4unr: Difference between revisions
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==Mtb TMK in complex with compound 23== | ==Mtb TMK in complex with compound 23== | ||
<StructureSection load='4unr' size='340' side='right' caption='[[4unr]], [[Resolution|resolution]] 1.98Å' scene=''> | <StructureSection load='4unr' size='340' side='right'caption='[[4unr]], [[Resolution|resolution]] 1.98Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4unr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UNR OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4unr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UNR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UNR FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=QZE:4-[3-CYANO-2-OXO-7-(1H-PYRAZOL-4-YL)-5,6-DIHYDRO-1H-BENZO[H]QUINOLIN-4-YL]BENZOIC+ACID'>QZE</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=QZE:4-[3-CYANO-2-OXO-7-(1H-PYRAZOL-4-YL)-5,6-DIHYDRO-1H-BENZO[H]QUINOLIN-4-YL]BENZOIC+ACID'>QZE</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=4unr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4unr OCA], [https://pdbe.org/4unr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4unr RCSB], [https://www.ebi.ac.uk/pdbsum/4unr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4unr ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/KTHY_MYCTU KTHY_MYCTU] Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with ITP, GTP, CTP and UTP.[HAMAP-Rule:MF_00165] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Thymidylate kinase|Thymidylate kinase]] | *[[Thymidylate kinase 3D structures|Thymidylate kinase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Gingell | [[Category: Mycobacterium tuberculosis]] | ||
[[Category: Hussein | [[Category: Gingell H]] | ||
[[Category: Read | [[Category: Hussein S]] | ||
[[Category: Tucker | [[Category: Read JA]] | ||
[[Category: Tucker J]] | |||
Latest revision as of 13:31, 10 January 2024
Mtb TMK in complex with compound 23Mtb TMK in complex with compound 23
Structural highlights
FunctionKTHY_MYCTU Catalyzes the reversible phosphorylation of deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP), using ATP as its preferred phosphoryl donor. Situated at the junction of both de novo and salvage pathways of deoxythymidine triphosphate (dTTP) synthesis, is essential for DNA synthesis and cellular growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with ITP, GTP, CTP and UTP.[HAMAP-Rule:MF_00165] Publication Abstract from PubMedM. tuberculosis thymidylate kinase (Mtb TMK) has been shown in vitro to be an essential enzyme in DNA synthesis. In order to identify novel leads for Mtb TMK, we performed a high throughput biochemical screen and an NMR based fragment screen through which we discovered two novel classes of inhibitors, 3-cyanopyridones and 1,6-naphthyridin-2-ones, respectively. We describe three cyanopyridone subseries that arose during our hit to lead campaign, along with cocrystal structures of representatives with Mtb TMK. Structure aided optimization of the cyanopyridones led to single digit nanomolar inhibitors of Mtb TMK. Fragment based lead generation, augmented by crystal structures and the SAR from the cyanopyridones, enabled us to drive the potency of our 1,6-naphthyridin-2-one fragment hit from 500 muM to 200 nM while simultaneously improving the ligand efficiency. Cyanopyridone derivatives containing sulfoxides and sulfones showed cellular activity against M. tuberculosis. To the best of our knowledge, these compounds are the first reports of non-thymidine-like inhibitors of Mtb TMK. Structure guided lead generation for M. tuberculosis thymidylate kinase (Mtb TMK): discovery of 3-cyanopyridone and 1,6-naphthyridin-2-one as potent inhibitors.,Naik M, Raichurkar A, Bandodkar BS, Varun BV, Bhat S, Kalkhambkar R, Murugan K, Menon R, Bhat J, Paul B, Iyer H, Hussein S, Tucker JA, Vogtherr M, Embrey KJ, McMiken H, Prasad S, Gill A, Ugarkar BG, Venkatraman J, Read J, Panda M J Med Chem. 2015 Jan 22;58(2):753-66. doi: 10.1021/jm5012947. Epub 2014 Dec 23. PMID:25486447[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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