6b88 - Revision history

OCA at 14:35, 4 October 2023

OCA — Wed, 04 Oct 2023 14:35:19 GMT

←Older revision		Revision as of 14:35, 4 October 2023
Line 1:		Line 1:

	==E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phenyl)-4-methylpyrimidine-5-carboxamido)-N-methylbutanamido)-16,26-bis(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl-6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide)==		==E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phenyl)-4-methylpyrimidine-5-carboxamido)-N-methylbutanamido)-16,26-bis(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl-6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide)==
-	<StructureSection load='6b88' size='340' side='right' caption='[[6b88]], [[Resolution\|resolution]] 2.41Å' scene=''>	+	<StructureSection load='6b88' size='340' side='right'caption='[[6b88]], [[Resolution\|resolution]] 2.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b88]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B88 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6B88 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b88]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6B88 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CZD:(8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide'>CZD</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]] 2.407Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lepB, b2568, JW2552 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CZD:(8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide'>CZD</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Signal_peptidase_I Signal peptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.89 3.4.21.89] </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=6b88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b88 OCA], [https://pdbe.org/6b88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6b88 RCSB], [https://www.ebi.ac.uk/pdbsum/6b88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6b88 ProSAT]</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=6b88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b88 OCA], [~~http~~://pdbe.org/6b88 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6b88 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6b88 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6b88 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LEP_ECOLI LEP_ECOLI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Signal peptidase I~~]]	+	[[Category: Large Structures]]
-	[[Category: Murray~~, J M~~]]	+	[[Category: Murray JM]]
-	[[Category: Rouge, L]]	+	[[Category: Rouge L]]
-	~~[[Category: Antibiotic]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Sbdd]]~~	+
-	~~[[Category: Signal peptidase~~]]	+

OCA at 06:42, 24 October 2018

OCA — Wed, 24 Oct 2018 06:42:54 GMT

←Older revision		Revision as of 06:42, 24 October 2018
Line 3:		Line 3:
	<StructureSection load='6b88' size='340' side='right' caption='[[6b88]], [[Resolution\|resolution]] 2.41Å' scene=''>		<StructureSection load='6b88' size='340' side='right' caption='[[6b88]], [[Resolution\|resolution]] 2.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b88]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B88 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b88]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B88 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CZD:(8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide'>CZD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CZD:(8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide'>CZD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lepB, b2568, JW2552 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Signal_peptidase_I Signal peptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.89 3.4.21.89] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Signal_peptidase_I Signal peptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.89 3.4.21.89] </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=6b88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b88 OCA], [http://pdbe.org/6b88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b88 RCSB], [http://www.ebi.ac.uk/pdbsum/6b88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b88 ProSAT]</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=6b88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b88 OCA], [http://pdbe.org/6b88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b88 RCSB], [http://www.ebi.ac.uk/pdbsum/6b88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b88 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Multidrug-resistant bacteria are spreading at alarming rates, and despite extensive efforts no new class of antibiotic with activity against Gram-negative bacteria has been approved in over fifty years. Natural products and their derivatives have a key role in combating Gram-negative pathogens. Here we report chemical optimization of the arylomycins-a class of natural products with weak activity and limited spectrum-to obtain G0775, a molecule with potent, broad-spectrum activity against Gram-negative bacteria. G0775 inhibits the essential bacterial type I signal peptidase, a new antibiotic target, through an unprecedented molecular mechanism. It circumvents existing antibiotic resistance mechanisms and retains activity against contemporary multidrug-resistant Gram-negative clinical isolates in vitro and in several in vivo infection models. These findings demonstrate that optimized arylomycin analogues such as G0775 could translate into new therapies to address the growing threat of multidrug-resistant Gram-negative infections.
		+
		+	Optimized arylomycins are a new class of Gram-negative antibiotics.,Smith PA, Koehler MFT, Girgis HS, Yan D, Chen Y, Chen Y, Crawford JJ, Durk MR, Higuchi RI, Kang J, Murray J, Paraselli P, Park S, Phung W, Quinn JG, Roberts TC, Rouge L, Schwarz JB, Skippington E, Wai J, Xu M, Yu Z, Zhang H, Tan MW, Heise CE Nature. 2018 Sep;561(7722):189-194. doi: 10.1038/s41586-018-0483-6. Epub 2018 Sep, 12. PMID:30209367<ref>PMID:30209367</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6b88" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Signal peptidase I]]		[[Category: Signal peptidase I]]
	[[Category: Murray, J M]]		[[Category: Murray, J M]]

OCA at 08:04, 10 October 2018

OCA — Wed, 10 Oct 2018 08:04:14 GMT

←Older revision		Revision as of 08:04, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6b88 is ~~ON HOLD until Paper Publication~~	+	==E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phenyl)-4-methylpyrimidine-5-carboxamido)-N-methylbutanamido)-16,26-bis(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl-6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide)==
-		+	<StructureSection load='6b88' size='340' side='right' caption='[[6b88]], [[Resolution\|resolution]] 2.41Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6b88]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B88 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CZD:(8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide'>CZD</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Signal_peptidase_I Signal peptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.89 3.4.21.89] </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=6b88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b88 OCA], [http://pdbe.org/6b88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b88 RCSB], [http://www.ebi.ac.uk/pdbsum/6b88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b88 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Signal peptidase I]]
		+	[[Category: Murray, J M]]
		+	[[Category: Rouge, L]]
		+	[[Category: Antibiotic]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Sbdd]]
		+	[[Category: Signal peptidase]]

OCA at 03:41, 8 March 2018

OCA — Thu, 08 Mar 2018 03:41:17 GMT

←Older revision		Revision as of 03:41, 8 March 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6b88 is ON HOLD	+	The entry 6b88 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6b88" [edit=sysop:move=sysop]

OCA — Wed, 11 Oct 2017 05:40:11 GMT

Protected "6b88" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 11 October 2017

OCA: New page: '''Unreleased structure''' The entry 6b88 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 11 Oct 2017 05:40:09 GMT

New page: '''Unreleased structure''' The entry 6b88 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6b88 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]