6bfb - Revision history

OCA at 14:32, 6 March 2024

2024-03-06T14:32:34Z

← Older revision		Revision as of 14:32, 6 March 2024
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	<StructureSection load='6bfb' size='340' side='right'caption='[[6bfb]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='6bfb' size='340' side='right'caption='[[6bfb]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bfb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BFB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6BFB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bfb]] 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=6BFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BFB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DKM:5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic+acid'>DKM</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]] 2.82Å</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=6bfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bfb OCA], [~~http~~://pdbe.org/6bfb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bfb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bfb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bfb ProSAT]</span></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DKM:5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic+acid'>DKM</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=6bfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bfb OCA], [https://pdbe.org/6bfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bfb RCSB], [https://www.ebi.ac.uk/pdbsum/6bfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bfb ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Recent advances in understanding the relevance of noncoding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA. Affinity-selection mass spectrometry (AS-MS) is theoretically applicable to high-throughput screening (HTS) of small molecules binding to ncRNA. Here, we report the first application of the Automated Ligand Detection System (ALIS), an indirect AS-MS technique, for the selective detection of small molecule-ncRNA interactions, high-throughput screening against large unbiased small-molecule libraries, and identification and characterization of novel compounds (structurally distinct from both FMN and ribocil) that target the FMN riboswitch. Crystal structures reveal that different compounds induce various conformations of the FMN riboswitch, leading to different activity profiles. Our findings validate the ALIS platform for HTS screening for RNA-binding small molecules and further demonstrate that ncRNA can be broadly targeted by chemically diverse yet selective small molecules as therapeutics.

	Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry.,Rizvi NF, Howe JA, Nahvi A, Klein DJ, Fischmann TO, Kim HY, McCoy MA, Walker SS, Hruza A, Richards MP, Chamberlin C, Saradjian P, Butko MT, Mercado G, Burchard J, Strickland C, Dandliker PJ, Smith GF, Nickbarg EB ACS Chem Biol. 2018 Feb 14. doi: 10.1021/acschembio.7b01013. PMID:29412640<ref>PMID:29412640</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6bfb" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]		*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Fusobacterium nucleatum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fischmann~~, T O~~]]		[[Category: Fischmann TO]]
	[[Category: Rizvi~~, N F]]~~		[[Category: Rizvi NF]]
	~~[[Category: Rna]]~~
	~~[[Category: Rna-inhibitor complex]]~~
	~~[[Category: Translation~~]]

OCA at 08:49, 11 November 2020

2020-11-11T08:49:27Z

← Older revision		Revision as of 08:49, 11 November 2020
Line 1:		Line 1:

	==Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3==		==Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3==
	<StructureSection load='6bfb' size='340' side='right' caption='[[6bfb]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='6bfb' size='340' side='right'caption='[[6bfb]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bfb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BFB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BFB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bfb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BFB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BFB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DKM:5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic+acid'>DKM</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=DKM:5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic+acid'>DKM</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=6bfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bfb OCA], [http://pdbe.org/6bfb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bfb RCSB], [http://www.ebi.ac.uk/pdbsum/6bfb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bfb 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=6bfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bfb OCA], [http://pdbe.org/6bfb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bfb RCSB], [http://www.ebi.ac.uk/pdbsum/6bfb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bfb 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 6bfb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bfb" 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: Rizvi, N F]]		[[Category: Rizvi, N F]]

OCA at 07:26, 22 February 2018

2018-02-22T07:26:41Z

← Older revision		Revision as of 07:26, 22 February 2018
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6bfb is ~~ON HOLD until Paper~~ Publication		==Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3==
			<StructureSection load='6bfb' size='340' side='right' caption='[[6bfb]], [[Resolution\|resolution]] 2.82Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[6bfb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BFB FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DKM:5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic+acid'>DKM</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=6bfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bfb OCA], [http://pdbe.org/6bfb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bfb RCSB], [http://www.ebi.ac.uk/pdbsum/6bfb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bfb ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Recent advances in understanding the relevance of noncoding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA. Affinity-selection mass spectrometry (AS-MS) is theoretically applicable to high-throughput screening (HTS) of small molecules binding to ncRNA. Here, we report the first application of the Automated Ligand Detection System (ALIS), an indirect AS-MS technique, for the selective detection of small molecule-ncRNA interactions, high-throughput screening against large unbiased small-molecule libraries, and identification and characterization of novel compounds (structurally distinct from both FMN and ribocil) that target the FMN riboswitch. Crystal structures reveal that different compounds induce various conformations of the FMN riboswitch, leading to different activity profiles. Our findings validate the ALIS platform for HTS screening for RNA-binding small molecules and further demonstrate that ncRNA can be broadly targeted by chemically diverse yet selective small molecules as therapeutics.

	~~Authors:~~ Rizvi, ~~N.F.~~, Fischmann, T.O.		Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry.,Rizvi NF, Howe JA, Nahvi A, Klein DJ, Fischmann TO, Kim HY, McCoy MA, Walker SS, Hruza A, Richards MP, Chamberlin C, Saradjian P, Butko MT, Mercado G, Burchard J, Strickland C, Dandliker PJ, Smith GF, Nickbarg EB ACS Chem Biol. 2018 Feb 14. doi: 10.1021/acschembio.7b01013. PMID:29412640<ref>PMID:29412640</ref>

	~~Description: Crystal structure~~ of ~~a F~~. ~~nucleatum FMN riboswitch bound to WG~~-3		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased Structures~~]]		</div>
	[[Category: Rizvi, N.F]]		<div class="pdbe-citations 6bfb" style="background-color:#fffaf0;"></div>
	[[Category: ~~Fischmann, T.O~~]]		== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Fischmann, T O]]
			[[Category: Rizvi, N F]]
			[[Category: Rna]]
			[[Category: Rna-inhibitor complex]]
			[[Category: Translation]]

OCA at 06:31, 22 November 2017

2017-11-22T06:31:48Z

← Older revision		Revision as of 06:31, 22 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6bfb is ON HOLD		The entry 6bfb is ON HOLD until Paper Publication

	Authors: Rizvi, N.F., Fischmann, T.O.		Authors: Rizvi, N.F., Fischmann, T.O.

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

2017-11-01T05:01:46Z

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

← Older revision	Revision as of 05:01, 1 November 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6bfb is ON HOLD Authors: Rizvi, N.F., Fischmann, T.O. Description: Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3 [[Category: Unr...

2017-11-01T05:01:45Z

New page: '''Unreleased structure''' The entry 6bfb is ON HOLD Authors: Rizvi, N.F., Fischmann, T.O. Description: Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3 [[Category: Unr...

New page

'''Unreleased structure'''

The entry 6bfb is ON HOLD

Authors: Rizvi, N.F., Fischmann, T.O.

Description: Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3
[[Category: Unreleased Structures]]
[[Category: Rizvi, N.F]]
[[Category: Fischmann, T.O]]