6yen - Revision history

OCA at 13:25, 24 January 2024

OCA — Wed, 24 Jan 2024 13:25:16 GMT

←Older revision		Revision as of 13:25, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6yen' size='340' side='right'caption='[[6yen]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='6yen' size='340' side='right'caption='[[6yen]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yen]] is a 1 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=6YEN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YEN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yen]] is a 1 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=6YEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YEN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K9K:(10aR)-2-(((1r,4R)-4-((2-aminoethyl)amino)cyclohexyl)methyl)-6-carboxy-4-hydroxy-4,10a-dihydro-10H-benzo[5,6][1,2]oxaborinino[2,3-b][1,4,2]oxazaborol-4-uide'>K9K</scene>, <scene name='pdbligand=KJK:(3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic+acid'>KJK</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.418Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA, b4150, JW4111 ([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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K9K:(10aR)-2-(((1r,4R)-4-((2-aminoethyl)amino)cyclohexyl)methyl)-6-carboxy-4-hydroxy-4,10a-dihydro-10H-benzo[5,6][1,2]oxaborinino[2,3-b][1,4,2]oxazaborol-4-uide'>K9K</scene>, <scene name='pdbligand=KJK:(3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic+acid'>KJK</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://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=6yen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yen OCA], [https://pdbe.org/6yen PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yen RCSB], [https://www.ebi.ac.uk/pdbsum/6yen PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yen ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6yen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yen OCA], [~~http~~://pdbe.org/6yen PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yen RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yen PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yen ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI]] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.	+	[https://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta~~-~~lactamase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brem, J]]	+	[[Category: Brem J]]
-	[[Category: Lang~~, P A~~]]	+	[[Category: Lang PA]]
-	[[Category: Schofield~~, C J]]~~	+	[[Category: Schofield CJ]]
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Beta lactamase]]~~	+
-	~~[[Category: Bicyclic boronate]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:49, 30 September 2020

OCA — Wed, 30 Sep 2020 07:49:43 GMT

←Older revision		Revision as of 07:49, 30 September 2020
Line 1:		Line 1:

	==Crystal structure of AmpC from E. coli with Taniborbactam (VNRX-5133)==		==Crystal structure of AmpC from E. coli with Taniborbactam (VNRX-5133)==
-	<StructureSection load='6yen' size='340' side='right'caption='[[6yen]]' scene=''>	+	<StructureSection load='6yen' size='340' side='right'caption='[[6yen]], [[Resolution\|resolution]] 1.42Å' 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=6YEN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yen]] is a 1 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=6YEN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEN FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yen OCA], [http://pdbe.org/6yen PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yen RCSB], [http://www.ebi.ac.uk/pdbsum/6yen PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yen 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K9K:(10aR)-2-(((1r,4R)-4-((2-aminoethyl)amino)cyclohexyl)methyl)-6-carboxy-4-hydroxy-4,10a-dihydro-10H-benzo[5,6][1,2]oxaborinino[2,3-b][1,4,2]oxazaborol-4-uide'>K9K</scene>, <scene name='pdbligand=KJK:(3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic+acid'>KJK</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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">ampC, ampA, b4150, JW4111 ([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/Beta-lactamase Beta-lactamase], with EC number [http://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'>[http://proteopedia.org/fgij/fg.htm?mol=6yen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yen OCA], [http://pdbe.org/6yen PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yen RCSB], [http://www.ebi.ac.uk/pdbsum/6yen PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yen ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI]] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Resistance to beta-lactam antibacterials, importantly via production of beta-lactamases, threatens their widespread use. Bicyclic boronates show promise as clinically useful, dual-action inhibitors of both serine- (SBL) and metallo- (MBL) beta-lactamases. In combination with cefepime, the bicyclic boronate taniborbactam is in phase 3 clinical trials for treatment of complicated urinary tract infections. We report kinetic and crystallographic studies on the inhibition of AmpC, the class C betalactamase from Escherichia coli, by bicyclic boronates, including taniborbactam, with different C-3 side chains. The combined studies reveal that an acylamino side chain is not essential for potent AmpC inhibition by active site binding bicyclic boronates. The tricyclic form of taniborbactam was observed bound to the surface of crystalline AmpC, but not at the active site, where the bicyclic form was observed. Structural comparisons reveal insights into why active site binding of a tricyclic form has been observed with the NDM-1 MBL, but not with other studied beta-lactamases. Together with reported studies on the structural basis of inhibition of class A, B and D betalactamases, our data support the proposal that bicyclic boronates are broad-spectrum betalactamase inhibitors that work by mimicking a high energy 'tetrahedral' intermediate. These results suggest further SAR guided development could improve the breadth of clinically useful beta-lactamase inhibition.
		+
		+	Bicyclic Boronates as Potent Inhibitors of AmpC, the Class C beta-Lactamase from Escherichia coli.,Lang PA, Parkova A, Leissing TM, Calvopina K, Cain R, Krajnc A, Panduwawala TD, Philippe J, Fishwick CWG, Trapencieris P, Page MGP, Schofield CJ, Brem J Biomolecules. 2020 Jun 12;10(6). pii: biom10060899. doi: 10.3390/biom10060899. PMID:32545682<ref>PMID:32545682</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yen" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brem J]]	+	[[Category: Brem, J]]
-	[[Category: Lang PA]]	+	[[Category: Lang, P A]]
-	[[Category: Schofield CJ]]	+	[[Category: Schofield, C J]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Beta lactamase]]
		+	[[Category: Bicyclic boronate]]
		+	[[Category: Hydrolase]]

