5dts - Revision history

OCA at 21:58, 28 June 2023

2023-06-28T21:58:55Z

←Older revision		Revision as of 21:58, 28 June 2023
Line 3:		Line 3:
	<StructureSection load='5dts' size='340' side='right'caption='[[5dts]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='5dts' size='340' side='right'caption='[[5dts]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dts]] is a 4 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=5DTS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DTS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dts]] is a 4 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=5DTS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DTS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=5F8:3~~-~~(PYRIDIN-3-YL)BENZOIC+ACID'>5F8</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.9401587Å</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=5F8:3-(PYRIDIN-3-YL)BENZOIC+ACID'>5F8</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[5dva\|5dva]]</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=5dts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dts OCA], [https://pdbe.org/5dts PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dts RCSB], [https://www.ebi.ac.uk/pdbsum/5dts PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dts ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">bla OXA-48~~, ~~blaOXA-48, KPE71T_00045 ([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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5dts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dts OCA], [~~http~~://pdbe.org/5dts PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dts RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dts PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dts 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 ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta-lactamase~~]]	+	[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Christopeit, T]]	+	[[Category: Christopeit T]]
-	[[Category: Leiros, H ~~K.S~~]]	+	[[Category: Leiros H-KS]]
-	[[Category: Lund~~, B A]]~~	+	[[Category: Lund BA]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Fragment]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Lactamase~~]]	+

OCA at 08:05, 15 April 2020

2020-04-15T08:05:38Z

←Older revision		Revision as of 08:05, 15 April 2020
Line 1:		Line 1:

	==Fragments bound to the OXA-48 beta-lactamase: Compound 2==		==Fragments bound to the OXA-48 beta-lactamase: Compound 2==
-	<StructureSection load='5dts' size='340' side='right' caption='[[5dts]], [[Resolution\|resolution]] 1.94Å' scene=''>	+	<StructureSection load='5dts' size='340' side='right'caption='[[5dts]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dts]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DTS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DTS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dts]] is a 4 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=5DTS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DTS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5F8:3-(PYRIDIN-3-YL)BENZOIC+ACID'>5F8</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5F8:3-(PYRIDIN-3-YL)BENZOIC+ACID'>5F8</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dva\|5dva]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dva\|5dva]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla OXA-48, blaOXA-48, KPE71T_00045 ([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=5dts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dts OCA], [http://pdbe.org/5dts PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dts RCSB], [http://www.ebi.ac.uk/pdbsum/5dts PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dts 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=5dts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dts OCA], [http://pdbe.org/5dts PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dts RCSB], [http://www.ebi.ac.uk/pdbsum/5dts PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dts ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5dts" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dts" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
	[[Category: Christopeit, T]]		[[Category: Christopeit, T]]
	[[Category: Leiros, H K.S]]		[[Category: Leiros, H K.S]]

OCA at 02:34, 13 July 2016

2016-07-13T02:34:27Z

←Older revision		Revision as of 02:34, 13 July 2016
Line 8:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dva\|5dva]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dva\|5dva]]</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=5dts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dts OCA], [http://pdbe.org/5dts PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dts RCSB], [http://www.ebi.ac.uk/pdbsum/5dts PDBsum]</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=5dts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dts OCA], [http://pdbe.org/5dts PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dts RCSB], [http://www.ebi.ac.uk/pdbsum/5dts PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dts ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:55, 1 June 2016

2016-06-01T22:55:34Z

←Older revision		Revision as of 22:55, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5dts is ~~ON HOLD until Paper~~ Publication	+	==Fragments bound to the OXA-48 beta-lactamase: Compound 2==
		+	<StructureSection load='5dts' size='340' side='right' caption='[[5dts]], [[Resolution\|resolution]] 1.94Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dts]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DTS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DTS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5F8:3-(PYRIDIN-3-YL)BENZOIC+ACID'>5F8</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dva\|5dva]]</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=5dts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dts OCA], [http://pdbe.org/5dts PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dts RCSB], [http://www.ebi.ac.uk/pdbsum/5dts PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The spread of antibiotic resistant bacteria is a global threat that shakes the foundations of modern healthcare. beta-Lactamases are enzymes that confer resistance to beta-lactam antibiotics in bacteria, and there is a critical need for new inhibitors of these enzymes for combination therapy together with an antibiotic. With this in mind, we have screened a library of 490 fragments to identify starting points for the development of new inhibitors of the class D beta-lactamase oxacillinase-48 (OXA-48) through surface plasmon resonance (SPR), dose-rate inhibition assays, and X-ray crystallography. Furthermore, we have uncovered structure-activity relationships and used alternate conformations from a crystallographic structure to grow a fragment into a more potent compound with a KD of 50 muM and an IC50 of 18 muM.

