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| | <StructureSection load='4p5d' size='340' side='right'caption='[[4p5d]], [[Resolution|resolution]] 2.11Å' scene=''> | | <StructureSection load='4p5d' size='340' side='right'caption='[[4p5d]], [[Resolution|resolution]] 2.11Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4p5d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P5D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4p5d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P5D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=N6P:6-(NAPHTHALEN-2-YL)-9-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-9H-PURINE'>N6P</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N6P:6-(NAPHTHALEN-2-YL)-9-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-9H-PURINE'>N6P</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fyi|4fyi]]</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=4p5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p5d OCA], [https://pdbe.org/4p5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p5d RCSB], [https://www.ebi.ac.uk/pdbsum/4p5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p5d ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dnph1, Rcl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
| + | |
| - | <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=4p5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p5d OCA], [http://pdbe.org/4p5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4p5d RCSB], [http://www.ebi.ac.uk/pdbsum/4p5d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4p5d ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DNPH1_RAT DNPH1_RAT]] Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.<ref>PMID:17234634</ref> | + | [https://www.uniprot.org/uniprot/DNPH1_RAT DNPH1_RAT] Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.<ref>PMID:17234634</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Buffalo rat]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kaminski, P A]] | + | [[Category: Rattus norvegicus]] |
| - | [[Category: Labesse, G]] | + | [[Category: Kaminski PA]] |
| - | [[Category: Padilla, A]] | + | [[Category: Labesse G]] |
| - | [[Category: Hydrolase]] | + | [[Category: Padilla A]] |
| - | [[Category: Inhibitor]]
| + | |
| - | [[Category: N-glycosidase]]
| + | |
| Structural highlights
Function
DNPH1_RAT Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.[1]
Publication Abstract from PubMed
The 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) has been proposed as a new molecular target for cancer treatment. Here, we describe the synthesis of a series of novel 6-aryl- and 6-heteroarylpurine riboside 5'-monophosphates via Suzuki-Miyaura cross-coupling reactions, and their ability to inhibit recombinant rat and human DNPH1. Enzymatic inhibition studies revealed competitive inhibitors in the low micromolar range. Crystal structures of human and rat DNPH1 in complex with one nucleotide from this series, the 6-naphthylpurine derivative, provided detailed structural information, in particular regarding the possible conformations of a long and flexible loop wrapping around the large hydrophobic substituent. Taking advantage of these high-resolution structures, we performed virtual docking studies in order to evaluate enzyme-inhibitor interactions for the whole compound series. Among the synthesized compounds, several molecules exhibited significant in vitro cytotoxicity against human colon cancer (HCT15, HCT116) and human promyelocytic leukemia (HL60) cell lines with IC50 values in the low micromolar range, which correlated with in vitro DNPH1 inhibitory potency.
6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: Synthesis, structural studies and cytotoxic activities.,Amiable C, Paoletti J, Haouz A, Padilla A, Labesse G, Kaminski PA, Pochet S Eur J Med Chem. 2014 Aug 1;85C:418-437. doi: 10.1016/j.ejmech.2014.07.110. PMID:25108359[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ghiorghi YK, Zeller KI, Dang CV, Kaminski PA. The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase. J Biol Chem. 2007 Mar 16;282(11):8150-6. Epub 2007 Jan 18. PMID:17234634 doi:http://dx.doi.org/10.1074/jbc.M610648200
- ↑ Amiable C, Paoletti J, Haouz A, Padilla A, Labesse G, Kaminski PA, Pochet S. 6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: Synthesis, structural studies and cytotoxic activities. Eur J Med Chem. 2014 Aug 1;85C:418-437. doi: 10.1016/j.ejmech.2014.07.110. PMID:25108359 doi:http://dx.doi.org/10.1016/j.ejmech.2014.07.110
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