4ivr - Revision history

OCA at 15:32, 20 September 2023

OCA — Wed, 20 Sep 2023 15:32:03 GMT

←Older revision		Revision as of 15:32, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ivr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_17 Human alphaherpesvirus 1 strain 17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IVR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ivr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_17 Human alphaherpesvirus 1 strain 17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IVR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N50:2-[(2,6-DIMETHOXY-5-METHYLPYRIMIDIN-4-YL)METHYLIDENE]PROPANE-1,3-DIOL'>N50</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]] 2.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N50:2-[(2,6-DIMETHOXY-5-METHYLPYRIMIDIN-4-YL)METHYLIDENE]PROPANE-1,3-DIOL'>N50</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4ivr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ivr OCA], [https://pdbe.org/4ivr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ivr RCSB], [https://www.ebi.ac.uk/pdbsum/4ivr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ivr 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=4ivr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ivr OCA], [https://pdbe.org/4ivr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ivr RCSB], [https://www.ebi.ac.uk/pdbsum/4ivr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ivr ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:14, 16 November 2022

OCA — Wed, 16 Nov 2022 21:14:48 GMT

←Older revision		Revision as of 21:14, 16 November 2022
Line 1:		Line 1:

	==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10==		==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10==
-	<StructureSection load='4ivr' size='340' side='right' caption='[[4ivr]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4ivr' size='340' side='right'caption='[[4ivr]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ivr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hhv-1 Hhv-~~1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IVR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ivr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1_strain_17 Human alphaherpesvirus 1 strain 17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IVR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N50:2-[(2,6-DIMETHOXY-5-METHYLPYRIMIDIN-4-YL)METHYLIDENE]PROPANE-1,3-DIOL'>N50</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" id="ligandDat"><scene name='pdbligand=N50:2-[(2,6-DIMETHOXY-5-METHYLPYRIMIDIN-4-YL)METHYLIDENE]PROPANE-1,3-DIOL'>N50</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f0t\|3f0t]], [[3rdp\|3rdp]], [[1e2p\|1e2p]], [[4ivp\|4ivp]], [[4ivq\|4ivq]]</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=4ivr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ivr OCA], [https://pdbe.org/4ivr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ivr RCSB], [https://www.ebi.ac.uk/pdbsum/4ivr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ivr ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK, TK (UL23), UL23 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=4ivr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ivr OCA], [~~http~~://pdbe.org/4ivr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ivr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ivr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ivr ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11]] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).	+	[https://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Molecular modeling and phosphorylation assay in vitro were employed to select a novel unsaturated 1,3-dihydroxyisobutenyl thymine derivative 6 as ligand for HSV-1 TK which may be of interest as lead for the development of an positron emission tomography (PET) imaging agent. Compound 6 was successfully prepared using modified approaches. A significant improvement over the syntheses involving pathways A and B (1% and 3% overall yield, respectively), was observed using synthetic route C (14% overall yield).	+

-	A new N-methyl thymine derivative comprising a dihydroxyisobutenyl unit as ligand for thymidine kinase of herpes simplex virus type 1 (HSV-1 TK).,Kristafor S, Novakovic I, Gazivoda Kraljevic T, Kraljevic Pavelic S, Lucin P, Westermaier Y, Pernot L, Scapozza L, Ametamey SM, Raic-Malic S Bioorg Med Chem Lett. 2011 Oct 15;21(20):6161-5. doi: 10.1016/j.bmcl.2011.07.115., Epub 2011 Aug 6. PMID:21911293<ref>PMID:21911293</ref>	+	==See Also==
-		+	*[[Thymidine kinase 3D structures\|Thymidine kinase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 4ivr" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hhv-~~1]]	+	[[Category: Human alphaherpesvirus 1 strain 17]]
-	[[Category: ~~Thymidine kinase~~]]	+	[[Category: Large Structures]]
-	[[Category: Novakovic, I]]	+	[[Category: Novakovic I]]
-	[[Category: Pernot, L]]	+	[[Category: Pernot L]]
-	[[Category: Perozzo, R]]	+	[[Category: Perozzo R]]
-	[[Category: Raic-Malic, S]]	+	[[Category: Raic-Malic S]]
-	[[Category: Scapozza, L]]	+	[[Category: Scapozza L]]
-	[[Category: Westermaier, Y]]	+	[[Category: Westermaier Y]]
-	~~[[Category: Atp binding]]~~	+
-	~~[[Category: Dna synthesis]]~~	+
-	~~[[Category: Nucleotide binding]]~~	+
-	~~[[Category: Pet imaging tracer]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:02, 15 November 2017