-	~~Authors:~~ Lund~~, B.A.~~, Christopeit, T., Leiros~~, H~~.~~-K.S~~.	+	Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening.,Lund BA, Christopeit T, Guttormsen Y, Bayer A, Leiros HS J Med Chem. 2016 May 20. PMID:27165692<ref>PMID:27165692</ref>

-	~~Description: Fragments bound to~~ the ~~OXA~~-~~48 beta~~-~~lactamase~~: ~~Compound 2~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Leiros, H.~~-~~K.S~~]]	+	<div class="pdbe-citations 5dts" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
	[[Category: Christopeit, T]]		[[Category: Christopeit, T]]
-	[[Category: Lund, B.A]]	+	[[Category: Leiros, H K.S]]
		+	[[Category: Lund, B A]]
		+	[[Category: Complex]]
		+	[[Category: Fragment]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Lactamase]]

OCA at 11:25, 16 December 2015

2015-12-16T11:25:00Z

←Older revision		Revision as of 11:25, 16 December 2015
Line 7:		Line 7:
	Description: Fragments bound to the OXA-48 beta-lactamase: Compound 2		Description: Fragments bound to the OXA-48 beta-lactamase: Compound 2
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Lund, B.A]]
	[[Category: Leiros, H.-K.S]]		[[Category: Leiros, H.-K.S]]
	[[Category: Christopeit, T]]		[[Category: Christopeit, T]]
		+	[[Category: Lund, B.A]]

OCA at 04:04, 22 October 2015

2015-10-22T04:04:39Z

←Older revision		Revision as of 04:04, 22 October 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Lund, B.A., Christopeit, T., Leiros, H.-K.S.		Authors: Lund, B.A., Christopeit, T., Leiros, H.-K.S.

-	Description: Fragments bound to the OXA-48 beta-lactamase: Compound 3	+	Description: Fragments bound to the OXA-48 beta-lactamase: Compound 2
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Lund, B.A]]		[[Category: Lund, B.A]]
	[[Category: Leiros, H.-K.S]]		[[Category: Leiros, H.-K.S]]
	[[Category: Christopeit, T]]		[[Category: Christopeit, T]]

OCA at 02:40, 16 October 2015

2015-10-16T02:40:59Z

←Older revision		Revision as of 02:40, 16 October 2015
Line 5:		Line 5:
	Authors: Lund, B.A., Christopeit, T., Leiros, H.-K.S.		Authors: Lund, B.A., Christopeit, T., Leiros, H.-K.S.

-	Description: OXA-48 beta-lactamase ~~in complex with carboxylate TC240~~	+	Description: Fragments bound to the OXA-48 beta-lactamase: Compound 3
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Lund, B.A]]		[[Category: Lund, B.A]]
	[[Category: Leiros, H.-K.S]]		[[Category: Leiros, H.-K.S]]
	[[Category: Christopeit, T]]		[[Category: Christopeit, T]]

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

2015-09-30T13:31:15Z

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

←Older revision

Revision as of 13:31, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dts is ON HOLD Authors: Lund, B.A., Christopeit, T., Leiros, H.-K.S. Description: OXA-48 beta-lactamase in complex with carboxylate TC240 [[Catego...

2015-09-30T13:31:14Z

New page: '''Unreleased structure''' The entry 5dts is ON HOLD Authors: Lund, B.A., Christopeit, T., Leiros, H.-K.S. Description: OXA-48 beta-lactamase in complex with carboxylate TC240 [[Catego...

New page

'''Unreleased structure'''

The entry 5dts is ON HOLD

Authors: Lund, B.A., Christopeit, T., Leiros, H.-K.S.

Description: OXA-48 beta-lactamase in complex with carboxylate TC240
[[Category: Unreleased Structures]]
[[Category: Lund, B.A]]
[[Category: Leiros, H.-K.S]]
[[Category: Christopeit, T]]