6qr6 - Revision history

OCA at 12:06, 24 January 2024

OCA — Wed, 24 Jan 2024 12:06:50 GMT

←Older revision		Revision as of 12:06, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6qr6' size='340' side='right'caption='[[6qr6]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='6qr6' size='340' side='right'caption='[[6qr6]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qr6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"mycobacterium_abcessus"_moore_and_frerichs_1953 "mycobacterium abcessus" moore and frerichs 1953~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QR6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6QR6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qr6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacteroides_abscessus Mycobacteroides abscessus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QR6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JCK:5-azanyl-3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile'>JCK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.71Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6nvr\|6nvr]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JCK:5-azanyl-3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile'>JCK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trmD, MAB_3226c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36809 "Mycobacterium abcessus" Moore and Frerichs 1953])</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=6qr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qr6 OCA], [https://pdbe.org/6qr6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qr6 RCSB], [https://www.ebi.ac.uk/pdbsum/6qr6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qr6 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/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </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=6qr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qr6 OCA], [~~http~~://pdbe.org/6qr6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qr6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qr6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qr6 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9]] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]	+	[https://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium abcessus moore and frerichs 1953]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abell, C]]	+	[[Category: Mycobacteroides abscessus]]
-	[[Category: Blundell~~, T L~~]]	+	[[Category: Abell C]]
-	[[Category: Coyne~~, A G~~]]	+	[[Category: Blundell TL]]
-	[[Category: Mendes, V]]	+	[[Category: Coyne AG]]
-	[[Category: Thomas~~, S E~~]]	+	[[Category: Mendes V]]
-	[[Category: Whitehouse~~, A J]]~~	+	[[Category: Thomas SE]]
-	~~[[Category: Spout methyltransferase]]~~	+	[[Category: Whitehouse AJ]]
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Trmd]]~~	+
-	~~[[Category: Trna methyltransferase~~]]	+

OCA at 05:50, 5 August 2020

OCA — Wed, 05 Aug 2020 05:50:10 GMT

←Older revision		Revision as of 05:50, 5 August 2020
Line 3:		Line 3:
	<StructureSection load='6qr6' size='340' side='right'caption='[[6qr6]], [[Resolution\|resolution]] 1.71Å' scene=''>		<StructureSection load='6qr6' size='340' side='right'caption='[[6qr6]], [[Resolution\|resolution]] 1.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qr6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QR6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QR6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qr6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_abcessus"_moore_and_frerichs_1953 "mycobacterium abcessus" moore and frerichs 1953]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QR6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6QR6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JCK:5-azanyl-3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile'>JCK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JCK:5-azanyl-3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile'>JCK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6nvr\|6nvr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6nvr\|6nvr]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trmD, MAB_3226c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36809 "Mycobacterium abcessus" Moore and Frerichs 1953])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </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=6qr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qr6 OCA], [http://pdbe.org/6qr6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qr6 RCSB], [http://www.ebi.ac.uk/pdbsum/6qr6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qr6 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=6qr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qr6 OCA], [http://pdbe.org/6qr6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qr6 RCSB], [http://www.ebi.ac.uk/pdbsum/6qr6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qr6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9]] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]		[[http://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9]] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Translational frameshift errors are often deleterious to the synthesis of functional proteins and could therefore be promoted therapeutically to kill bacteria. TrmD (tRNA-(N(1)G37) methyltransferase) is an essential tRNA modification enzyme in bacteria that prevents +1 errors in the reading frame during protein translation and represents an attractive potential target for the development of new antibiotics. Here, we describe the application of a structure-guided fragment-based drug discovery approach to the design of a new class of inhibitors against TrmD in Mycobacterium abscessus. Fragment library screening, followed by structure-guided chemical elaboration of hits, led to the rapid development of drug-like molecules with potent in vitro TrmD inhibitory activity. Several of these compounds exhibit activity against planktonic M. abscessus and M. tuberculosis as well as against intracellular M. abscessus and M. leprae, indicating their potential as the basis for a novel class of broad-spectrum mycobacterial drugs.
		+
		+	Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification.,Thomas SE, Whitehouse AJ, Brown K, Burbaud S, Belardinelli JM, Sangen J, Lahiri R, Libardo MDJ, Gupta P, Malhotra S, Boshoff HIM, Jackson M, Abell C, Coyne AG, Blundell TL, Floto RA, Mendes V Nucleic Acids Res. 2020 Jun 30. pii: 5865065. doi: 10.1093/nar/gkaa539. PMID:32602532<ref>PMID:32602532</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6qr6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Mycobacterium abcessus moore and frerichs 1953]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Abell, C]]		[[Category: Abell, C]]

