4mbc - Revision history

OCA at 12:25, 1 March 2024

2024-03-01T12:25:11Z

←Older revision		Revision as of 12:25, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4mbc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_GA47373 Streptococcus pneumoniae GA47373]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MBC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4mbc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_GA47373 Streptococcus pneumoniae GA47373]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MBC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=28G:1-{5-[2-(MORPHOLIN-4-YL)ETHOXY]-6-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-B]PYRIDIN-2-YL}-3-PROP-2-EN-1-YLUREA'>28G</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]] 1.75Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=28G:1-{5-[2-(MORPHOLIN-4-YL)ETHOXY]-6-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-B]PYRIDIN-2-YL}-3-PROP-2-EN-1-YLUREA'>28G</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=4mbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mbc OCA], [https://pdbe.org/4mbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mbc RCSB], [https://www.ebi.ac.uk/pdbsum/4mbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mbc 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=4mbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mbc OCA], [https://pdbe.org/4mbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mbc RCSB], [https://www.ebi.ac.uk/pdbsum/4mbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mbc ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A pharmacophore-based search led to the identification of thiazolopyridine ureas as a novel scaffold with antitubercular activity acting through inhibition of DNA Gyrase B (GyrB) ATPase. Evaluation of the binding mode of thiazolopyridines in a Mycobacterium tuberculosis (Mtb) GyrB homology model prompted exploration of side-chains at the thiazolopyridine ring C-5 position to access the ribose/solvent pocket. Potent compounds with GyrB IC50 </=1 nM and Mtb MIC </=0.1 microM were obtained with certain combinations of side-chains at C-5 position and heterocycles at C-6 position of the thiazolopyridine core. Substitutions at C-5 also enabled optimization of physicochemical properties. Representative compounds were co-crystallized with Streptococcus pneumoniae (Spn) ParE; these confirmed the binding modes predicted by the homology model. The target link to GyrB was confirmed by genetic mapping of mutations conferring resistance to thiazolopyridine ureas. The compounds are bactericidal in vitro and efficacious in vivo in an acute murine model of tuberculosis.
-
-	Thiazolopyridine Ureas as Novel Antitubercular Agents Acting Through Inhibition of DNA Gyrase B.,Ghorpade SR, Kale M, Raichurkar A, Hameed P S, Waterson D, McKinney D, Mramaiah M, Koushik K, Jena LK, Shinde V, Rudrapatna S, Humnabadkar V, Madhavapeddi P, Basavarajappa H, Ghosh A, Murthy R, Guptha S, Sharma S, Vachaspati P, K N MK, Giridhar J, Reddy J, Panduga V, Ganguly S, Ahuja V, Gaonkar S, C N NK, Ogg D, Tucker JA, Boriack-Sjodin PA, de Sousa SM, Sambandamurthy V, Kranthi U, Barde S J Med Chem. 2013 Oct 3. PMID:24088190<ref>PMID:24088190</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4mbc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Topoisomerase 3D structures\|Topoisomerase 3D structures]]		*[[Topoisomerase 3D structures\|Topoisomerase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:07, 21 December 2022

2022-12-21T11:07:14Z

←Older revision		Revision as of 11:07, 21 December 2022
Line 1:		Line 1:

	==Structure of Streptococcus pneumonia ParE in complex with AZ13053807==		==Structure of Streptococcus pneumonia ParE in complex with AZ13053807==
-	<StructureSection load='4mbc' size='340' side='right' caption='[[4mbc]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='4mbc' size='340' side='right'caption='[[4mbc]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4mbc]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Streptococcus_pneumoniae_ga47373~~ Streptococcus pneumoniae ~~ga47373~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MBC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MBC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4mbc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_GA47373 Streptococcus pneumoniae GA47373]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MBC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=28G:1-{5-[2-(MORPHOLIN-4-YL)ETHOXY]-6-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-B]PYRIDIN-2-YL}-3-PROP-2-EN-1-YLUREA'>28G</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=28G:1-{5-[2-(MORPHOLIN-4-YL)ETHOXY]-6-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-B]PYRIDIN-2-YL}-3-PROP-2-EN-1-YLUREA'>28G</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4emv\|4emv]], [[4em7\|4em7]], [[4mb9\|4mb9]]</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=4mbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mbc OCA], [https://pdbe.org/4mbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mbc RCSB], [https://www.ebi.ac.uk/pdbsum/4mbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mbc ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAR94_0831 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=760835 Streptococcus pneumoniae GA47373])</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=4mbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mbc OCA], [~~http~~://pdbe.org/4mbc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4mbc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4mbc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4mbc ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4mbc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4mbc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Topoisomerase 3D structures\|Topoisomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptococcus pneumoniae ga47373~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ogg, D~~]]	+	[[Category: Streptococcus pneumoniae GA47373]]
-	[[Category: ~~Tucker, J~~]]	+	[[Category: Ogg D]]
-	[[Category: ~~Antimicrobial]]~~	+	[[Category: Tucker J]]
-	~~[[Category: Atp binding]]~~	+
-	~~[[Category: Isomerase-isomerase inhibitor complex]]~~	+
-	~~[[Category: Structure-based drug design~~]]	+

