7zi7 - Revision history

OCA at 08:03, 7 February 2024

OCA — Wed, 07 Feb 2024 08:03:56 GMT

←Older revision		Revision as of 08:03, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7zi7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZI7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7zi7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZI7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JCM:4-(4-azanylpyrimidin-2-yl)-N-[2-methyl-5-[4-[2-(4-methylpiperazin-1-yl)ethyl]phenyl]phenyl]-N-propyl-1,3-thiazol-2-amine'>JCM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JCM:4-(4-azanylpyrimidin-2-yl)-N-[2-methyl-5-[4-[2-(4-methylpiperazin-1-yl)ethyl]phenyl]phenyl]-N-propyl-1,3-thiazol-2-amine'>JCM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></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=7zi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zi7 OCA], [https://pdbe.org/7zi7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zi7 RCSB], [https://www.ebi.ac.uk/pdbsum/7zi7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zi7 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=7zi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zi7 OCA], [https://pdbe.org/7zi7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zi7 RCSB], [https://www.ebi.ac.uk/pdbsum/7zi7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zi7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</ref>		[https://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Cancer cells utilize the main de novo pathway and the alternative salvage pathway for deoxyribonucleotide biosynthesis to achieve adequate nucleotide pools. Deoxycytidine kinase is the rate-limiting enzyme of the salvage pathway and it has recently emerged as a target for anti-proliferative therapies for cancers where it is essential. Here, we present the development of a potent inhibitor applying an iterative multidisciplinary approach, which relies on computational design coupled with experimental evaluations. This strategy allows an acceleration of the hit-to-lead process by gradually implementing key chemical modifications to increase affinity and activity. Our lead compound, OR0642, is more than 1000 times more potent than its initial parent compound, masitinib, previously identified from a drug repositioning approach. OR0642 in combination with a physiological inhibitor of the de novo pathway doubled the survival rate in a human T-cell acute lymphoblastic leukemia patient-derived xenograft mouse model, demonstrating the proof-of-concept of this drug design strategy.
-
-	From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia.,Saez-Ayala M, Hoffer L, Abel S, Ben Yaala K, Sicard B, Andrieu GP, Latiri M, Davison EK, Ciufolini MA, Bremond P, Rebuffet E, Roche P, Derviaux C, Voisset E, Montersino C, Castellano R, Collette Y, Asnafi V, Betzi S, Dubreuil P, Combes S, Morelli X Nat Commun. 2023 May 29;14(1):3079. doi: 10.1038/s41467-023-38668-2. PMID:37248212<ref>PMID:37248212</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7zi7" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 05:36, 7 June 2023

OCA — Wed, 07 Jun 2023 05:36:16 GMT

←Older revision		Revision as of 05:36, 7 June 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7zi7 is ~~ON HOLD until 2024~~-07-07	+	==Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0345 inhibitor==
		+	<StructureSection load='7zi7' size='340' side='right'caption='[[7zi7]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7zi7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZI7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JCM:4-(4-azanylpyrimidin-2-yl)-N-[2-methyl-5-[4-[2-(4-methylpiperazin-1-yl)ethyl]phenyl]phenyl]-N-propyl-1,3-thiazol-2-amine'>JCM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></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=7zi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zi7 OCA], [https://pdbe.org/7zi7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zi7 RCSB], [https://www.ebi.ac.uk/pdbsum/7zi7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zi7 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cancer cells utilize the main de novo pathway and the alternative salvage pathway for deoxyribonucleotide biosynthesis to achieve adequate nucleotide pools. Deoxycytidine kinase is the rate-limiting enzyme of the salvage pathway and it has recently emerged as a target for anti-proliferative therapies for cancers where it is essential. Here, we present the development of a potent inhibitor applying an iterative multidisciplinary approach, which relies on computational design coupled with experimental evaluations. This strategy allows an acceleration of the hit-to-lead process by gradually implementing key chemical modifications to increase affinity and activity. Our lead compound, OR0642, is more than 1000 times more potent than its initial parent compound, masitinib, previously identified from a drug repositioning approach. OR0642 in combination with a physiological inhibitor of the de novo pathway doubled the survival rate in a human T-cell acute lymphoblastic leukemia patient-derived xenograft mouse model, demonstrating the proof-of-concept of this drug design strategy.

-	~~Authors~~:	+	From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia.,Saez-Ayala M, Hoffer L, Abel S, Ben Yaala K, Sicard B, Andrieu GP, Latiri M, Davison EK, Ciufolini MA, Bremond P, Rebuffet E, Roche P, Derviaux C, Voisset E, Montersino C, Castellano R, Collette Y, Asnafi V, Betzi S, Dubreuil P, Combes S, Morelli X Nat Commun. 2023 May 29;14(1):3079. doi: 10.1038/s41467-023-38668-2. PMID:37248212<ref>PMID:37248212</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 7zi7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome P450 3D structures\|Cytochrome P450 3D structures]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Ben-Yaala K]]
		+	[[Category: Betzi S]]
		+	[[Category: Morelli X]]
		+	[[Category: Rebuffet E]]
		+	[[Category: Saez-Ayala M]]

OCA at 18:33, 12 April 2023

OCA — Wed, 12 Apr 2023 18:33:11 GMT

←Older revision		Revision as of 18:33, 12 April 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7zi7 is ON HOLD until 2024-04-07	+	The entry 7zi7 is ON HOLD until 2024-07-07

	Authors:		Authors:

OCA at 03:44, 3 August 2022

OCA — Wed, 03 Aug 2022 03:44:01 GMT

←Older revision		Revision as of 03:44, 3 August 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7zi7 is ON HOLD	+	The entry 7zi7 is ON HOLD until 2024-04-07

	Authors:		Authors:

OCA at 05:05, 12 May 2022

OCA — Thu, 12 May 2022 05:05:16 GMT

←Older revision		Revision as of 05:05, 12 May 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7zi7 is ON HOLD ~~until sometime in the future~~	+	The entry 7zi7 is ON HOLD

	Authors:		Authors:

OCA at 11:46, 4 May 2022

OCA — Wed, 04 May 2022 11:46:34 GMT

←Older revision		Revision as of 11:46, 4 May 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7zi7 is ON HOLD	+	The entry 7zi7 is ON HOLD until sometime in the future

	Authors:		Authors:

OCA: Protected "7zi7" [edit=sysop:move=sysop]

OCA — Wed, 13 Apr 2022 08:51:27 GMT

Protected "7zi7" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:51, 13 April 2022

OCA: New page: '''Unreleased structure''' The entry 7zi7 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Apr 2022 08:51:26 GMT

New page: '''Unreleased structure''' The entry 7zi7 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7zi7 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]