6td1 - Revision history

OCA at 13:00, 24 January 2024

OCA — Wed, 24 Jan 2024 13:00:05 GMT

←Older revision		Revision as of 13:00, 24 January 2024
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	<StructureSection load='6td1' size='340' side='right'caption='[[6td1]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='6td1' size='340' side='right'caption='[[6td1]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6td1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus~~ pneumoniae~~" (schroeter 1886) flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TD1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6TD1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6td1]] is a 1 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=6TD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TD1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=SO4:SULFATE+ION'>SO4</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]] 1.2Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla, kpc, kpc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=SO4:SULFATE+ION'>SO4</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=6td1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6td1 OCA], [https://pdbe.org/6td1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6td1 RCSB], [https://www.ebi.ac.uk/pdbsum/6td1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6td1 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=6td1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6td1 OCA], [~~http~~://pdbe.org/6td1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6td1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6td1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6td1 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BLKPC_KLEPN BLKPC_KLEPN]] Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency.	+	[https://www.uniprot.org/uniprot/BLKPC_KLEPN BLKPC_KLEPN] Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Klebsiella pneumoniae carbapenemase-2 (KPC-2) is a serine-beta-lactamase (SBL) capable of hydrolysing almost all beta-lactam antibiotics. We compare KPC-2 inhibition by vaborbactam, a clinically-approved monocyclic boronate, and VNRX-5133 (taniborbactam), a bicyclic boronate in late-stage clinical development. Vaborbactam inhibition is slowly reversible, whereas taniborbactam has an off-rate indicating essentially irreversible complex formation and a 15-fold higher on-rate, although both potentiate beta-lactam activity against KPC-2-expressing K. pneumoniae. High resolution X-ray crystal structures reveal closely related binding modes for both inhibitors to KPC-2, with differences apparent only in positioning of the endocyclic boronate ester oxygen. The results indicate the bicyclic boronate scaffold as both an efficient, long-lasting, KPC-2 inhibitor and capable of supporting further iterations that may improve potency against specific enzyme targets and pre-empt the emergence of inhibitor resistant KPC-2 variants.
		+
		+	Cyclic boronates as versatile scaffolds for KPC-2 beta-lactamase inhibition.,Tooke CL, Hinchliffe P, Krajnc A, Mulholland AJ, Brem J, Schofield CJ, Spencer J RSC Med Chem. 2020 Jan 10;11(4):491-496. doi: 10.1039/c9md00557a. eCollection , 2020 Apr 1. PMID:33479650<ref>PMID:33479650</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6td1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta-lactamase~~]]	+	[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hinchliffe, P]]	+	[[Category: Hinchliffe P]]
-	[[Category: Spencer, J]]	+	[[Category: Spencer J]]
-	[[Category: Tooke~~, C L]]~~	+	[[Category: Tooke CL]]
-	~~[[Category: Antimicrobial protein]]~~	+
-	~~[[Category: Boronate]]~~	+
-	~~[[Category: Inhibitor~~]]	+

OCA at 10:43, 27 March 2020

OCA — Fri, 27 Mar 2020 10:43:46 GMT

←Older revision		Revision as of 10:43, 27 March 2020
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	<StructureSection load='6td1' size='340' side='right'caption='[[6td1]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='6td1' size='340' side='right'caption='[[6td1]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6td1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TD1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6td1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TD1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla, kpc, kpc1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</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='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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6td1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6td1 OCA], [http://pdbe.org/6td1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6td1 RCSB], [http://www.ebi.ac.uk/pdbsum/6td1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6td1 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=6td1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6td1 OCA], [http://pdbe.org/6td1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6td1 RCSB], [http://www.ebi.ac.uk/pdbsum/6td1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6td1 ProSAT]</span></td></tr>

OCA at 16:19, 22 January 2020

OCA — Wed, 22 Jan 2020 16:19:58 GMT

←Older revision		Revision as of 16:19, 22 January 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6td1 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of VNRX-5133 (taniborbactam) bound to KPC-2==
-		+	<StructureSection load='6td1' size='340' side='right'caption='[[6td1]], [[Resolution\|resolution]] 1.20Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6td1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TD1 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=SO4:SULFATE+ION'>SO4</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/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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6td1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6td1 OCA], [http://pdbe.org/6td1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6td1 RCSB], [http://www.ebi.ac.uk/pdbsum/6td1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6td1 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BLKPC_KLEPN BLKPC_KLEPN]] Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
		+	[[Category: Hinchliffe, P]]
		+	[[Category: Spencer, J]]
		+	[[Category: Tooke, C L]]
		+	[[Category: Antimicrobial protein]]
		+	[[Category: Boronate]]
		+	[[Category: Inhibitor]]

OCA at 13:36, 20 November 2019

OCA — Wed, 20 Nov 2019 13:36:18 GMT

←Older revision		Revision as of 13:36, 20 November 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6td1 is ON HOLD	+	The entry 6td1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6td1" [edit=sysop:move=sysop]

OCA — Wed, 13 Nov 2019 09:30:12 GMT

Protected "6td1" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:30, 13 November 2019

OCA: New page: '''Unreleased structure''' The entry 6td1 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Nov 2019 09:30:11 GMT

New page: '''Unreleased structure''' The entry 6td1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6td1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]