7dv1 - Revision history

OCA at 16:39, 29 November 2023

OCA — Wed, 29 Nov 2023 16:39:58 GMT

←Older revision		Revision as of 16:39, 29 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7dv1]] 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=7DV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DV1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dv1]] 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=7DV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DV1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=HN9:1-[(4-hydroxyphenyl)methyl]imidazole-2-carboxylic+acid'>HN9</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]] 1.966Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=HN9:1-[(4-hydroxyphenyl)methyl]imidazole-2-carboxylic+acid'>HN9</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'>[https://proteopedia.org/fgij/fg.htm?mol=7dv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dv1 OCA], [https://pdbe.org/7dv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dv1 RCSB], [https://www.ebi.ac.uk/pdbsum/7dv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dv1 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=7dv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dv1 OCA], [https://pdbe.org/7dv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dv1 RCSB], [https://www.ebi.ac.uk/pdbsum/7dv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dv1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q9K2N0_PSEAI Q9K2N0_PSEAI]]	+	[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 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7dv1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7dv1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:46, 8 September 2022

OCA — Thu, 08 Sep 2022 03:46:16 GMT

←Older revision		Revision as of 03:46, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7dv1' size='340' side='right'caption='[[7dv1]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='7dv1' size='340' side='right'caption='[[7dv1]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7dv1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dv1]] 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=7DV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DV1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=HN9:1-[(4-hydroxyphenyl)methyl]imidazole-2-carboxylic+acid'>HN9</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" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=HN9:1-[(4-hydroxyphenyl)methyl]imidazole-2-carboxylic+acid'>HN9</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'>[https://proteopedia.org/fgij/fg.htm?mol=7dv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dv1 OCA], [https://pdbe.org/7dv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dv1 RCSB], [https://www.ebi.ac.uk/pdbsum/7dv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dv1 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=7dv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dv1 OCA], [https://pdbe.org/7dv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dv1 RCSB], [https://www.ebi.ac.uk/pdbsum/7dv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dv1 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 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Li, G B~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Yan, Y H]]~~	+	[[Category: Li G-B]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Yan Y-H]]
-	~~[[Category: Metallo~~-~~beta-lactamase vim-2~~]]	+
-	[[Category: ~~Vim~~-2]]	+

OCA at 04:58, 3 August 2022

OCA — Wed, 03 Aug 2022 04:58:12 GMT

←Older revision		Revision as of 04:58, 3 August 2022
Line 1:		Line 1:

	==Crystal structure of VIM-2 MBL in complex with 1-(4-hydroxybenzyl)-1H-imidazole-2-carboxylic acid==		==Crystal structure of VIM-2 MBL in complex with 1-(4-hydroxybenzyl)-1H-imidazole-2-carboxylic acid==
-	<StructureSection load='7dv1' size='340' side='right'caption='[[7dv1]]' scene=''>	+	<StructureSection load='7dv1' size='340' side='right'caption='[[7dv1]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DV1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dv1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DV1 FirstGlance]. <br>
-	</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=7dv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dv1 OCA], [https://pdbe.org/7dv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dv1 RCSB], [https://www.ebi.ac.uk/pdbsum/7dv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dv1 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=HN9:1-[(4-hydroxyphenyl)methyl]imidazole-2-carboxylic+acid'>HN9</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'>[https://proteopedia.org/fgij/fg.htm?mol=7dv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dv1 OCA], [https://pdbe.org/7dv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dv1 RCSB], [https://www.ebi.ac.uk/pdbsum/7dv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dv1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Production of metallo-beta-lactamases (MBLs) in bacterial pathogens is an important cause of resistance to the 'last-resort' carbapenem antibiotics. Development of effective MBL inhibitors to reverse carbapenem resistance in Gram-negative bacteria is still needed. We herein report X-ray structure-guided optimization of 1H-imidazole-2-carboxylic acid (ICA) derivatives by considering how to engage with the active-site flexible loops and improve penetration into Gram-negative bacteria. Structure-activity relationship studies revealed the importance of appropriate substituents at ICA 1-position to achieve potent inhibition to class B1 MBLs, particularly the Verona Integron-encoded MBLs (VIMs), mainly by involving ingenious interactions with the flexible active site loops as observed by crystallographic analyses. Of the tested ICA inhibitors, 55 displayed potent synergistic antibacterial activity with meropenem against engineered Escherichia coli strains and even intractable clinically isolated Pseudomonas aeruginosa producing VIM-2 MBL. The morphologic and internal structural changes of bacterial cells after treatment further demonstrated that 55 crossed the outer membrane and reversed the activity of meropenem. Moreover, 55 showed good pharmacokinetic and safety profile in vivo, which could be a potential candidate for combating VIM-mediated Gram-negative carbapenem resistance.
		+
		+	Structure-guided optimization of 1H-imidazole-2-carboxylic acid derivatives affording potent VIM-Type metallo-beta-lactamase inhibitors.,Yan YH, Li W, Chen W, Li C, Zhu KR, Deng J, Dai QQ, Yang LL, Wang Z, Li GB Eur J Med Chem. 2022 Jan 15;228:113965. doi: 10.1016/j.ejmech.2021.113965. Epub, 2021 Nov 2. PMID:34763944<ref>PMID:34763944</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dv1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li G-B]]	+	[[Category: Li, G B]]
-	[[Category: Yan Y-H]]	+	[[Category: Yan, Y H]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallo-beta-lactamase vim-2]]
		+	[[Category: Vim-2]]

