S4M:5-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5-DEOXYADENOSINE'>S4M</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]] 1.58Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BSX:2-(2-FLUOROPHENYL)ETHANAMINE'>BSX</scene>, <scene name='pdbligand=S4M:5-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5-DEOXYADENOSINE'>S4M</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=5b1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b1s OCA], [https://pdbe.org/5b1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b1s RCSB], [https://www.ebi.ac.uk/pdbsum/5b1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b1s 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=5b1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b1s OCA], [https://pdbe.org/5b1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b1s RCSB], [https://www.ebi.ac.uk/pdbsum/5b1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b1s ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:35, 31 May 2023

OCA — Wed, 31 May 2023 06:35:54 GMT

←Older revision		Revision as of 06:35, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5b1s' size='340' side='right'caption='[[5b1s]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='5b1s' size='340' side='right'caption='[[5b1s]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b1s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B1S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5B1S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b1s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_cruzi_strain_CL_Brener Trypanosoma cruzi strain CL Brener]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B1S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BSX:2-(2-FLUOROPHENYL)ETHANAMINE'>BSX</scene>, <scene name='pdbligand=S4M:5-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5-DEOXYADENOSINE'>S4M</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BSX:2-(2-FLUOROPHENYL)ETHANAMINE'>BSX</scene>, <scene name='pdbligand=S4M:5-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5-DEOXYADENOSINE'>S4M</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Spermidine_synthase Spermidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.16 2.5.1.16] </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=5b1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b1s OCA], [https://pdbe.org/5b1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b1s RCSB], [https://www.ebi.ac.uk/pdbsum/5b1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b1s 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=5b1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b1s OCA], [~~http~~://pdbe.org/5b1s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5b1s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5b1s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5b1s ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4DA73_TRYCC Q4DA73_TRYCC]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Spermidine synthase~~]]	+	[[Category: Trypanosoma cruzi strain CL Brener]]
-	[[Category: Amano, Y]]	+	[[Category: Amano Y]]
-	[[Category: Tateishi, Y]]	+	[[Category: Tateishi Y]]
-	~~[[Category: Polyamine synthesis]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:44, 11 March 2020

OCA — Wed, 11 Mar 2020 08:44:52 GMT

←Older revision		Revision as of 08:44, 11 March 2020
Line 1:		Line 1:

	==Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 2-(2-fluorophenyl)ethanamine==		==Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 2-(2-fluorophenyl)ethanamine==
-	<StructureSection load='5b1s' size='340' side='right' caption='[[5b1s]], [[Resolution\|resolution]] 1.58Å' scene=''>	+	<StructureSection load='5b1s' size='340' side='right'caption='[[5b1s]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b1s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B1S FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b1s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B1S FirstGlance]. <br>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5b1s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5b1s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Spermidine synthase 3D structures\|Spermidine synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Spermidine synthase]]		[[Category: Spermidine synthase]]
	[[Category: Amano, Y]]		[[Category: Amano, Y]]

OCA at 06:02, 17 August 2017

OCA — Thu, 17 Aug 2017 06:02:59 GMT

←Older revision		Revision as of 06:02, 17 August 2017
Line 8:		Line 8:
	<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=5b1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b1s OCA], [http://pdbe.org/5b1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b1s RCSB], [http://www.ebi.ac.uk/pdbsum/5b1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b1s 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=5b1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b1s OCA], [http://pdbe.org/5b1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b1s RCSB], [http://www.ebi.ac.uk/pdbsum/5b1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b1s ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chagas disease results from infection by Trypanosoma cruzi and is a neglected tropical disease (NTD). Although some treatment drugs are available, their use is associated with severe problems, including adverse effects and limited effectiveness during the chronic disease phase. To develop a novel anti-Chagas drug, we virtually screened 4.8 million small molecules against spermidine synthase (SpdSyn) as the target protein using our super computer "TSUBAME2.5" and conducted in vitro enzyme assays to determine the half-maximal inhibitory concentration values. We identified four hit compounds that inhibit T. cruzi SpdSyn (TcSpdSyn) by in silico and in vitro screening. We also determined the TcSpdSyn-hit compound complex structure using X-ray crystallography, which shows that the hit compound binds to the putrescine-binding site and interacts with Asp171 through a salt bridge.
		+
		+	In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease.,Yoshino R, Yasuo N, Hagiwara Y, Ishida T, Inaoka DK, Amano Y, Tateishi Y, Ohno K, Namatame I, Niimi T, Orita M, Kita K, Akiyama Y, Sekijima M Sci Rep. 2017 Jul 27;7(1):6666. doi: 10.1038/s41598-017-06411-9. PMID:28751689<ref>PMID:28751689</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5b1s" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:35, 22 December 2016

OCA — Thu, 22 Dec 2016 21:35:49 GMT

←Older revision		Revision as of 21:35, 22 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5b1s is ON HOLD until Paper Publication~~	+	==Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 2-(2-fluorophenyl)ethanamine==
-		+	<StructureSection load='5b1s' size='340' side='right' caption='[[5b1s]], [[Resolution\|resolution]] 1.58Å' scene=''>
-	~~Authors: Amano, Y., Tateishi, Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5b1s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B1S FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 2-(2-fluorophenyl)ethanamine	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BSX:2-(2-FLUOROPHENYL)ETHANAMINE'>BSX</scene>, <scene name='pdbligand=S4M:5-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5-DEOXYADENOSINE'>S4M</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/Spermidine_synthase Spermidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.16 2.5.1.16] </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=5b1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b1s OCA], [http://pdbe.org/5b1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b1s RCSB], [http://www.ebi.ac.uk/pdbsum/5b1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b1s ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Spermidine synthase]]
	[[Category: Amano, Y]]		[[Category: Amano, Y]]
	[[Category: Tateishi, Y]]		[[Category: Tateishi, Y]]
		+	[[Category: Polyamine synthesis]]
		+	[[Category: Transferase]]

OCA at 14:30, 30 December 2015

OCA — Wed, 30 Dec 2015 14:30:10 GMT

←Older revision		Revision as of 14:30, 30 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5b1s is ON HOLD	+	The entry 5b1s is ON HOLD until Paper Publication

	Authors: Amano, Y., Tateishi, Y.		Authors: Amano, Y., Tateishi, Y.

OCA: Protected "5b1s" [edit=sysop:move=sysop]

OCA — Wed, 23 Dec 2015 08:44:24 GMT

Protected "5b1s" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:44, 23 December 2015

OCA: New page: '''Unreleased structure''' The entry 5b1s is ON HOLD Authors: Amano, Y., Tateishi, Y. Description: Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 2-(2-fluor...

OCA — Wed, 23 Dec 2015 08:44:23 GMT

New page: '''Unreleased structure''' The entry 5b1s is ON HOLD Authors: Amano, Y., Tateishi, Y. Description: Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 2-(2-fluor...

New page

'''Unreleased structure'''

The entry 5b1s is ON HOLD

Authors: Amano, Y., Tateishi, Y.

Description: Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 2-(2-fluorophenyl)ethanamine
[[Category: Unreleased Structures]]
[[Category: Amano, Y]]
[[Category: Tateishi, Y]]