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| | ==HUMAN PEROXIREDOXIN 5 with a fragment== | | ==HUMAN PEROXIREDOXIN 5 with a fragment== |
| - | <StructureSection load='4k7i' size='340' side='right' caption='[[4k7i]], [[Resolution|resolution]] 2.25Å' scene=''> | + | <StructureSection load='4k7i' size='340' side='right'caption='[[4k7i]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4k7i]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K7I FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4k7i]] is a 3 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=4K7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K7I FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</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]] 2.25Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4k7n|4k7n]], [[4k7o|4k7o]], [[4mmm|4mmm]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAQ:CATECHOL'>CAQ</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PRDX5, ACR1, SBBI10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4k7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k7i OCA], [https://pdbe.org/4k7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k7i RCSB], [https://www.ebi.ac.uk/pdbsum/4k7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k7i ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></td></tr>
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| - | <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=4k7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k7i OCA], [http://pdbe.org/4k7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k7i RCSB], [http://www.ebi.ac.uk/pdbsum/4k7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k7i ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PRDX5_HUMAN PRDX5_HUMAN]] Reduces hydrogen peroxide and alkyl hydroperoxides with reducing equivalents provided through the thioredoxin system. Involved in intracellular redox signaling. | + | [https://www.uniprot.org/uniprot/PRDX5_HUMAN PRDX5_HUMAN] Reduces hydrogen peroxide and alkyl hydroperoxides with reducing equivalents provided through the thioredoxin system. Involved in intracellular redox signaling. |
| | <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== |
| - | *[[Peroxiredoxin|Peroxiredoxin]] | + | *[[Peroxiredoxin 3D structures|Peroxiredoxin 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Peroxiredoxin]] | + | [[Category: Large Structures]] |
| - | [[Category: Guichou, J F]] | + | [[Category: Guichou JF]] |
| - | [[Category: Cytosol]]
| + | |
| - | [[Category: Enzyme]]
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| - | [[Category: Oxidoreductase]]
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| Structural highlights
Function
PRDX5_HUMAN Reduces hydrogen peroxide and alkyl hydroperoxides with reducing equivalents provided through the thioredoxin system. Involved in intracellular redox signaling.
Publication Abstract from PubMed
Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD) experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP) calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.
Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5.,Aguirre C, Brink TT, Guichou JF, Cala O, Krimm I PLoS One. 2014 Jul 15;9(7):e102300. doi: 10.1371/journal.pone.0102300., eCollection 2014. PMID:25025339[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Aguirre C, Brink TT, Guichou JF, Cala O, Krimm I. Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5. PLoS One. 2014 Jul 15;9(7):e102300. doi: 10.1371/journal.pone.0102300., eCollection 2014. PMID:25025339 doi:http://dx.doi.org/10.1371/journal.pone.0102300
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