OCA at 09:46, 18 March 2020

OCA — Wed, 18 Mar 2020 09:46:52 GMT

←Older revision		Revision as of 09:46, 18 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qr6 ~~is ON HOLD~~	+	==Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor==
-		+	<StructureSection load='6qr6' size='340' side='right'caption='[[6qr6]], [[Resolution\|resolution]] 1.71Å' scene=''>
-	~~Authors~~: ~~Thomas, S~~.E., ~~Whitehouse~~, A.J., ~~Coyne, A~~.G., ~~Abell~~, C., ~~Mendes, V~~., ~~Blundell, T~~.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6qr6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QR6 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of TrmD, a tRNA~~-~~(N1G37) methyltransferase, from Mycobacterium abscessus~~ in ~~complex with inhibitor~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JCK:5-azanyl-3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile'>JCK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6nvr\|6nvr]]</td></tr>
-	[[Category: Blundell, T.L]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(37)-N(1))-methyltransferase tRNA (guanine(37)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.228 2.1.1.228] </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=6qr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qr6 OCA], [http://pdbe.org/6qr6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qr6 RCSB], [http://www.ebi.ac.uk/pdbsum/6qr6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qr6 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9]] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Abell, C]]
		+	[[Category: Blundell, T L]]
		+	[[Category: Coyne, A G]]
	[[Category: Mendes, V]]		[[Category: Mendes, V]]
-	[[Category: Thomas, S.E]]	+	[[Category: Thomas, S E]]
-	[[Category: ~~Abell~~, C]]	+	[[Category: Whitehouse, A J]]
-	[[Category: ~~Whitehouse, A.J~~]]	+	[[Category: Spout methyltransferase]]
-	[[Category: ~~Coyne, A.G~~]]	+	[[Category: Transferase]]
		+	[[Category: Trmd]]
		+	[[Category: Trna methyltransferase]]

OCA: Protected "6qr6" [edit=sysop:move=sysop]

OCA — Wed, 27 Feb 2019 13:58:20 GMT

Protected "6qr6" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:58, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qr6 is ON HOLD Authors: Thomas, S.E., Whitehouse, A.J., Coyne, A.G., Abell, C., Mendes, V., Blundell, T.L. Description: Crystal structure of TrmD,...

OCA — Wed, 27 Feb 2019 13:58:18 GMT

New page: '''Unreleased structure''' The entry 6qr6 is ON HOLD Authors: Thomas, S.E., Whitehouse, A.J., Coyne, A.G., Abell, C., Mendes, V., Blundell, T.L. Description: Crystal structure of TrmD,...

New page

'''Unreleased structure'''

The entry 6qr6 is ON HOLD

Authors: Thomas, S.E., Whitehouse, A.J., Coyne, A.G., Abell, C., Mendes, V., Blundell, T.L.

Description: Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor
[[Category: Unreleased Structures]]
[[Category: Blundell, T.L]]
[[Category: Mendes, V]]
[[Category: Thomas, S.E]]
[[Category: Abell, C]]
[[Category: Whitehouse, A.J]]
[[Category: Coyne, A.G]]