PMC:7594251 / 97021-98106 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T211","span":{"begin":427,"end":434},"obj":"Body_part"}],"attributes":[{"id":"A211","pred":"fma_id","subj":"T211","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"3.6.5. SALMON\nSolvent accessibility, ligand binding, and mapping of ligand orientation by NMR spectroscopy (SALMON) is another method based on the data obtained via nuclear Overhauser effect. This method utilizes WaterLOGSY [401] to probe for solvent accessibility to the ligand and determine the orientation of the ligand by analyzing signal changes in WaterLOGSY spectra (positive signal from unbound ligand vs. negative for protein-bound ligands). This method was first used to determine the orientation of prodrug called tretazicar ((5-(aziridin-1-yl)-2,4-dinitrobenzamide) known as CB1954 in NQO2 (quinone oxidoreductase 2) binding site. Previous attempts had been made to obtain the orientation of tretazicar bounded to NQO2, however the results obtained from X-ray crystallography were inconclusive as two orientations of tretazicar could be possible. The information obtained via SALMON showed that the side chain of asparagine at position 161 formed a hydrogen bond with 2-nitrogroup of tretazicar, and that the aziridine moiety of tretazicar pointed toward the solvent [401]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T682","span":{"begin":336,"end":342},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T683","span":{"begin":383,"end":389},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T684","span":{"begin":959,"end":960},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"3.6.5. SALMON\nSolvent accessibility, ligand binding, and mapping of ligand orientation by NMR spectroscopy (SALMON) is another method based on the data obtained via nuclear Overhauser effect. This method utilizes WaterLOGSY [401] to probe for solvent accessibility to the ligand and determine the orientation of the ligand by analyzing signal changes in WaterLOGSY spectra (positive signal from unbound ligand vs. negative for protein-bound ligands). This method was first used to determine the orientation of prodrug called tretazicar ((5-(aziridin-1-yl)-2,4-dinitrobenzamide) known as CB1954 in NQO2 (quinone oxidoreductase 2) binding site. Previous attempts had been made to obtain the orientation of tretazicar bounded to NQO2, however the results obtained from X-ray crystallography were inconclusive as two orientations of tretazicar could be possible. The information obtained via SALMON showed that the side chain of asparagine at position 161 formed a hydrogen bond with 2-nitrogroup of tretazicar, and that the aziridine moiety of tretazicar pointed toward the solvent [401]."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T652","span":{"begin":37,"end":43},"obj":"Chemical"},{"id":"T653","span":{"begin":68,"end":74},"obj":"Chemical"},{"id":"T654","span":{"begin":233,"end":238},"obj":"Chemical"},{"id":"T655","span":{"begin":243,"end":250},"obj":"Chemical"},{"id":"T656","span":{"begin":272,"end":278},"obj":"Chemical"},{"id":"T657","span":{"begin":316,"end":322},"obj":"Chemical"},{"id":"T658","span":{"begin":403,"end":409},"obj":"Chemical"},{"id":"T659","span":{"begin":427,"end":434},"obj":"Chemical"},{"id":"T660","span":{"begin":441,"end":448},"obj":"Chemical"},{"id":"T661","span":{"begin":510,"end":517},"obj":"Chemical"},{"id":"T662","span":{"begin":603,"end":610},"obj":"Chemical"},{"id":"T663","span":{"begin":925,"end":935},"obj":"Chemical"},{"id":"T664","span":{"begin":961,"end":969},"obj":"Chemical"},{"id":"T665","span":{"begin":1021,"end":1030},"obj":"Chemical"},{"id":"T666","span":{"begin":1071,"end":1078},"obj":"Chemical"}],"attributes":[{"id":"A652","pred":"chebi_id","subj":"T652","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A653","pred":"chebi_id","subj":"T653","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A654","pred":"chebi_id","subj":"T654","obj":"http://purl.obolibrary.org/obo/CHEBI_50406"},{"id":"A655","pred":"chebi_id","subj":"T655","obj":"http://purl.obolibrary.org/obo/CHEBI_46787"},{"id":"A656","pred":"chebi_id","subj":"T656","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A657","pred":"chebi_id","subj":"T657","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A658","pred":"chebi_id","subj":"T658","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A659","pred":"chebi_id","subj":"T659","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A660","pred":"chebi_id","subj":"T660","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A661","pred":"chebi_id","subj":"T661","obj":"http://purl.obolibrary.org/obo/CHEBI_50266"},{"id":"A662","pred":"chebi_id","subj":"T662","obj":"http://purl.obolibrary.org/obo/CHEBI_36141"},{"id":"A663","pred":"chebi_id","subj":"T663","obj":"http://purl.obolibrary.org/obo/CHEBI_22653"},{"id":"A664","pred":"chebi_id","subj":"T664","obj":"http://purl.obolibrary.org/obo/CHEBI_49637"},{"id":"A665","pred":"chebi_id","subj":"T665","obj":"http://purl.obolibrary.org/obo/CHEBI_30969"},{"id":"A666","pred":"chebi_id","subj":"T666","obj":"http://purl.obolibrary.org/obo/CHEBI_46787"}],"text":"3.6.5. SALMON\nSolvent accessibility, ligand binding, and mapping of ligand orientation by NMR spectroscopy (SALMON) is another method based on the data obtained via nuclear Overhauser effect. This