5kx9 - Revision history

OCA at 09:14, 25 October 2023

OCA — Wed, 25 Oct 2023 09:14:29 GMT

←Older revision		Revision as of 09:14, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kx9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusobacterium_nucleatum Fusobacterium nucleatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KX9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kx9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusobacterium_nucleatum Fusobacterium nucleatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KX9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6YG:2-[(3~{S})-1-[(2-METHOXYPYRIMIDIN-5-YL)METHYL]PIPERIDIN-3-YL]-6-THIOPHEN-2-YL-1~{H}-PYRIMIDIN-4-ONE'>6YG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6YG:2-[(3~{S})-1-[(2-METHOXYPYRIMIDIN-5-YL)METHYL]PIPERIDIN-3-YL]-6-THIOPHEN-2-YL-1~{H}-PYRIMIDIN-4-ONE'>6YG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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'>[https://proteopedia.org/fgij/fg.htm?mol=5kx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kx9 OCA], [https://pdbe.org/5kx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kx9 RCSB], [https://www.ebi.ac.uk/pdbsum/5kx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kx9 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=5kx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kx9 OCA], [https://pdbe.org/5kx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kx9 RCSB], [https://www.ebi.ac.uk/pdbsum/5kx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kx9 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:50, 22 February 2023

OCA — Wed, 22 Feb 2023 12:50:30 GMT

←Older revision		Revision as of 12:50, 22 February 2023
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	<StructureSection load='5kx9' size='340' side='right'caption='[[5kx9]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5kx9' size='340' side='right'caption='[[5kx9]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kx9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KX9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kx9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusobacterium_nucleatum Fusobacterium nucleatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KX9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6YG:2-[(3~{S})-1-[(2-METHOXYPYRIMIDIN-5-YL)METHYL]PIPERIDIN-3-YL]-6-THIOPHEN-2-YL-1~{H}-PYRIMIDIN-4-ONE'>6YG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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" id="ligandDat"><scene name='pdbligand=6YG:2-[(3~{S})-1-[(2-METHOXYPYRIMIDIN-5-YL)METHYL]PIPERIDIN-3-YL]-6-THIOPHEN-2-YL-1~{H}-PYRIMIDIN-4-ONE'>6YG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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~~://proteopedia.org/fgij/fg.htm?mol=5kx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kx9 OCA], [~~http~~://pdbe.org/5kx9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kx9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kx9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kx9 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=5kx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kx9 OCA], [https://pdbe.org/5kx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kx9 RCSB], [https://www.ebi.ac.uk/pdbsum/5kx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kx9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Fusobacterium nucleatum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fischmann~~, T O]]~~	+	[[Category: Fischmann TO]]
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna-inhibitor complex]]~~	+
-	~~[[Category: Translation~~]]	+

OCA at 06:36, 5 August 2020

OCA — Wed, 05 Aug 2020 06:36:40 GMT

←Older revision		Revision as of 06:36, 5 August 2020
Line 1:		Line 1:

	==Selective Small Molecule Inhibition of the FMN Riboswitch==		==Selective Small Molecule Inhibition of the FMN Riboswitch==
-	<StructureSection load='5kx9' size='340' side='right' caption='[[5kx9]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5kx9' size='340' side='right'caption='[[5kx9]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kx9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KX9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kx9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KX9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KX9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6YG:2-[(3~{S})-1-[(2-METHOXYPYRIMIDIN-5-YL)METHYL]PIPERIDIN-3-YL]-6-THIOPHEN-2-YL-1~{H}-PYRIMIDIN-4-ONE'>6YG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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" id="ligandDat"><scene name='pdbligand=6YG:2-[(3~{S})-1-[(2-METHOXYPYRIMIDIN-5-YL)METHYL]PIPERIDIN-3-YL]-6-THIOPHEN-2-YL-1~{H}-PYRIMIDIN-4-ONE'>6YG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=5kx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kx9 OCA], [http://pdbe.org/5kx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kx9 RCSB], [http://www.ebi.ac.uk/pdbsum/5kx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kx9 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=5kx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kx9 OCA], [http://pdbe.org/5kx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kx9 RCSB], [http://www.ebi.ac.uk/pdbsum/5kx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kx9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5kx9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kx9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fischmann, T O]]		[[Category: Fischmann, T O]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Rna-inhibitor complex]]		[[Category: Rna-inhibitor complex]]
	[[Category: Translation]]		[[Category: Translation]]

