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| | ==The crystal structure of human HDHD4 IN COMPLEX WITH MAGNESIUM AND THE PHOSPHATE MIMETIC VANADATE== | | ==The crystal structure of human HDHD4 IN COMPLEX WITH MAGNESIUM AND THE PHOSPHATE MIMETIC VANADATE== |
| - | <StructureSection load='4knw' size='340' side='right' caption='[[4knw]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='4knw' size='340' side='right'caption='[[4knw]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4knw]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KNW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KNW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4knw]] 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=4KNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KNW 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=VO4:VANADATE+ION'>VO4</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]] 2.699Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4knv|4knv]]</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=VO4:VANADATE+ION'>VO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">C20orf147, HDHD4, NANP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=4knw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4knw OCA], [https://pdbe.org/4knw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4knw RCSB], [https://www.ebi.ac.uk/pdbsum/4knw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4knw 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/N-acylneuraminate-9-phosphatase N-acylneuraminate-9-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.29 3.1.3.29] </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=4knw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4knw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4knw RCSB], [http://www.ebi.ac.uk/pdbsum/4knw PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/NANP_HUMAN NANP_HUMAN] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4knw" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Homo sapiens]] | | [[Category: Homo sapiens]] |
| - | [[Category: N-acylneuraminate-9-phosphatase]] | + | [[Category: Large Structures]] |
| - | [[Category: Klei, H E]] | + | [[Category: Klei HE]] |
| - | [[Category: Carbohydrate metabolism]]
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| - | [[Category: Hdhd4]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: N-acetylneuraminate]]
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| - | [[Category: N-acetylneuraminic acid phosphatase]]
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| - | [[Category: Nanp]]
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| - | [[Category: Neu5ac-9-phosphate]]
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| Structural highlights
Function
NANP_HUMAN
Publication Abstract from PubMed
The design, synthesis and characterization of a phosphonate inhibitor of N-acetylneuraminate-9-phosphate phosphatase (HDHD4) is described. Compound 3, where the substrate C-9 oxygen was replaced with a nonlabile CH2 group, inhibits HDHD4 with a binding affinity (IC50 11muM) in the range of the native substrate Neu5Ac-9-P (compound 1, Km 47muM). Combined SAR, modeling and NMR studies are consistent with the phosphonate group in inhibitor 3 forming a stable complex with native Mg(2+). In addition to this key interaction, the C-1 carboxylate of the sugar interacts with a cluster of basic residues, K141, R104 and R72. Comparative NMR studies of compounds 3 and 1 with Ca(2+) and Mg(2+) are indicative of a highly dynamic process in the active site for the HDHD4/Mg(2+)/3 complex. Possible explanations for this observation are discussed.
Design, synthesis, functional and structural characterization of an inhibitor of N-acetylneuraminate-9-phosphate phosphatase: Observation of extensive dynamics in an enzyme/inhibitor complex.,Kim SH, Constantine KL, Duke GJ, Goldfarb V, Hunt JT, Johnson S, Kish K, Klei HE, McDonnell PA, Metzler WJ, Mueller L, Poss MA, Fairchild CR, Bhide RS Bioorg Med Chem Lett. 2013 Jul 15;23(14):4107-11. doi:, 10.1016/j.bmcl.2013.05.052. Epub 2013 May 23. PMID:23747226[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kim SH, Constantine KL, Duke GJ, Goldfarb V, Hunt JT, Johnson S, Kish K, Klei HE, McDonnell PA, Metzler WJ, Mueller L, Poss MA, Fairchild CR, Bhide RS. Design, synthesis, functional and structural characterization of an inhibitor of N-acetylneuraminate-9-phosphate phosphatase: Observation of extensive dynamics in an enzyme/inhibitor complex. Bioorg Med Chem Lett. 2013 Jul 15;23(14):4107-11. doi:, 10.1016/j.bmcl.2013.05.052. Epub 2013 May 23. PMID:23747226 doi:10.1016/j.bmcl.2013.05.052
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