5mmo - Revision history

OCA at 17:38, 8 November 2023

OCA — Wed, 08 Nov 2023 17:38:47 GMT

←Older revision		Revision as of 17:38, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='5mmo' size='340' side='right'caption='[[5mmo]], [[Resolution\|resolution]] 1.81Å' scene=''>		<StructureSection load='5mmo' size='340' side='right'caption='[[5mmo]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mmo]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Eco57 Eco57~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MMO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5MMO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mmo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MMO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9JG:PROP-2-YNYL+~{N}-[[3-(ETHYLCARBAMOYLAMINO)-5-PYRIDIN-4-YL-ISOQUINOLIN-8-YL]METHYL]CARBAMATE'>9JG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.81Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB, Z5190, ECs4634 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9JG:PROP-2-YNYL+~{N}-[[3-(ETHYLCARBAMOYLAMINO)-5-PYRIDIN-4-YL-ISOQUINOLIN-8-YL]METHYL]CARBAMATE'>9JG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=5mmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mmo OCA], [https://pdbe.org/5mmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mmo RCSB], [https://www.ebi.ac.uk/pdbsum/5mmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mmo 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=5mmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mmo OCA], [~~http~~://pdbe.org/5mmo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mmo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mmo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mmo ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GYRB_ECO57 GYRB_ECO57]] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.[HAMAP-Rule:MF_01898]	+	[https://www.uniprot.org/uniprot/GYRB_ECO57 GYRB_ECO57] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.[HAMAP-Rule:MF_01898]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Eco57~~]]	+	[[Category: Escherichia coli O157:H7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blumstein, A C]]	+	[[Category: Blumstein A-C]]
-	[[Category: Bruyere, T]]	+	[[Category: Bruyere T]]
-	[[Category: Bur, D]]	+	[[Category: Bur D]]
-	[[Category: Chambovey, A]]	+	[[Category: Chambovey A]]
-	[[Category: Ertel~~, E A~~]]	+	[[Category: Ertel EA]]
-	[[Category: Gude, M]]	+	[[Category: Gude M]]
-	[[Category: Hubschwerlen, C]]	+	[[Category: Hubschwerlen C]]
-	[[Category: Jacob, L]]	+	[[Category: Jacob L]]
-	[[Category: Kimmerlin, T]]	+	[[Category: Kimmerlin T]]
-	[[Category: Panchaud, P]]	+	[[Category: Panchaud P]]
-	[[Category: Pfeifer, T]]	+	[[Category: Pfeifer T]]
-	[[Category: Prade, L]]	+	[[Category: Prade L]]
-	[[Category: Ritz, D]]	+	[[Category: Ritz D]]
-	[[Category: Rueedi, G]]	+	[[Category: Rueedi G]]
-	[[Category: Seiler, P]]	+	[[Category: Seiler P]]
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 07:23, 19 August 2020

OCA — Wed, 19 Aug 2020 07:23:22 GMT

←Older revision		Revision as of 07:23, 19 August 2020
Line 1:		Line 1:

	==E. coli DNA Gyrase B 24 kDa ATPase domain in complex with [3-(3-ethyl-ureido)-5-(pyridin-4-yl)-isoquinolin-8-yl-methyl]-carbamic acid prop-2-ynyl ester==		==E. coli DNA Gyrase B 24 kDa ATPase domain in complex with [3-(3-ethyl-ureido)-5-(pyridin-4-yl)-isoquinolin-8-yl-methyl]-carbamic acid prop-2-ynyl ester==
-	<StructureSection load='5mmo' size='340' side='right' caption='[[5mmo]], [[Resolution\|resolution]] 1.81Å' scene=''>	+	<StructureSection load='5mmo' size='340' side='right'caption='[[5mmo]], [[Resolution\|resolution]] 1.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mmo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MMO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MMO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mmo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MMO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MMO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9JG:PROP-2-YNYL+~{N}-[[3-(ETHYLCARBAMOYLAMINO)-5-PYRIDIN-4-YL-ISOQUINOLIN-8-YL]METHYL]CARBAMATE'>9JG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9JG:PROP-2-YNYL+~{N}-[[3-(ETHYLCARBAMOYLAMINO)-5-PYRIDIN-4-YL-ISOQUINOLIN-8-YL]METHYL]CARBAMATE'>9JG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gyrB, Z5190, ECs4634 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=5mmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mmo OCA], [http://pdbe.org/5mmo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mmo RCSB], [http://www.ebi.ac.uk/pdbsum/5mmo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mmo 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=5mmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mmo OCA], [http://pdbe.org/5mmo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mmo RCSB], [http://www.ebi.ac.uk/pdbsum/5mmo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mmo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5mmo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mmo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Gyrase 3D Structures\|Gyrase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Eco57]]
		+	[[Category: Large Structures]]
	[[Category: Blumstein, A C]]		[[Category: Blumstein, A C]]
	[[Category: Bruyere, T]]		[[Category: Bruyere, T]]