OCA — Wed, 15 Nov 2017 09:02:49 GMT

←Older revision		Revision as of 09:02, 15 November 2017
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 4ivr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ivr" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Thymidine kinase\|Thymidine kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:04, 4 August 2016

OCA — Thu, 04 Aug 2016 23:04:30 GMT

←Older revision		Revision as of 23:04, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10==		==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10==
	<StructureSection load='4ivr' size='340' side='right' caption='[[4ivr]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4ivr' size='340' side='right' caption='[[4ivr]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ivr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Herpes_simplex_virus_(type_1_/_strain_17) Herpes simplex virus (type~~ 1 ~~/ strain 17)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IVR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ivr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hhv-1 Hhv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IVR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N50:2-[(2,6-DIMETHOXY-5-METHYLPYRIMIDIN-4-YL)METHYLIDENE]PROPANE-1,3-DIOL'>N50</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=N50:2-[(2,6-DIMETHOXY-5-METHYLPYRIMIDIN-4-YL)METHYLIDENE]PROPANE-1,3-DIOL'>N50</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f0t\|3f0t]], [[3rdp\|3rdp]], [[1e2p\|1e2p]], [[4ivp\|4ivp]], [[4ivq\|4ivq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f0t\|3f0t]], [[3rdp\|3rdp]], [[1e2p\|1e2p]], [[4ivp\|4ivp]], [[4ivq\|4ivq]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK, TK (UL23), UL23 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 ~~Herpes simplex virus (type~~ 1 ~~/ strain 17)~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK, TK (UL23), UL23 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 HHV-1])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=4ivr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ivr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ivr RCSB], [http://www.ebi.ac.uk/pdbsum/4ivr 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=4ivr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ivr OCA], [http://pdbe.org/4ivr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ivr RCSB], [http://www.ebi.ac.uk/pdbsum/4ivr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ivr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Novel C~~-6 ~~substituted pyrimidine derivatives are good substrates~~ of ~~herpes simplex virus type 1 thymidine kinase~~ (~~HSV1-TK~~). ~~Enzyme kinetic experiments showed that our lead compound, N-methyl DHBT (N-methyl-~~6-(1,3~~-dihydroxyisobutyl) thymine; N-Me DHBT)~~, ~~is phosphorylated at a similar rate compared to "gold standard" 9-[4-fluoro-3-(hydroxymethyl~~)~~butyl]guanine, FHBG~~, (~~K(m~~) = 10 +/- 0.3 muM; k(cat) = 0.036 +/- 0.015 sec(-1)). Additionally, it does not show cytotoxic properties on B16F1 cells up to a concentration of 10 mM. The x-ray analysis of the crystal structures of HSV1-TK with N-Me DHBT and of HSV1-TK with the fluorinated derivative N-Me FHBT confirmed the binding mode predicted by docking studies and their substrate characteristics. Moreover, the crystal structure of HSV1-TK with N-Me DHBT revealed an additional water-mediated H-bond interesting for the design of further analogues.	+	Molecular modeling and phosphorylation assay in vitro were employed to select a novel unsaturated 1,3-dihydroxyisobutenyl thymine derivative 6 as ligand for HSV-1 TK which may be of interest as lead for the development of an positron emission tomography (PET) imaging agent. Compound 6 was successfully prepared using modified approaches. A significant improvement over the syntheses involving pathways A and B (1% and 3% overall yield, respectively), was observed using synthetic route C (14% overall yield).

