5dhr - Revision history

OCA at 21:42, 28 June 2023

OCA — Wed, 28 Jun 2023 21:42:17 GMT

←Older revision		Revision as of 21:42, 28 June 2023
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	<StructureSection load='5dhr' size='340' side='right'caption='[[5dhr]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='5dhr' size='340' side='right'caption='[[5dhr]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dhr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DHR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DHR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dhr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes_EGD-e Listeria monocytogenes EGD-e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DHR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AJ:5-AZIDO-8-[(2-{[2-(1H-BENZIMIDAZOL-2-YL)ETHYL]AMINO}-2-OXOETHYL)SULFANYL]-5-DEOXYADENOSINE'>5AJ</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.31Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dhu\|5dhu]], [[5dht\|5dht]], [[5dhs\|5dhs]], [[5dhq\|5dhq]], [[5dhp\|5dhp]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AJ:5-AZIDO-8-[(2-{[2-(1H-BENZIMIDAZOL-2-YL)ETHYL]AMINO}-2-OXOETHYL)SULFANYL]-5-DEOXYADENOSINE'>5AJ</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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=5dhr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dhr OCA], [https://pdbe.org/5dhr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dhr RCSB], [https://www.ebi.ac.uk/pdbsum/5dhr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dhr 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=5dhr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dhr OCA], [~~http~~://pdbe.org/5dhr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dhr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dhr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dhr ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>	+	[https://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Assairi, L]]	+	[[Category: Listeria monocytogenes EGD-e]]
-	[[Category: Gelin, M]]	+	[[Category: Assairi L]]
-	[[Category: Huteau, V]]	+	[[Category: Gelin M]]
-	[[Category: Labesse, G]]	+	[[Category: Huteau V]]
-	[[Category: Paoletti, J]]	+	[[Category: Labesse G]]
-	[[Category: Pochet, S]]	+	[[Category: Paoletti J]]
-	~~[[Category: Tetrameric nad kinase]]~~	+	[[Category: Pochet S]]
-	~~[[Category: Transferase~~]]	+

OCA at 08:04, 8 April 2020

OCA — Wed, 08 Apr 2020 08:04:02 GMT

←Older revision		Revision as of 08:04, 8 April 2020
Line 1:		Line 1:

	==Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor==		==Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor==
-	<StructureSection load='5dhr' size='340' side='right' caption='[[5dhr]], [[Resolution\|resolution]] 2.31Å' scene=''>	+	<StructureSection load='5dhr' size='340' side='right'caption='[[5dhr]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dhr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DHR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DHR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dhr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DHR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DHR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AJ:5-AZIDO-8-[(2-{[2-(1H-BENZIMIDAZOL-2-YL)ETHYL]AMINO}-2-OXOETHYL)SULFANYL]-5-DEOXYADENOSINE'>5AJ</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AJ:5-AZIDO-8-[(2-{[2-(1H-BENZIMIDAZOL-2-YL)ETHYL]AMINO}-2-OXOETHYL)SULFANYL]-5-DEOXYADENOSINE'>5AJ</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dhu\|5dhu]], [[5dht\|5dht]], [[5dhs\|5dhs]], [[5dhq\|5dhq]], [[5dhp\|5dhp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dhu\|5dhu]], [[5dht\|5dht]], [[5dhs\|5dhs]], [[5dhq\|5dhq]], [[5dhp\|5dhp]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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=5dhr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dhr OCA], [http://pdbe.org/5dhr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dhr RCSB], [http://www.ebi.ac.uk/pdbsum/5dhr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dhr 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=5dhr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dhr OCA], [http://pdbe.org/5dhr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dhr RCSB], [http://www.ebi.ac.uk/pdbsum/5dhr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dhr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Assairi, L]]		[[Category: Assairi, L]]
	[[Category: Gelin, M]]		[[Category: Gelin, M]]

OCA at 03:46, 6 September 2017

OCA — Wed, 06 Sep 2017 03:46:26 GMT

←Older revision		Revision as of 03:46, 6 September 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5dhr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dhr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[NAD kinase\|NAD kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:04, 9 December 2016