OCA at 07:26, 19 January 2022

OCA — Wed, 19 Jan 2022 07:26:52 GMT

←Older revision		Revision as of 07:26, 19 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7dv1 is ON HOLD until Paper Publication~~	+	==Crystal structure of VIM-2 MBL in complex with 1-(4-hydroxybenzyl)-1H-imidazole-2-carboxylic acid==
-		+	<StructureSection load='7dv1' size='340' side='right'caption='[[7dv1]]' scene=''>
-	~~Authors: Li, G.-B., Yan, Y.-H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DV1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DV1 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of VIM-2 MBL in complex with 1-(4-hydroxybenzyl)-1H-imidazole-2-carboxylic acid	+	</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=7dv1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dv1 OCA], [https://pdbe.org/7dv1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dv1 RCSB], [https://www.ebi.ac.uk/pdbsum/7dv1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dv1 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Yan~~, Y.-H]]	+	__TOC__
-	[[Category: Li, G.-B]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Li G-B]]
		+	[[Category: Yan Y-H]]

OCA at 09:17, 3 February 2021

OCA — Wed, 03 Feb 2021 09:17:57 GMT

←Older revision		Revision as of 09:17, 3 February 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7dv1 is ON HOLD	+	The entry 7dv1 is ON HOLD until Paper Publication

	Authors: Li, G.-B., Yan, Y.-H.		Authors: Li, G.-B., Yan, Y.-H.

OCA: Protected "7dv1" [edit=sysop:move=sysop]

OCA — Wed, 20 Jan 2021 06:48:46 GMT

Protected "7dv1" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:48, 20 January 2021

OCA: New page: '''Unreleased structure''' The entry 7dv1 is ON HOLD Authors: Li, G.-B., Yan, Y.-H. Description: Crystal structure of VIM-2 MBL in complex with 1-(4-hydroxybenzyl)-1H-imidazole-2-carbo...

OCA — Wed, 20 Jan 2021 06:48:45 GMT

New page: '''Unreleased structure''' The entry 7dv1 is ON HOLD Authors: Li, G.-B., Yan, Y.-H. Description: Crystal structure of VIM-2 MBL in complex with 1-(4-hydroxybenzyl)-1H-imidazole-2-carbo...

New page

'''Unreleased structure'''

The entry 7dv1 is ON HOLD

Authors: Li, G.-B., Yan, Y.-H.

Description: Crystal structure of VIM-2 MBL in complex with 1-(4-hydroxybenzyl)-1H-imidazole-2-carboxylic acid
[[Category: Unreleased Structures]]
[[Category: Yan, Y.-H]]
[[Category: Li, G.-B]]