OCA at 18:49, 1 February 2017

2017-02-01T18:49:30Z

←Older revision		Revision as of 18:49, 1 February 2017
Line 1:		Line 1:
		+
	==Structure of Streptococcus pneumonia ParE in complex with AZ13053807==		==Structure of Streptococcus pneumonia ParE in complex with AZ13053807==
	<StructureSection load='4mbc' size='340' side='right' caption='[[4mbc]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4mbc' size='340' side='right' caption='[[4mbc]], [[Resolution\|resolution]] 1.75Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4emv\|4emv]], [[4em7\|4em7]], [[4mb9\|4mb9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4emv\|4emv]], [[4em7\|4em7]], [[4mb9\|4mb9]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAR94_0831 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=760835 Streptococcus pneumoniae GA47373])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAR94_0831 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=760835 Streptococcus pneumoniae GA47373])</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=4mbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mbc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mbc RCSB], [http://www.ebi.ac.uk/pdbsum/4mbc PDBsum]</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=4mbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mbc OCA], [http://pdbe.org/4mbc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mbc RCSB], [http://www.ebi.ac.uk/pdbsum/4mbc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mbc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
-		+	<div class="pdbe-citations 4mbc" style="background-color:#fffaf0;"></div>
-	==~~See Also==~~	+
-	*[[Topoisomerase\|Topoisomerase]]	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:47, 5 January 2015

2015-01-05T09:47:47Z

←Older revision		Revision as of 09:47, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4mbc\| PDB=4mbc \| SCENE= }}~~	+	==Structure of Streptococcus pneumonia ParE in complex with AZ13053807==
-	===Structure of Streptococcus pneumonia ParE in complex with AZ13053807===	+	<StructureSection load='4mbc' size='340' side='right' caption='[[4mbc]], [[Resolution\|resolution]] 1.75Å' scene=''>
-	{~~{ABSTRACT_PUBMED_24088190}~~}	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4mbc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_ga47373 Streptococcus pneumoniae ga47373]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MBC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=28G:1-{5-[2-(MORPHOLIN-4-YL)ETHOXY]-6-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-B]PYRIDIN-2-YL}-3-PROP-2-EN-1-YLUREA'>28G</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4emv\|4emv]], [[4em7\|4em7]], [[4mb9\|4mb9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAR94_0831 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=760835 Streptococcus pneumoniae GA47373])</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=4mbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mbc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mbc RCSB], [http://www.ebi.ac.uk/pdbsum/4mbc PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A pharmacophore-based search led to the identification of thiazolopyridine ureas as a novel scaffold with antitubercular activity acting through inhibition of DNA Gyrase B (GyrB) ATPase. Evaluation of the binding mode of thiazolopyridines in a Mycobacterium tuberculosis (Mtb) GyrB homology model prompted exploration of side-chains at the thiazolopyridine ring C-5 position to access the ribose/solvent pocket. Potent compounds with GyrB IC50 </=1 nM and Mtb MIC </=0.1 microM were obtained with certain combinations of side-chains at C-5 position and heterocycles at C-6 position of the thiazolopyridine core. Substitutions at C-5 also enabled optimization of physicochemical properties. Representative compounds were co-crystallized with Streptococcus pneumoniae (Spn) ParE; these confirmed the binding modes predicted by the homology model. The target link to GyrB was confirmed by genetic mapping of mutations conferring resistance to thiazolopyridine ureas. The compounds are bactericidal in vitro and efficacious in vivo in an acute murine model of tuberculosis.