method utilizes WaterLOGSY [401] to probe for solvent accessibility to the ligand and determine the orientation of the ligand by analyzing signal changes in WaterLOGSY spectra (positive signal from unbound ligand vs. negative for protein-bound ligands). This method was first used to determine the orientation of prodrug called tretazicar ((5-(aziridin-1-yl)-2,4-dinitrobenzamide) known as CB1954 in NQO2 (quinone oxidoreductase 2) binding site. Previous attempts had been made to obtain the orientation of tretazicar bounded to NQO2, however the results obtained from X-ray crystallography were inconclusive as two orientations of tretazicar could be possible. The information obtained via SALMON showed that the side chain of asparagine at position 161 formed a hydrogen bond with 2-nitrogroup of tretazicar, and that the aziridine moiety of tretazicar pointed toward the solvent [401]."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1032","span":{"begin":597,"end":601},"obj":"Gene"},{"id":"1033","span":{"begin":726,"end":730},"obj":"Gene"},{"id":"1034","span":{"begin":525,"end":535},"obj":"Chemical"},{"id":"1035","span":{"begin":537,"end":576},"obj":"Chemical"},{"id":"1036","span":{"begin":587,"end":593},"obj":"Chemical"},{"id":"1037","span":{"begin":704,"end":714},"obj":"Chemical"},{"id":"1038","span":{"begin":829,"end":839},"obj":"Chemical"},{"id":"1039","span":{"begin":925,"end":935},"obj":"Chemical"},{"id":"1040","span":{"begin":961,"end":969},"obj":"Chemical"},{"id":"1041","span":{"begin":996,"end":1006},"obj":"Chemical"},{"id":"1042","span":{"begin":1021,"end":1030},"obj":"Chemical"},{"id":"1043","span":{"begin":1041,"end":1051},"obj":"Chemical"}],"attributes":[{"id":"A1032","pred":"tao:has_database_id","subj":"1032","obj":"Gene:4835"},{"id":"A1033","pred":"tao:has_database_id","subj":"1033","obj":"Gene:4835"},{"id":"A1034","pred":"tao:has_database_id","subj":"1034","obj":"MESH:C100099"},{"id":"A1035","pred":"tao:has_database_id","subj":"1035","obj":"MESH:C100099"},{"id":"A1036","pred":"tao:has_database_id","subj":"1036","obj":"MESH:C100099"},{"id":"A1037","pred":"tao:has_database_id","subj":"1037","obj":"MESH:C100099"},{"id":"A1038","pred":"tao:has_database_id","subj":"1038","obj":"MESH:C100099"},{"id":"A1039","pred":"tao:has_database_id","subj":"1039","obj":"MESH:D001216"},{"id":"A1040","pred":"tao:has_database_id","subj":"1040","obj":"MESH:D006859"},{"id":"A1041","pred":"tao:has_database_id","subj":"1041","obj":"MESH:C100099"},{"id":"A1042","pred":"tao:has_database_id","subj":"1042","obj":"MESH:C033132"},{"id":"A1043","pred":"tao:has_database_id","subj":"1043","obj":"MESH:C100099"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"3.6.5. SALMON\nSolvent accessibility, ligand binding, and mapping of ligand orientation by NMR spectroscopy (SALMON) is another method based on the data obtained via nuclear Overhauser effect. This method utilizes WaterLOGSY [401] to probe for solvent accessibility to the ligand and determine the orientation of the ligand by analyzing signal changes in WaterLOGSY spectra (positive signal from unbound ligand vs. negative for protein-bound ligands). This method was first used to determine the orientation of prodrug called tretazicar ((5-(aziridin-1-yl)-2,4-dinitrobenzamide) known as CB1954 in NQO2 (quinone oxidoreductase 2) binding site. Previous attempts had been made to obtain the orientation of tretazicar bounded to NQO2, however the results obtained from X-ray crystallography were inconclusive as two orientations of tretazicar could be possible. The information obtained via SALMON showed that the side chain of asparagine at position 161 formed a hydrogen bond with 2-nitrogroup of tretazicar, and that the aziridine moiety of tretazicar pointed toward the solvent [401]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T635","span":{"begin":0,"end":6},"obj":"Sentence"},{"id":"T636","span":{"begin":7,"end":13},"obj":"Sentence"},{"id":"T637","span":{"begin":14,"end":191},"obj":"Sentence"},{"id":"T638","span":{"begin":192,"end":450},"obj":"Sentence"},{"id":"T639","span":{"begin":451,"end":642},"obj":"Sentence"},{"id":"T640","span":{"begin":643,"end":858},"obj":"Sentence"},{"id":"T641","span":{"begin":859,"end":1085},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.6.5. SALMON\nSolvent accessibility, ligand binding, and mapping of ligand orientation by NMR spectroscopy (SALMON) is another method based on the data obtained via nuclear Overhauser effect. This method utilizes WaterLOGSY [401] to probe for solvent accessibility to the ligand and determine the orientation of the ligand by analyzing signal changes in WaterLOGSY spectra (positive signal from unbound ligand vs. negative for protein-bound ligands). This method was first used to determine the orientation of prodrug called tretazicar ((5-(aziridin-1-yl)-2,4-dinitrobenzamide) known as CB1954 in NQO2 (quinone oxidoreductase 2) binding site. Previous attempts had been made to obtain the orientation of tretazicar bounded to NQO2, however the results obtained from X-ray crystallography were inconclusive as two orientations of tretazicar could be possible. The information obtained via SALMON showed that the side chain of asparagine at position 161 formed a hydrogen bond with 2-nitrogroup of tretazicar, and that the aziridine moiety of tretazicar pointed toward the solvent [401]."}