OCA at 06:54, 10 September 2016

OCA — Sat, 10 Sep 2016 06:54:51 GMT

←Older revision		Revision as of 06:54, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kx9 is ~~ON HOLD~~	+	==Selective Small Molecule Inhibition of the FMN Riboswitch==
		+	<StructureSection load='5kx9' size='340' side='right' caption='[[5kx9]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kx9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KX9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6YG:2-[(3~{S})-1-[(2-METHOXYPYRIMIDIN-5-YL)METHYL]PIPERIDIN-3-YL]-6-THIOPHEN-2-YL-1~{H}-PYRIMIDIN-4-ONE'>6YG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=5kx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kx9 OCA], [http://pdbe.org/5kx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kx9 RCSB], [http://www.ebi.ac.uk/pdbsum/5kx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kx9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, has led to efforts to develop small-molecules that mimic natural riboswitch ligands to inhibit metabolic pathways and bacterial growth. Recently, we reported the results of a phenotypic screen targeting the riboflavin biosynthesis pathway in the Gram-negative bacteria Escherichia coli that led to the identification of ribocil, a small molecule inhibitor of the flavin mononucleotide (FMN) riboswitch controlling expression of this biosynthetic pathway. Although ribocil is structurally distinct from FMN, ribocil functions as a potent and highly selective synthetic mimic of the natural ligand to repress riboswitch-mediated ribB gene expression and inhibit bacterial growth both in vitro and in vivo. Herein, we expand our analysis of ribocil; including mode of binding in the FMN binding pocket of the riboswitch, mechanisms of resistance and structure-activity relationship guided efforts to generate more potent analogs.

-	~~Authors~~: Fischmann, T.O.	+	Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch.,Howe JA, Xiao L, Fischmann TO, Wang H, Tang H, Villafania A, Zhang R, Barbieri CM, Roemer T RNA Biol. 2016 Aug 2:1-9. PMID:27485612<ref>PMID:27485612</ref>

-	~~Description: Selective Small Molecule Inhibition~~ of the ~~FMN Riboswitch~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Fischmann, T.O~~]]	+	<div class="pdbe-citations 5kx9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fischmann, T O]]
		+	[[Category: Rna]]
		+	[[Category: Rna-inhibitor complex]]
		+	[[Category: Translation]]

OCA at 02:09, 4 August 2016

OCA — Thu, 04 Aug 2016 02:09:00 GMT

←Older revision		Revision as of 02:09, 4 August 2016
Line 3:		Line 3:
	The entry 5kx9 is ON HOLD		The entry 5kx9 is ON HOLD

-	Authors: ~~Thierry~~ Fischmann	+	Authors: Fischmann, T.O.

	Description: Selective Small Molecule Inhibition of the FMN Riboswitch		Description: Selective Small Molecule Inhibition of the FMN Riboswitch
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Thierry~~ Fischmann]]	+	[[Category: Fischmann, T.O]]

OCA: Protected "5kx9" [edit=sysop:move=sysop]

OCA — Wed, 27 Jul 2016 13:29:50 GMT

Protected "5kx9" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:29, 27 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kx9 is ON HOLD Authors: Thierry Fischmann Description: Selective Small Molecule Inhibition of the FMN Riboswitch [[Category: Unreleased Structures...

OCA — Wed, 27 Jul 2016 13:29:48 GMT

New page: '''Unreleased structure''' The entry 5kx9 is ON HOLD Authors: Thierry Fischmann Description: Selective Small Molecule Inhibition of the FMN Riboswitch [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 5kx9 is ON HOLD

Authors: Thierry Fischmann

Description: Selective Small Molecule Inhibition of the FMN Riboswitch
[[Category: Unreleased Structures]]
[[Category: Thierry Fischmann]]