-	~~==About this Structure==~~	+	Thiazolopyridine Ureas as Novel Antitubercular Agents Acting Through Inhibition of DNA Gyrase B.,Ghorpade SR, Kale M, Raichurkar A, Hameed P S, Waterson D, McKinney D, Mramaiah M, Koushik K, Jena LK, Shinde V, Rudrapatna S, Humnabadkar V, Madhavapeddi P, Basavarajappa H, Ghosh A, Murthy R, Guptha S, Sharma S, Vachaspati P, K N MK, Giridhar J, Reddy J, Panduga V, Ganguly S, Ahuja V, Gaonkar S, C N NK, Ogg D, Tucker JA, Boriack-Sjodin PA, de Sousa SM, Sambandamurthy V, Kranthi U, Barde S J Med Chem. 2013 Oct 3. PMID:24088190<ref>PMID:24088190</ref>
-	~~[[4mbc]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptococcus_pneumoniae_ga47373 Streptococcus pneumoniae ga47373]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4MBC OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:024088190</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Topoisomerase\|Topoisomerase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Streptococcus pneumoniae ga47373]]		[[Category: Streptococcus pneumoniae ga47373]]
-	[[Category: Ogg, D.]]	+	[[Category: Ogg, D]]
-	[[Category: Tucker, J.]]	+	[[Category: Tucker, J]]
	[[Category: Antimicrobial]]		[[Category: Antimicrobial]]
	[[Category: Atp binding]]		[[Category: Atp binding]]
	[[Category: Isomerase-isomerase inhibitor complex]]		[[Category: Isomerase-isomerase inhibitor complex]]
	[[Category: Structure-based drug design]]		[[Category: Structure-based drug design]]

OCA at 07:58, 16 October 2013

2013-10-16T07:58:06Z

←Older revision		Revision as of 07:58, 16 October 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4mbc\| PDB=4mbc \| SCENE= }}
		+	===Structure of Streptococcus pneumonia ParE in complex with AZ13053807===
		+	{{ABSTRACT_PUBMED_24088190}}

-	~~The entry~~ 4mbc is ~~ON HOLD~~	+	==About this Structure==
		+	[[4mbc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_ga47373 Streptococcus pneumoniae ga47373]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MBC OCA].

-	~~Authors~~: Ogg, D., Tucker, J.	+	==Reference==
-		+	<ref group="xtra">PMID:024088190</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Structure of Streptococcus pneumonia ParE in~~ complex ~~with AZ13053807~~	+	[[Category: Streptococcus pneumoniae ga47373]]
		+	[[Category: Ogg, D.]]
		+	[[Category: Tucker, J.]]
		+	[[Category: Antimicrobial]]
		+	[[Category: Atp binding]]
		+	[[Category: Isomerase-isomerase inhibitor complex]]
		+	[[Category: Structure-based drug design]]

OCA at 03:36, 20 September 2013

2013-09-20T03:36:47Z

←Older revision		Revision as of 03:36, 20 September 2013
Line 3:		Line 3:
	The entry 4mbc is ON HOLD		The entry 4mbc is ON HOLD

-	Authors: Ogg, ~~Derek~~, Tucker, ~~Julie~~	+	Authors: Ogg, D., Tucker, J.

	Description: Structure of Streptococcus pneumonia ParE in complex with AZ13053807		Description: Structure of Streptococcus pneumonia ParE in complex with AZ13053807

OCA: Protected "4mbc" [edit=sysop:move=sysop]

2013-08-28T06:56:22Z

Protected "4mbc" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:56, 28 August 2013

OCA: New page: '''Unreleased structure''' The entry 4mbc is ON HOLD Authors: Ogg, Derek, Tucker, Julie Description: Structure of Streptococcus pneumonia ParE in complex with AZ13053807

2013-08-28T06:56:20Z

New page: '''Unreleased structure''' The entry 4mbc is ON HOLD Authors: Ogg, Derek, Tucker, Julie Description: Structure of Streptococcus pneumonia ParE in complex with AZ13053807

New page

'''Unreleased structure'''

The entry 4mbc is ON HOLD

Authors: Ogg, Derek, Tucker, Julie

Description: Structure of Streptococcus pneumonia ParE in complex with AZ13053807