OCA — Fri, 09 Dec 2016 20:04:08 GMT

←Older revision		Revision as of 20:04, 9 December 2016
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>		[[http://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Increased resistance of pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials. Biosynthetic pathways of several cofactors important for bacterial growth, such as nicotinamide adenine dinucleotide phosphate (NADP), have been proposed as a promising source of antibiotic targets. Nicotinamide adenine dinucleotide kinases (NADK; EC 2.7.1.23) are attractive for inhibitor development, since they catalyze the phosphorylation of NAD to NADP, which is an essential step of NADP metabolism. We previously synthesized diadenosine derivatives that inhibited NADK from two human pathogens, Listeria monocytogenes and Staphylococcus aureus, in the micromolar range. They behave as NAD mimics with the 5',5'-diphosphate group substituted by a 8,5' thioglycolic bridge. In an attempt to improve inhibitory potency, we designed new NAD mimics based on a single adenosine moiety harboring a larger derivatization attached to the C8 position and a small group at the 5' position. Here we report the synthesis of a series of 8-thioalkyl-adenosine derivatives containing various aryl and heteroaryl moieties and their evaluation as inhibitors of L. monocytogenes NADK1, S. aureus NADK and their human counterpart. Novel, sub-micromolar inhibitors of LmNADK1 were identified. Surprisingly, most LmNADK1 inhibitors demonstrated a high selectivity index against the close staphylococcal ortholog and the human NADK. Structural characterization of enzyme-inhibitor complexes revealed the original binding mode of these novel NAD mimics.
		+
		+	8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.,Paoletti J, Assairi L, Gelin M, Huteau V, Nahori MA, Dussurget O, Labesse G, Pochet S Eur J Med Chem. 2016 Nov 29;124:1041-1056. doi: 10.1016/j.ejmech.2016.10.033., Epub 2016 Oct 18. PMID:27783975<ref>PMID:27783975</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5dhr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:28, 14 September 2016

OCA — Wed, 14 Sep 2016 15:28:51 GMT

←Older revision		Revision as of 15:28, 14 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5dhr is ~~ON HOLD~~	+	==Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor==
-		+	<StructureSection load='5dhr' size='340' side='right' caption='[[5dhr]], [[Resolution\|resolution]] 2.31Å' scene=''>
-	~~Authors~~: ~~Gelin~~, M., ~~Paoletti~~, J., ~~Assairi~~, L., ~~Huteau~~, V.~~, Pochet, S~~., ~~Labesse~~, G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5dhr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DHR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DHR FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of NAD ~~kinase 1 from Listeria monocytogenes in complex with~~ a ~~novel inhibitor~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5AJ:5-AZIDO-8-[(2-{[2-(1H-BENZIMIDAZOL-2-YL)ETHYL]AMINO}-2-OXOETHYL)SULFANYL]-5-DEOXYADENOSINE'>5AJ</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dhu\|5dhu]], [[5dht\|5dht]], [[5dhs\|5dhs]], [[5dhq\|5dhq]], [[5dhp\|5dhp]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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=5dhr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dhr OCA], [http://pdbe.org/5dhr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dhr RCSB], [http://www.ebi.ac.uk/pdbsum/5dhr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dhr ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NADK1_LISMO NADK1_LISMO]] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.[HAMAP-Rule:MF_00361]<ref>PMID:17686780</ref> <ref>PMID:22608967</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Assairi, L]]
		+	[[Category: Gelin, M]]
	[[Category: Huteau, V]]		[[Category: Huteau, V]]
	[[Category: Labesse, G]]		[[Category: Labesse, G]]
-	[[Category: ~~Assairi~~, L]]	+	[[Category: Paoletti, J]]
	[[Category: Pochet, S]]		[[Category: Pochet, S]]
-	[[Category: ~~Paoletti, J~~]]	+	[[Category: Tetrameric nad kinase]]
-	[[Category: ~~Gelin, M~~]]	+	[[Category: Transferase]]

OCA at 11:09, 16 December 2015

OCA — Wed, 16 Dec 2015 11:09:44 GMT

←Older revision		Revision as of 11:09, 16 December 2015
Line 7:		Line 7:
	Description: Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor		Description: Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Huteau, V]]
	[[Category: Labesse, G]]		[[Category: Labesse, G]]
		+	[[Category: Assairi, L]]
	[[Category: Pochet, S]]		[[Category: Pochet, S]]
	[[Category: Paoletti, J]]		[[Category: Paoletti, J]]
	[[Category: Gelin, M]]		[[Category: Gelin, M]]
-	[[Category: Huteau, V]]
-	[[Category: Assairi, L]]

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

OCA — Wed, 09 Sep 2015 10:13:25 GMT

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

←Older revision

Revision as of 10:13, 9 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dhr is ON HOLD Authors: Gelin, M., Paoletti, J., Assairi, L., Huteau, V., Pochet, S., Labesse, G. Description: Crystal structure of NAD kinase 1 f...

OCA — Wed, 09 Sep 2015 10:13:24 GMT

New page: '''Unreleased structure''' The entry 5dhr is ON HOLD Authors: Gelin, M., Paoletti, J., Assairi, L., Huteau, V., Pochet, S., Labesse, G. Description: Crystal structure of NAD kinase 1 f...

New page

'''Unreleased structure'''

The entry 5dhr is ON HOLD

Authors: Gelin, M., Paoletti, J., Assairi, L., Huteau, V., Pochet, S., Labesse, G.

Description: Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor
[[Category: Unreleased Structures]]
[[Category: Labesse, G]]
[[Category: Pochet, S]]
[[Category: Paoletti, J]]
[[Category: Gelin, M]]
[[Category: Huteau, V]]
[[Category: Assairi, L]]