7k5v - Revision history

OCA at 15:18, 18 October 2023

OCA — Wed, 18 Oct 2023 15:18:15 GMT

←Older revision		Revision as of 15:18, 18 October 2023
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	<StructureSection load='7k5v' size='340' side='right'caption='[[7k5v]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='7k5v' size='340' side='right'caption='[[7k5v]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7k5v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7k5v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K5V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BIH:NAPHTHALENE-2,6-DISULFONIC+ACID'>BIH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.8Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BIH:NAPHTHALENE-2,6-DISULFONIC+ACID'>BIH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6]~~ </~~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=7k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k5v OCA], [https://pdbe.org/7k5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k5v RCSB], [https://www.ebi.ac.uk/pdbsum/7k5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k5v 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=7k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k5v OCA], [https://pdbe.org/7k5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k5v RCSB], [https://www.ebi.ac.uk/pdbsum/7k5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k5v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6XEC0_KLEPN Q6XEC0_KLEPN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7k5v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7k5v" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta-lactamase~~]]	+	[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hu, L]]	+	[[Category: Hu L]]
-	[[Category: Palzkill, T]]	+	[[Category: Palzkill T]]
-	[[Category: Prasad~~, B V.V~~]]	+	[[Category: Prasad BVV]]
-	[[Category: Taylor~~, D M]]~~	+	[[Category: Taylor DM]]
-	~~[[Category: Beta-lactamase inhibitor]]~~	+
-	~~[[Category: Carbapenemase]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Oxacillinase~~]]	+

OCA at 10:05, 8 December 2021

OCA — Wed, 08 Dec 2021 10:05:03 GMT

←Older revision		Revision as of 10:05, 8 December 2021
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	==OXA-48 bound by Compound 3.1==		==OXA-48 bound by Compound 3.1==
-	<StructureSection load='7k5v' size='340' side='right'caption='[[7k5v]]' scene=''>	+	<StructureSection load='7k5v' size='340' side='right'caption='[[7k5v]], [[Resolution\|resolution]] 2.80Å' 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=7K5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7k5v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K5V 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=7k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k5v OCA], [https://pdbe.org/7k5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k5v RCSB], [https://www.ebi.ac.uk/pdbsum/7k5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k5v 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=BIH:NAPHTHALENE-2,6-DISULFONIC+ACID'>BIH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=7k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k5v OCA], [https://pdbe.org/7k5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k5v RCSB], [https://www.ebi.ac.uk/pdbsum/7k5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k5v ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Despite the advances in beta-lactamase inhibitor development, limited options exist for the class D carbapenemase known as OXA-48. OXA-48 is one of the most prevalent carbapenemases in carbapenem-resistant Enterobacteriaceae infections and is not susceptible to most available beta-lactamase inhibitors. Here, we screened various low-molecular-weight compounds (fragments) against OXA-48 to identify functional scaffolds for inhibitor development. Several biphenyl-, naphthalene-, fluorene-, anthraquinone-, and azobenzene-based compounds were found to inhibit OXA-48 with low micromolar potency despite their small size. Co-crystal structures of OXA-48 with several of these compounds revealed key interactions with the carboxylate-binding pocket, Arg214, and various hydrophobic residues of beta-lactamase that can be exploited in future inhibitor development. A number of the low-micromolar-potency inhibitors, across different scaffolds, synergize with ampicillin to kill Escherichia coli expressing OXA-48, albeit at high concentrations of the respective inhibitors. Additionally, several compounds demonstrated micromolar potency toward the OXA-24 and OXA-58 class D carbapenemases that are prevalent in Acinetobacter baumannii. This work provides foundational information on a variety of chemical scaffolds that can guide the design of effective OXA-48 inhibitors that maintain efficacy as well as potency toward other major class D carbapenemases.
		+
		+	Unique Diacidic Fragments Inhibit the OXA-48 Carbapenemase and Enhance the Killing of Escherichia coli Producing OXA-48.,Taylor DM, Anglin J, Hu L, Wang L, Sankaran B, Wang J, Matzuk MM, Prasad BVV, Palzkill T ACS Infect Dis. 2021 Nov 24. doi: 10.1021/acsinfecdis.1c00501. PMID:34817169<ref>PMID:34817169</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7k5v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hu L]]	+	[[Category: Hu, L]]
-	[[Category: Palzkill T]]	+	[[Category: Palzkill, T]]
-	[[Category: Prasad ~~BVV~~]]	+	[[Category: Prasad, B V.V]]
-	[[Category: Taylor DM]]	+	[[Category: Taylor, D M]]
		+	[[Category: Beta-lactamase inhibitor]]
		+	[[Category: Carbapenemase]]
		+	[[Category: Complex]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Oxacillinase]]

OCA at 06:19, 1 December 2021

OCA — Wed, 01 Dec 2021 06:19:21 GMT

←Older revision		Revision as of 06:19, 1 December 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7k5v is ~~ON HOLD until Paper Publication~~	+	==OXA-48 bound by Compound 3.1==
-		+	<StructureSection load='7k5v' size='340' side='right'caption='[[7k5v]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K5V FirstGlance]. <br>
-	~~Description~~:	+	</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=7k5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k5v OCA], [https://pdbe.org/7k5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k5v RCSB], [https://www.ebi.ac.uk/pdbsum/7k5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k5v ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hu L]]
		+	[[Category: Palzkill T]]
		+	[[Category: Prasad BVV]]
		+	[[Category: Taylor DM]]

OCA at 04:44, 7 October 2020

OCA — Wed, 07 Oct 2020 04:44:07 GMT

←Older revision		Revision as of 04:44, 7 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7k5v is ON HOLD	+	The entry 7k5v is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7k5v" [edit=sysop:move=sysop]

OCA — Wed, 23 Sep 2020 09:18:13 GMT

Protected "7k5v" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:18, 23 September 2020

OCA: New page: '''Unreleased structure''' The entry 7k5v is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 23 Sep 2020 09:18:11 GMT

New page: '''Unreleased structure''' The entry 7k5v is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7k5v is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]