5y6e - Revision history

OCA at 08:23, 22 November 2023

OCA — Wed, 22 Nov 2023 08:23:22 GMT

←Older revision		Revision as of 08:23, 22 November 2023
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	==VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 12)==		==VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 12)==
-	<StructureSection load='5y6e' size='340' side='right' caption='[[5y6e]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5y6e' size='340' side='right'caption='[[5y6e]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y6e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y6E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y6e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y6E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8PO:(2R)-2-(4-hydroxyphenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic+acid'>8PO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.8Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8PO:(2R)-2-(4-hydroxyphenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic+acid'>8PO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5y6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6e OCA], [~~http~~://pdbe.org/5y6e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y6e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y6e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6e 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=5y6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6e OCA], [https://pdbe.org/5y6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y6e RCSB], [https://www.ebi.ac.uk/pdbsum/5y6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6e ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9K2N0_PSEAI Q9K2N0_PSEAI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5y6e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5y6e" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Li, G B~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Hydrolase~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Metallo~~-~~beta-lactamase vim-2~~]]	+	[[Category: Li G-B]]

OCA at 06:46, 7 February 2018

OCA — Wed, 07 Feb 2018 06:46:57 GMT

←Older revision		Revision as of 06:46, 7 February 2018
Line 3:		Line 3:
	<StructureSection load='5y6e' size='340' side='right' caption='[[5y6e]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5y6e' size='340' side='right' caption='[[5y6e]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y6e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y6E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y6e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y6E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8PO:(2R)-2-(4-hydroxyphenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic+acid'>8PO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8PO:(2R)-2-(4-hydroxyphenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic+acid'>8PO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=5y6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6e OCA], [http://pdbe.org/5y6e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y6e RCSB], [http://www.ebi.ac.uk/pdbsum/5y6e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6e 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=5y6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6e OCA], [http://pdbe.org/5y6e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y6e RCSB], [http://www.ebi.ac.uk/pdbsum/5y6e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6e ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The emergence and global spread of metallo-beta-lactamase (MBL) mediated resistance to almost all beta-lactam antibacterials poses a serious threat to public health. Since no clinically useful MBL inhibitors have been reported, there is an urgent need to develop new potent broad-spectrum MBL inhibitors effective against antibacterial resistance. Herein, we synthesized a set of 2-substituted ((S)-3-mercapto-2-methylpropanamido) acetic acid derivatives, some of which displayed potent inhibition with high ligand efficiency to the clinically relevant MBL subtypes, Verona Integron-encoded MBL (VIM)-2 and New Delhi MBL (NDM)-1. Kinetic studies revealed that the inhibitors are not strong zinc chelators in solution, and they bind reversibly to VIM-2 but dissociate very slowly. Crystallographic analyses revealed that they inhibit VIM-2 via chelating the active site zinc ions and interacting with catalytically important residues. Further cell- and zebrafish-based assays revealed that the inhibitors slightly increase susceptibility of E. coli cells expressing VIM-2 to meropenem, and they have no apparent toxicity to the viability of HEK293T cells and the zebrafish embryogenesis.
		+
		+	((S)-3-Mercapto-2-methylpropanamido)acetic acid derivatives as metallo-beta-lactamase inhibitors: Synthesis, kinetic and crystallographic studies.,Liu S, Jing L, Yu ZJ, Wu C, Zheng Y, Zhang E, Chen Q, Yu Y, Guo L, Wu Y, Li GB Eur J Med Chem. 2018 Feb 10;145:649-660. doi: 10.1016/j.ejmech.2018.01.032. Epub , 2018 Jan 11. PMID:29353720<ref>PMID:29353720</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y6e" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:27, 24 January 2018

OCA — Wed, 24 Jan 2018 18:27:49 GMT

←Older revision		Revision as of 18:27, 24 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5y6e is ON HOLD until Paper Publication~~	+	==VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 12)==
-		+	<StructureSection load='5y6e' size='340' side='right' caption='[[5y6e]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors: Li, G.-B.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y6e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y6E FirstGlance]. <br>
-	~~Description:~~ VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 12)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8PO:(2R)-2-(4-hydroxyphenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic+acid'>8PO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5y6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6e OCA], [http://pdbe.org/5y6e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y6e RCSB], [http://www.ebi.ac.uk/pdbsum/5y6e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6e ProSAT]</span></td></tr>
-	[[Category: Li, G.-B]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Li, G B]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallo-beta-lactamase vim-2]]

OCA at 05:29, 17 January 2018

OCA — Wed, 17 Jan 2018 05:29:44 GMT

←Older revision		Revision as of 05:29, 17 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5y6e is ON HOLD	+	The entry 5y6e is ON HOLD until Paper Publication

	Authors: Li, G.-B.		Authors: Li, G.-B.

OCA: Protected "5y6e" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:11:33 GMT

Protected "5y6e" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:11, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y6e is ON HOLD Authors: Li, G.-B. Description: VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylprop...

OCA — Wed, 27 Sep 2017 16:11:32 GMT

New page: '''Unreleased structure''' The entry 5y6e is ON HOLD Authors: Li, G.-B. Description: VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylprop...

New page

'''Unreleased structure'''

The entry 5y6e is ON HOLD

Authors: Li, G.-B.

Description: VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 12)
[[Category: Unreleased Structures]]
[[Category: Li, G.-B]]