6ykv - Revision history

OCA at 13:29, 24 January 2024

2024-01-24T13:29:29Z

←Older revision		Revision as of 13:29, 24 January 2024
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	<StructureSection load='6ykv' size='340' side='right'caption='[[6ykv]], [[Resolution\|resolution]] 2.43Å' scene=''>		<StructureSection load='6ykv' size='340' side='right'caption='[[6ykv]], [[Resolution\|resolution]] 2.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ykv]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"diplococcus_gonorrhoeae"_(zopf_1885)_lehmann_and_neumann_1896 "diplococcus~~ gonorrhoeae~~" (zopf 1885) lehmann and neumann 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YKV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YKV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ykv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_gonorrhoeae Neisseria gonorrhoeae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YKV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OVQ:[(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-(4-pyridin-3-yl-1,2,3-triazol-1-yl)propyl]oxan-2-yl]methyl+~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate'>OVQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.43Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ykl\|6ykl]], [[6ykn\|6ykn]], [[6yko\|6yko]], [[6ykq\|6ykq]], [[6yks\|6yks]], [[6ykt\|6ykt]], [[6yku\|6yku]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OVQ:[(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-(4-pyridin-3-yl-1,2,3-triazol-1-yl)propyl]oxan-2-yl]methyl+~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate'>OVQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">leuS, VT05_02036, WHOO_00006, WHOO_00455 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=485 "Diplococcus gonorrhoeae" (Zopf 1885) Lehmann and Neumann 1896])</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=6ykv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ykv OCA], [https://pdbe.org/6ykv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ykv RCSB], [https://www.ebi.ac.uk/pdbsum/6ykv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ykv ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Leucine--tRNA_ligase Leucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.4 6.1.1.4] </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=6ykv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ykv OCA], [~~http~~://pdbe.org/6ykv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ykv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ykv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ykv ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SYL_NEIG1 SYL_NEIG1]
	<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 6ykv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ykv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacyl tRNA synthetase 3D structures\|Aminoacyl tRNA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Leucine--tRNA ligase~~]]	+	[[Category: Neisseria gonorrhoeae]]
-	[[Category: Pang, L]]	+	[[Category: Pang L]]
-	[[Category: Strelkov~~, S V~~]]	+	[[Category: Strelkov SV]]
-	[[Category: Weeks~~, S D]]~~	+	[[Category: Weeks SD]]
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Protein-inhibitor complex]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Trna synthetase~~]]	+

OCA at 06:52, 9 December 2020

2020-12-09T06:52:08Z

←Older revision		Revision as of 06:52, 9 December 2020
Line 1:		Line 1:

