2yoh: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{STRUCTURE_2yoh|  PDB=2yoh  |  SCENE=  }}
-===Plasmodium falciparum thymidylate kinase in complex with a urea-alpha- deoxythymidine inhibitor===
-{{ABSTRACT_PUBMED_23240776}}
-==About this Structure==
+==Plasmodium falciparum thymidylate kinase in complex with a urea-alpha- deoxythymidine inhibitor==
-[[2yoh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Plasmodium_falciparum_3d7 Plasmodium falciparum 3d7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YOH OCA].
+<StructureSection load='2yoh' size='340' side='right'caption='[[2yoh]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2yoh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum_3D7 Plasmodium falciparum 3D7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YOH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YOH 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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=WMJ:1-[[(2R,3S,5S)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL]-3-(4-NITROPHENYL)UREA'>WMJ</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=2yoh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yoh OCA], [https://pdbe.org/2yoh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yoh RCSB], [https://www.ebi.ac.uk/pdbsum/2yoh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yoh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KTHY_PLAF7 KTHY_PLAF7] Catalyzes the phosphorylation of thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP), the immediate precursor for the DNA building block dTTP (PubMed:18477629, PubMed:19126267, PubMed:31934749, PubMed:20353400). Can also phosphorylate dGMP and to a lesser extent GMP, dUMP and dIMP (PubMed:18477629, PubMed:19126267, PubMed:31934749, PubMed:20353400). Can use either ATP or dATP as phosphate donors in presence of Mg(2+) (PubMed:18477629).<ref>PMID:18477629</ref> <ref>PMID:19126267</ref> <ref>PMID:20353400</ref> <ref>PMID:31934749</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Plasmodium falciparum thymidylate kinase (PfTMPK) is a key enzyme in pyrimidine nucleotide biosynthesis. 3-Trifluoromethyl-4-chloro-phenyl-urea-alpha-thymidine has been reported as an inhibitor of Mycobacterium tuberculosis TMPK (MtTMPK). Starting from this point, we designed, synthesized and evaluated a number of thymidine analogues as antimalarials. Both 5'-urea-alpha- and beta-thymidine derivatives were moderate inhibitors of PfTMPK and furthermore showed moderate inhibition of parasite growth. The structure of several enzyme-inhibitor complexes provides a basis for improved inhibitor design. However, we found that certain 5'-urea-alpha-thymidine analogues had antimalarial activity where inhibition of PfTMPK is not the major mode of action. Optimization of this series resulted in a compound with potent antimalarial activity (EC(50) = 28 nM; CC(50) = 29 muM).
-==Reference==
+Synthesis and evaluation of alpha-thymidine analogues as novel antimalarials.,Cui H, Carrero-Lerida J, Silva AP, Whittingham JL, Brannigan JA, Ruiz-Perez LM, Read KD, Wilson KS, Gonzalez-Pacanowska D, Gilbert IH J Med Chem. 2012 Dec 27;55(24):10948-57. doi: 10.1021/jm301328h. Epub 2012 Dec, 14. PMID:23240776<ref>PMID:23240776</ref>
-<ref group="xtra">PMID:023240776</ref><references group="xtra"/><references/>
-[[Category: Plasmodium falciparum 3d7]]
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: DTMP kinase]]
+</div>
-[[Category: Brannigan, J A.]]
+<div class="pdbe-citations 2yoh" style="background-color:#fffaf0;"></div>
-[[Category: Carrero-Lerida, J.]]
-[[Category: Gilbert, I H.]]
+==See Also==
-[[Category: Gonzalez-Pacanowska, D.]]
+*[[Thymidylate kinase 3D structures|Thymidylate kinase 3D structures]]
-[[Category: Huaqing, C.]]
+== References ==
-[[Category: Read, K D.]]
+<references/>
-[[Category: Ruiz-Perez, L M.]]
+__TOC__
-[[Category: Silva, A P.G.]]
+</StructureSection>
-[[Category: Whittingham, J L.]]
+[[Category: Large Structures]]
-[[Category: Wilson, K S.]]
+[[Category: Plasmodium falciparum 3D7]]
-[[Category: Inhibitor]]
+[[Category: Brannigan JA]]
-[[Category: Malaria]]
+[[Category: Carrero-Lerida J]]
-[[Category: Transferase]]
+[[Category: Gilbert IH]]
+[[Category: Gonzalez-Pacanowska D]]
+[[Category: Huaqing C]]
+[[Category: Read KD]]
+[[Category: Ruiz-Perez LM]]
+[[Category: Silva APG]]
+[[Category: Whittingham JL]]
+[[Category: Wilson KS]]