-	~~Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives:~~ new ~~lead structures~~ for ~~monitoring gene expression in vivo~~.,~~Martic M~~, ~~Pernot L~~, Westermaier Y, ~~Perozzo R~~, ~~Kraljevic TG~~, ~~Kristafor S~~, Raic-Malic S~~, Scapozza L, Ametamey S Nucleosides Nucleotides Nucleic Acids~~. 2011 ~~Apr~~;30(4):~~293~~-~~315~~. PMID:~~21623543~~<ref>PMID:~~21623543~~</ref>	+	A new N-methyl thymine derivative comprising a dihydroxyisobutenyl unit as ligand for thymidine kinase of herpes simplex virus type 1 (HSV-1 TK).,Kristafor S, Novakovic I, Gazivoda Kraljevic T, Kraljevic Pavelic S, Lucin P, Westermaier Y, Pernot L, Scapozza L, Ametamey SM, Raic-Malic S Bioorg Med Chem Lett. 2011 Oct 15;21(20):6161-5. doi: 10.1016/j.bmcl.2011.07.115., Epub 2011 Aug 6. PMID:21911293<ref>PMID:21911293</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4ivr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hhv-1]]
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
	[[Category: Novakovic, I]]		[[Category: Novakovic, I]]

OCA at 13:50, 25 December 2014

OCA — Thu, 25 Dec 2014 13:50:12 GMT

←Older revision		Revision as of 13:50, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4ivr\| PDB=4ivr \| SCENE= }}~~	+	==Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10==
-	===Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10===	+	<StructureSection load='4ivr' size='340' side='right' caption='[[4ivr]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21623543}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ivr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Herpes_simplex_virus_(type_1_/_strain_17) Herpes simplex virus (type 1 / strain 17)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IVR FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N50:2-[(2,6-DIMETHOXY-5-METHYLPYRIMIDIN-4-YL)METHYLIDENE]PROPANE-1,3-DIOL'>N50</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3f0t\|3f0t]], [[3rdp\|3rdp]], [[1e2p\|1e2p]], [[4ivp\|4ivp]], [[4ivq\|4ivq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK, TK (UL23), UL23 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10299 Herpes simplex virus (type 1 / strain 17)])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] </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=4ivr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ivr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ivr RCSB], [http://www.ebi.ac.uk/pdbsum/4ivr PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11]] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).		[[http://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11]] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Novel C-6 substituted pyrimidine derivatives are good substrates of herpes simplex virus type 1 thymidine kinase (HSV1-TK). Enzyme kinetic experiments showed that our lead compound, N-methyl DHBT (N-methyl-6-(1,3-dihydroxyisobutyl) thymine; N-Me DHBT), is phosphorylated at a similar rate compared to "gold standard" 9-[4-fluoro-3-(hydroxymethyl)butyl]guanine, FHBG, (K(m) = 10 +/- 0.3 muM; k(cat) = 0.036 +/- 0.015 sec(-1)). Additionally, it does not show cytotoxic properties on B16F1 cells up to a concentration of 10 mM. The x-ray analysis of the crystal structures of HSV1-TK with N-Me DHBT and of HSV1-TK with the fluorinated derivative N-Me FHBT confirmed the binding mode predicted by docking studies and their substrate characteristics. Moreover, the crystal structure of HSV1-TK with N-Me DHBT revealed an additional water-mediated H-bond interesting for the design of further analogues.

-	~~==About this Structure==~~	+	Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo.,Martic M, Pernot L, Westermaier Y, Perozzo R, Kraljevic TG, Kristafor S, Raic-Malic S, Scapozza L, Ametamey S Nucleosides Nucleotides Nucleic Acids. 2011 Apr;30(4):293-315. PMID:21623543<ref>PMID:21623543</ref>
-	~~[[4ivr]] is a 2 chain~~ structure ~~with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Herpes_simplex_virus_~~(~~type_1_/_strain_17~~) ~~Herpes simplex virus (type 1 / strain 17)]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4IVR OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Thymidine kinase\|Thymidine kinase]]		*[[Thymidine kinase\|Thymidine kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021623543</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
-	[[Category: Novakovic, I.]]	+	[[Category: Novakovic, I]]
-	[[Category: Pernot, L.]]	+	[[Category: Pernot, L]]
-	[[Category: Perozzo, R.]]	+	[[Category: Perozzo, R]]
-	[[Category: Raic-Malic, S.]]	+	[[Category: Raic-Malic, S]]
-	[[Category: Scapozza, L.]]	+	[[Category: Scapozza, L]]
-	[[Category: Westermaier, Y.]]	+	[[Category: Westermaier, Y]]
	[[Category: Atp binding]]		[[Category: Atp binding]]
	[[Category: Dna synthesis]]		[[Category: Dna synthesis]]