	==Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11g==		==Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11g==
-	<StructureSection load='6ykv' size='340' side='right'caption='[[6ykv]]' scene=''>	+	<StructureSection load='6ykv' size='340' side='right'caption='[[6ykv]], [[Resolution\|resolution]] 2.43Å' 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=6YKV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YKV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ykv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"diplococcus_gonorrhoeae"_(zopf_1885)_lehmann_and_neumann_1896 "diplococcus gonorrhoeae" (zopf 1885) lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YKV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YKV 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=6ykv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ykv OCA], [http://pdbe.org/6ykv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ykv RCSB], [http://www.ebi.ac.uk/pdbsum/6ykv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ykv 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OVQ:[(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-(4-pyridin-3-yl-1,2,3-triazol-1-yl)propyl]oxan-2-yl]methyl+~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate'>OVQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ykl\|6ykl]], [[6ykn\|6ykn]], [[6yko\|6yko]], [[6ykq\|6ykq]], [[6yks\|6yks]], [[6ykt\|6ykt]], [[6yku\|6yku]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">leuS, VT05_02036, WHOO_00006, WHOO_00455 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=485 "Diplococcus gonorrhoeae" (Zopf 1885) Lehmann and Neumann 1896])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Leucine--tRNA_ligase Leucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.4 6.1.1.4] </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=6ykv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ykv OCA], [http://pdbe.org/6ykv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ykv RCSB], [http://www.ebi.ac.uk/pdbsum/6ykv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ykv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Leucyl-tRNA synthetase (LeuRS) is a clinically validated target for the development of antimicrobials. This enzyme catalyzes the formation of charged tRNA(Leu) molecules, an essential substrate for protein translation. In the first step of catalysis LeuRS activates leucine using ATP, forming a leucyl-adenylate intermediate. Bi-substrate inhibitors that mimic this chemically labile phosphoanhydride-linked nucleoside have proven to be potent inhibitors of different members of the aminoacyl-tRNA synthetase family but, to date, they have demonstrated poor antibacterial activity. We synthesized a small series of 1,5-anhydrohexitol-based analogues coupled to a variety of triazoles and performed detailed structure-activity relationship studies with bacterial LeuRS. In an in vitro assay, Ki(app) values in the nanomolar range were demonstrated. Inhibitory activity differences between the compounds revealed that the polarity and size of the triazole substituents affect binding. X-ray crystallographic studies of N. gonorrhoeae LeuRS in complex with all the inhibitors highlighted the crucial interactions defining their relative enzyme inhibitory activities. We further examined their in vitro antimicrobial properties by screening against several bacterial and yeast strains. While only weak antibacterial activity against M. tuberculosis was detected, the extensive structural data which were obtained could make these LeuRS inhibitors a suitable starting point towards further antibiotic development.
		+
		+	Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors.,De Ruysscher D, Pang L, Lenders SMG, Cappoen D, Cos P, Rozenski J, Strelkov SV, Weeks SD, Van Aerschot A Eur J Med Chem. 2020 Nov 16:113021. doi: 10.1016/j.ejmech.2020.113021. PMID:33248851<ref>PMID:33248851</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ykv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pang L]]	+	[[Category: Leucine--tRNA ligase]]
-	[[Category: Strelkov SV]]	+	[[Category: Pang, L]]
-	[[Category: Weeks SD]]	+	[[Category: Strelkov, S V]]
		+	[[Category: Weeks, S D]]
		+	[[Category: Ligase]]
		+	[[Category: Protein-inhibitor complex]]
		+	[[Category: Rossmann fold]]
		+	[[Category: Trna synthetase]]

OCA at 07:47, 2 December 2020

2020-12-02T07:47:59Z

←Older revision		Revision as of 07:47, 2 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ykv ~~is ON HOLD until Paper Publication~~	+	==Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11g==
-		+	<StructureSection load='6ykv' size='340' side='right'caption='[[6ykv]]' scene=''>
-	~~Authors~~: ~~Pang~~, L., ~~Strelkov~~, S.V., ~~Weeks~~, S.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YKV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YKV FirstGlance]. <br>
-	~~Description: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11g~~	+	</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=6ykv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ykv OCA], [http://pdbe.org/6ykv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ykv RCSB], [http://www.ebi.ac.uk/pdbsum/6ykv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ykv ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Pang, L]]	+	__TOC__
-	[[Category: Strelkov~~, S.V~~]]	+	</StructureSection>
-	[[Category: Weeks~~, S.D~~]]	+	[[Category: Large Structures]]
		+	[[Category: Pang L]]
		+	[[Category: Strelkov SV]]
		+	[[Category: Weeks SD]]

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

2020-04-15T05:34:39Z

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

←Older revision

Revision as of 05:34, 15 April 2020

OCA: New page: '''Unreleased structure''' The entry 6ykv is ON HOLD until Paper Publication Authors: Pang, L., Strelkov, S.V., Weeks, S.D. Description: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in...

2020-04-15T05:34:38Z

New page: '''Unreleased structure''' The entry 6ykv is ON HOLD until Paper Publication Authors: Pang, L., Strelkov, S.V., Weeks, S.D. Description: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in...

New page

'''Unreleased structure'''

The entry 6ykv is ON HOLD until Paper Publication

Authors: Pang, L., Strelkov, S.V., Weeks, S.D.

Description: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11g
[[Category: Unreleased Structures]]
[[Category: Pang, L]]
[[Category: Strelkov, S.V]]
[[Category: Weeks, S.D]]