3sec

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<StructureSection load='3sec' size='340' side='right'caption='[[3sec]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='3sec' size='340' side='right'caption='[[3sec]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3sec]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SEC FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3sec]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SEC FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PFU:(1S)-1,4-ANHYDRO-1-(5-CARBAMOYL-4-HYDROXY-1H-PYRAZOL-3-YL)-5-O-PHOSPHONO-D-RIBITOL'>PFU</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3sgu|3sgu]], [[3ssj|3ssj]], [[3sw6|3sw6]], [[3mi2|3mi2]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PFU:(1S)-1,4-ANHYDRO-1-(5-CARBAMOYL-4-HYDROXY-1H-PYRAZOL-3-YL)-5-O-PHOSPHONO-D-RIBITOL'>PFU</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">1470090, MTH_129, pyrF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3sec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sec OCA], [https://pdbe.org/3sec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sec RCSB], [https://www.ebi.ac.uk/pdbsum/3sec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sec 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=3sec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sec OCA], [https://pdbe.org/3sec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sec RCSB], [https://www.ebi.ac.uk/pdbsum/3sec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sec ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
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[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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In recent years, orotidine-5'-monophosphate decarboxylase (ODCase) has gained renewed attention as a drug target. As a part of continuing efforts to design novel inhibitors of ODCase, we undertook a comprehensive study of potent, structurally diverse ligands of ODCase and analyzed their structural interactions in the active site of ODCase. These ligands comprise of pyrazole or pyrimidine nucleotides including the mononucleotide derivatives of pyrazofurin, barbiturate ribonucleoside, and 5-cyanouridine, as well as, in a computational approach, 1,4-dihydropyridine-based non-nucleoside inhibitors such as nifedipine and nimodipine. All these ligands bind in the active site of ODCase exhibiting distinct interactions paving the way to design novel inhibitors against this interesting enzyme. We propose an empirical model for the ligand structure for rational modifications in new drug design and potentially new lead structures.
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Structural determinants for the inhibitory ligands of orotidine-5'-monophosphate decarboxylase.,Meza-Avina ME, Wei L, Liu Y, Poduch E, Bello AM, Mishra RK, Pai EF, Kotra LP Bioorg Med Chem. 2010 Jun 1;18(11):4032-41. Epub 2010 Apr 9. PMID:20452222<ref>PMID:20452222</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3sec" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Metth]]
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[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
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[[Category: Orotidine-5'-phosphate decarboxylase]]
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[[Category: Kotra LP]]
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[[Category: Kotra, L P]]
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[[Category: Liu Y]]
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[[Category: Liu, Y]]
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[[Category: Pai EF]]
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[[Category: Pai, E F]]
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[[Category: Decarboxylase]]
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[[Category: Lyase-lyase inhibitor complex]]
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[[Category: Methanothermobacter thermautotrophicus]]
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[[Category: Orotidine 5'-monophosphate decarboxylase]]
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[[Category: Pyrazofurin monophosphate]]
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Current revision

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate

PDB ID 3sec

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