7z2i: Difference between revisions
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<StructureSection load='7z2i' size='340' side='right'caption='[[7z2i]], [[Resolution|resolution]] 1.09Å' scene=''> | <StructureSection load='7z2i' size='340' side='right'caption='[[7z2i]], [[Resolution|resolution]] 1.09Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'> | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z2I FirstGlance]. <br> | ||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.09Å</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]] 1.09Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=I9O:5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine'>I9O</scene></td></tr> | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=I9O:5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine'>I9O</scene></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=7z2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z2i OCA], [https://pdbe.org/7z2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z2i RCSB], [https://www.ebi.ac.uk/pdbsum/7z2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z2i 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=7z2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z2i OCA], [https://pdbe.org/7z2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z2i RCSB], [https://www.ebi.ac.uk/pdbsum/7z2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z2i ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | |||
Ligand-based (19) F NMR screening is a highly effective and well-established hit-finding approach. The high sensitivity to protein binding makes it particularly suitable for fragment screening. Different criteria can be considered for generating fluorinated fragment libraries. One common strategy is to assemble a large, diverse, well-designed and characterized fragment library which is screened in mixtures, generated based on experimental (19) F NMR chemical shifts. Here, we introduce a complementary knowledge-based (19) F NMR screening approach, named (19) Focused screening, enabling the efficient screening of putative active molecules selected by computational hit finding methodologies, in mixtures assembled and on-the-fly deconvoluted based on predicted (19) F NMR chemical shifts. In this study, we developed a novel approach, named LEFshift, for (19) F NMR chemical shift prediction using rooted topological fluorine torsion fingerprints in combination with a random forest machine learning method. A demonstration of this approach to a real test case is reported. | |||
Efficient Screening of Target-Specific Selected Compounds in Mixtures by (19) F NMR Binding Assay with Predicted (19) F NMR Chemical Shifts.,Vulpetti A, Lingel A, Dalvit C, Schiering N, Oberer L, Henry C, Lu Y ChemMedChem. 2022 Apr 27:e202200163. doi: 10.1002/cmdc.202200163. PMID:35475323<ref>PMID:35475323</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7z2i" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Trypsin 3D structures|Trypsin 3D structures]] | *[[Trypsin 3D structures|Trypsin 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Dalvit C]] | [[Category: Dalvit C]] | ||
[[Category: Schiering N]] | [[Category: Schiering N]] | ||
[[Category: Vulpetti A]] | [[Category: Vulpetti A]] | ||
Latest revision as of 12:23, 17 October 2024
TRYPSIN (BOVINE) COMPLEXED WITH compound 4TRYPSIN (BOVINE) COMPLEXED WITH compound 4
Structural highlights
Publication Abstract from PubMedLigand-based (19) F NMR screening is a highly effective and well-established hit-finding approach. The high sensitivity to protein binding makes it particularly suitable for fragment screening. Different criteria can be considered for generating fluorinated fragment libraries. One common strategy is to assemble a large, diverse, well-designed and characterized fragment library which is screened in mixtures, generated based on experimental (19) F NMR chemical shifts. Here, we introduce a complementary knowledge-based (19) F NMR screening approach, named (19) Focused screening, enabling the efficient screening of putative active molecules selected by computational hit finding methodologies, in mixtures assembled and on-the-fly deconvoluted based on predicted (19) F NMR chemical shifts. In this study, we developed a novel approach, named LEFshift, for (19) F NMR chemical shift prediction using rooted topological fluorine torsion fingerprints in combination with a random forest machine learning method. A demonstration of this approach to a real test case is reported. Efficient Screening of Target-Specific Selected Compounds in Mixtures by (19) F NMR Binding Assay with Predicted (19) F NMR Chemical Shifts.,Vulpetti A, Lingel A, Dalvit C, Schiering N, Oberer L, Henry C, Lu Y ChemMedChem. 2022 Apr 27:e202200163. doi: 10.1002/cmdc.202200163. PMID:35475323[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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