OCA at 13:48, 27 April 2017

OCA — Thu, 27 Apr 2017 13:48:06 GMT

←Older revision		Revision as of 13:48, 27 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mmo is ~~ON HOLD until Paper~~ Publication	+	==E. coli DNA Gyrase B 24 kDa ATPase domain in complex with [3-(3-ethyl-ureido)-5-(pyridin-4-yl)-isoquinolin-8-yl-methyl]-carbamic acid prop-2-ynyl ester==
		+	<StructureSection load='5mmo' size='340' side='right' caption='[[5mmo]], [[Resolution\|resolution]] 1.81Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5mmo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MMO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MMO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9JG:PROP-2-YNYL+~{N}-[[3-(ETHYLCARBAMOYLAMINO)-5-PYRIDIN-4-YL-ISOQUINOLIN-8-YL]METHYL]CARBAMATE'>9JG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </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=5mmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mmo OCA], [http://pdbe.org/5mmo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mmo RCSB], [http://www.ebi.ac.uk/pdbsum/5mmo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mmo ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GYRB_ECO57 GYRB_ECO57]] DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.[HAMAP-Rule:MF_01898]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Our strategy to combat resistant bacteria consisted of targeting the GyrB/ParE ATP-binding sites located on bacterial DNA gyrase and topoisomerase IV and not utilized by marketed antibiotics. Screening around the minimal ethyl urea binding motif led to the identification of isoquinoline ethyl urea 13 as a promising starting point for fragment evolution. The optimization was guided by structure-based design and focused on antibacterial activity in vitro and in vivo, culminating in the discovery of unprecedented substituents able to interact with conserved residues within the ATP-binding site. A detailed characterization of the lead compound highlighted the potential for treatment of the problematic fluoroquinolone-resistant MRSA, VRE, and S. pneumoniae, and the possibility to offer patients an intravenous-to-oral switch therapy was supported by the identification of a suitable prodrug concept. Eventually, hERG K-channel block was identified as the main limitation of this chemical series, and efforts toward its minimization are reported.

-	~~Authors~~:	+	Discovery and Optimization of Isoquinoline Ethyl Ureas as Antibacterial Agents.,Panchaud P, Bruyere T, Blumstein AC, Bur D, Chambovey A, Ertel EA, Gude M, Hubschwerlen C, Jacob L, Kimmerlin T, Pfeifer T, Prade L, Seiler P, Ritz D, Rueedi G J Med Chem. 2017 Apr 24. doi: 10.1021/acs.jmedchem.6b01834. PMID:28406299<ref>PMID:28406299</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5mmo" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Blumstein, A C]]
		+	[[Category: Bruyere, T]]
		+	[[Category: Bur, D]]
		+	[[Category: Chambovey, A]]
		+	[[Category: Ertel, E A]]
		+	[[Category: Gude, M]]
		+	[[Category: Hubschwerlen, C]]
		+	[[Category: Jacob, L]]
		+	[[Category: Kimmerlin, T]]
		+	[[Category: Panchaud, P]]
		+	[[Category: Pfeifer, T]]
		+	[[Category: Prade, L]]
		+	[[Category: Ritz, D]]
		+	[[Category: Rueedi, G]]
		+	[[Category: Seiler, P]]
		+	[[Category: Inhibitor]]
		+	[[Category: Isomerase]]

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

OCA — Thu, 22 Dec 2016 19:10:42 GMT

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

←Older revision

Revision as of 19:10, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mmo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Thu, 22 Dec 2016 19:10:41 GMT

New page: '''Unreleased structure''' The entry 5mmo is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5mmo is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]