3ipy: Difference between revisions
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== | ==X-Ray structure of Human Deoxycytidine Kinase in complex with an inhibitor== | ||
[[http://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN | <StructureSection load='3ipy' size='340' side='right'caption='[[3ipy]], [[Resolution|resolution]] 2.54Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ipy]] is a 2 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=3IPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IPY FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.54Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B87:4-(1-BENZOTHIOPHEN-2-YL)-6-[4-(2-OXO-2-PYRROLIDIN-1-YLETHYL)PIPERAZIN-1-YL]PYRIMIDINE'>B87</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</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=3ipy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ipy OCA], [https://pdbe.org/3ipy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ipy RCSB], [https://www.ebi.ac.uk/pdbsum/3ipy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ipy 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> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/3ipy_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ipy ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A series of deoxycytidine kinase inhibitors was simultaneously optimized for potency and PK properties. A co-crystal structure then allowed merging this series with a high throughput screening hit to afford a highly potent, selective and orally bioavailable inhibitor, compound 10. This compound showed dose dependent inhibition of deoxycytidine kinase in vivo. | |||
Lead optimization and structure-based design of potent and bioavailable deoxycytidine kinase inhibitors.,Jessop TC, Tarver JE, Carlsen M, Xu A, Healy JP, Heim-Riether A, Fu Q, Taylor JA, Augeri DJ, Shen M, Stouch TR, Swanson RV, Tari LW, Hunter M, Hoffman I, Keyes PE, Yu XC, Miranda M, Liu Q, Swaffield JC, David Kimball S, Nouraldeen A, Wilson AG, Foushee AM, Jhaver K, Finch R, Anderson S, Oravecz T, Carson KG Bioorg Med Chem Lett. 2009 Dec 1;19(23):6784-7. Epub 2009 Sep 25. PMID:19836232<ref>PMID:19836232</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
< | </div> | ||
[[ | <div class="pdbe-citations 3ipy" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Deoxycytidine kinase 3D structures|Deoxycytidine kinase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Carson | [[Category: Large Structures]] | ||
[[Category: Hoffman | [[Category: Carson KG]] | ||
[[Category: Hunter | [[Category: Hoffman I]] | ||
[[Category: Stouch | [[Category: Hunter M]] | ||
[[Category: Swanson | [[Category: Stouch TR]] | ||
[[Category: Tari | [[Category: Swanson RV]] | ||
[[Category: Tari LW]] | |||
Latest revision as of 10:56, 6 September 2023
X-Ray structure of Human Deoxycytidine Kinase in complex with an inhibitorX-Ray structure of Human Deoxycytidine Kinase in complex with an inhibitor
Structural highlights
FunctionDCK_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.[1] [2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedA series of deoxycytidine kinase inhibitors was simultaneously optimized for potency and PK properties. A co-crystal structure then allowed merging this series with a high throughput screening hit to afford a highly potent, selective and orally bioavailable inhibitor, compound 10. This compound showed dose dependent inhibition of deoxycytidine kinase in vivo. Lead optimization and structure-based design of potent and bioavailable deoxycytidine kinase inhibitors.,Jessop TC, Tarver JE, Carlsen M, Xu A, Healy JP, Heim-Riether A, Fu Q, Taylor JA, Augeri DJ, Shen M, Stouch TR, Swanson RV, Tari LW, Hunter M, Hoffman I, Keyes PE, Yu XC, Miranda M, Liu Q, Swaffield JC, David Kimball S, Nouraldeen A, Wilson AG, Foushee AM, Jhaver K, Finch R, Anderson S, Oravecz T, Carson KG Bioorg Med Chem Lett. 2009 Dec 1;19(23):6784-7. Epub 2009 Sep 25. PMID:19836232[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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