OCA at 06:31, 25 June 2020

OCA — Thu, 25 Jun 2020 06:31:58 GMT

←Older revision		Revision as of 06:31, 25 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6yen ~~is ON HOLD until Mar 25 2022~~	+	==Crystal structure of AmpC from E. coli with Taniborbactam (VNRX-5133)==
-		+	<StructureSection load='6yen' size='340' side='right'caption='[[6yen]]' scene=''>
-	~~Authors~~: ~~Lang~~, P.A., ~~Brem~~, J., ~~Schofield, C~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEN FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of AmpC from E~~. ~~coli with Taniborbactam (VNRX~~-~~5133)~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yen OCA], [http://pdbe.org/6yen PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yen RCSB], [http://www.ebi.ac.uk/pdbsum/6yen PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yen ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Brem, J]]	+	__TOC__
-	[[Category: ~~Schofield, C.J~~]]	+	</StructureSection>
-	[[Category: ~~Lang, P.A~~]]	+	[[Category: Large Structures]]
		+	[[Category: Brem J]]
		+	[[Category: Lang PA]]
		+	[[Category: Schofield CJ]]

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

OCA — Wed, 01 Apr 2020 07:45:28 GMT

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

←Older revision

Revision as of 07:45, 1 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yen is ON HOLD until Mar 25 2022 Authors: Lang, P.A., Brem, J., Schofield, C.J. Description: Crystal structure of AmpC from E. coli with Taniborba...

OCA — Wed, 01 Apr 2020 07:45:27 GMT

New page: '''Unreleased structure''' The entry 6yen is ON HOLD until Mar 25 2022 Authors: Lang, P.A., Brem, J., Schofield, C.J. Description: Crystal structure of AmpC from E. coli with Taniborba...

New page

'''Unreleased structure'''

The entry 6yen is ON HOLD until Mar 25 2022

Authors: Lang, P.A., Brem, J., Schofield, C.J.

Description: Crystal structure of AmpC from E. coli with Taniborbactam (VNRX-5133)
[[Category: Unreleased Structures]]
[[Category: Brem, J]]
[[Category: Schofield, C.J]]
[[Category: Lang, P.A]]