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| | ==The crystal structure of Glycogen Phosphorylase in complex with 10b== | | ==The crystal structure of Glycogen Phosphorylase in complex with 10b== |
| - | <StructureSection load='6f3l' size='340' side='right' caption='[[6f3l]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='6f3l' size='340' side='right'caption='[[6f3l]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6f3l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F3L FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6f3l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F3L FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CJW:6-[5-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-1~{H}-1,2,4-triazol-3-yl]naphthalene-2-carboxylic+acid'>CJW</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 1.9Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CJW:6-[5-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-1~{H}-1,2,4-triazol-3-yl]naphthalene-2-carboxylic+acid'>CJW</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></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=6f3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f3l OCA], [http://pdbe.org/6f3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f3l RCSB], [http://www.ebi.ac.uk/pdbsum/6f3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f3l 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=6f3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f3l OCA], [https://pdbe.org/6f3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f3l RCSB], [https://www.ebi.ac.uk/pdbsum/6f3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f3l ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PYGM_RABIT PYGM_RABIT]] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties. | + | [https://www.uniprot.org/uniprot/PYGM_RABIT PYGM_RABIT] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6f3l" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6f3l" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Glycogen phosphorylase 3D structures|Glycogen phosphorylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Oryctolagus cuniculus]] | | [[Category: Oryctolagus cuniculus]] |
| - | [[Category: Phosphorylase]]
| + | [[Category: Barkas TA]] |
| - | [[Category: Barkas, T A]] | + | [[Category: Kyriakis E]] |
| - | [[Category: Kyriakis, E]] | + | [[Category: Leonidas DD]] |
| - | [[Category: Leonidas, D D]] | + | [[Category: Skamnaki VT]] |
| - | [[Category: Skamnaki, V T]] | + | [[Category: Stravodimos GA]] |
| - | [[Category: Stravodimos, G A]] | + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PYGM_RABIT Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
Publication Abstract from PubMed
3-(beta-d-Glucopyranosyl)-5-substituted-1,2,4-triazoles have been revealed as an effective scaffold for the development of potent glycogen phosphorylase (GP) inhibitors but with the potency very sensitive to the nature of the alkyl/aryl 5-substituent (Kun et al., Eur. J. Med. Chem. 2014, 76, 567). For a training set of these ligands, quantum mechanics-polarized ligand docking (QM-PLD) demonstrated good potential to identify larger differences in potencies (predictive index PI=0.82) and potent inhibitors with Ki's<10muM (AU-ROC=0.86). Accordingly, in silico screening of 2335 new analogues exploiting the ZINC docking database was performed and nine predicted candidates selected for synthesis. The compounds were prepared in O-perbenzoylated forms by either ring transformation of 5-beta-d-glucopyranosyl tetrazole by N-benzyl-arenecarboximidoyl chlorides, ring closure of C-(beta-d-glucopyranosyl)formamidrazone with aroyl chlorides, or that of N-(beta-d-glucopyranosylcarbonyl)arenethiocarboxamides by hydrazine, followed by deprotections. Kinetics experiments against rabbit muscle GPb (rmGPb) and human liver GPa (hlGPa) revealed five compounds as potent low muM inhibitors with three of these on the submicromolar range for rmGPa. X-ray crystallographic analysis sourced the potency to a combination of favorable interactions from the 1,2,4-triazole and suitable aryl substituents in the GP catalytic site. The compounds also revealed promising calculated pharmacokinetic profiles.
A multidisciplinary study of 3-(beta-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors.,Kun S, Begum J, Kyriakis E, Stamati ECV, Barkas TA, Szennyes E, Bokor E, Szabo KE, Stravodimos GA, Sipos A, Docsa T, Gergely P, Moffatt C, Patraskaki MS, Kokolaki MC, Gkerdi A, Skamnaki VT, Leonidas DD, Somsak L, Hayes JM Eur J Med Chem. 2018 Mar 10;147:266-278. doi: 10.1016/j.ejmech.2018.01.095. Epub , 2018 Feb 2. PMID:29453094[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kun S, Begum J, Kyriakis E, Stamati ECV, Barkas TA, Szennyes E, Bokor E, Szabo KE, Stravodimos GA, Sipos A, Docsa T, Gergely P, Moffatt C, Patraskaki MS, Kokolaki MC, Gkerdi A, Skamnaki VT, Leonidas DD, Somsak L, Hayes JM. A multidisciplinary study of 3-(beta-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors. Eur J Med Chem. 2018 Mar 10;147:266-278. doi: 10.1016/j.ejmech.2018.01.095. Epub , 2018 Feb 2. PMID:29453094 doi:http://dx.doi.org/10.1016/j.ejmech.2018.01.095
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