OCA at 06:01, 2 October 2013

OCA — Wed, 02 Oct 2013 06:01:06 GMT

←Older revision		Revision as of 06:01, 2 October 2013
Line 1:		Line 1:
-	[[Image:4ivr.jpg\|left\|200px]]
-
	{{STRUCTURE_4ivr\| PDB=4ivr \| SCENE= }}		{{STRUCTURE_4ivr\| PDB=4ivr \| SCENE= }}
-
	===Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10===		===Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10===
-
	{{ABSTRACT_PUBMED_21623543}}		{{ABSTRACT_PUBMED_21623543}}
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/KITH_HHV11 KITH_HHV11]] In latent infection, may allow the virus to be reactivated and to grow in cells lacking a high concentration of phosphorylated nucleic acid precursors, such as nerve cells that do not replicate their genome (By similarity).

	==About this Structure==		==About this Structure==
	[[4ivr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Herpes_simplex_virus_(type_1_/_strain_17) Herpes simplex virus (type 1 / strain 17)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA].		[[4ivr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Herpes_simplex_virus_(type_1_/_strain_17) Herpes simplex virus (type 1 / strain 17)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA].
		+
		+	==See Also==
		+	*[[Thymidine kinase\|Thymidine kinase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021623543</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021623543</ref><references group="xtra"/><references/>
	[[Category: Thymidine kinase]]		[[Category: Thymidine kinase]]
	[[Category: Novakovic, I.]]		[[Category: Novakovic, I.]]
Line 18:		Line 20:
	[[Category: Raic-Malic, S.]]		[[Category: Raic-Malic, S.]]
	[[Category: Scapozza, L.]]		[[Category: Scapozza, L.]]
		+	[[Category: Westermaier, Y.]]
	[[Category: Atp binding]]		[[Category: Atp binding]]
	[[Category: Dna synthesis]]		[[Category: Dna synthesis]]

OCA at 13:08, 6 February 2013

OCA — Wed, 06 Feb 2013 13:08:56 GMT

←Older revision		Revision as of 13:08, 6 February 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4ivr.jpg\|left\|200px]]

-	~~The entry~~ 4ivr ~~is ON HOLD~~	+	{{STRUCTURE_4ivr\| PDB=4ivr \| SCENE= }}

-	~~Authors: Pernot, L., Novakovic, I., Perozzo, R., Raic-Malic, S., Scapozza, L.~~	+	===Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10===

-	~~Description: Crystal~~ structure ~~of thymidine kinase~~ from ~~herpes~~ simplex virus type 1 ~~in complex with IN52~~/10	+	{{ABSTRACT_PUBMED_21623543}}
		+
		+	==About this Structure==
		+	[[4ivr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Herpes_simplex_virus_(type_1_/_strain_17) Herpes simplex virus (type 1 / strain 17)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IVR OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021623543</ref><references group="xtra"/>
		+	[[Category: Thymidine kinase]]
		+	[[Category: Novakovic, I.]]
		+	[[Category: Pernot, L.]]
		+	[[Category: Perozzo, R.]]
		+	[[Category: Raic-Malic, S.]]
		+	[[Category: Scapozza, L.]]
		+	[[Category: Atp binding]]
		+	[[Category: Dna synthesis]]
		+	[[Category: Nucleotide binding]]
		+	[[Category: Pet imaging tracer]]
		+	[[Category: Transferase]]

OCA: Protected "4ivr" [edit=sysop:move=sysop]

OCA — Wed, 30 Jan 2013 12:06:24 GMT

Protected "4ivr" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:06, 30 January 2013

OCA: New page: '''Unreleased structure''' The entry 4ivr is ON HOLD Authors: Pernot, L., Novakovic, I., Perozzo, R., Raic-Malic, S., Scapozza, L. Description: Crystal structure of thymidine kinase fr...

OCA — Wed, 30 Jan 2013 12:06:23 GMT

New page: '''Unreleased structure''' The entry 4ivr is ON HOLD Authors: Pernot, L., Novakovic, I., Perozzo, R., Raic-Malic, S., Scapozza, L. Description: Crystal structure of thymidine kinase fr...

New page

'''Unreleased structure'''

The entry 4ivr is ON HOLD

Authors: Pernot, L., Novakovic, I., Perozzo, R., Raic-Malic, S., Scapozza, L.

Description: Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10