PMC:7784834 / 31961-33285 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7784834","sourcedb":"PMC","sourceid":"7784834","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7784834","text":"Further, hydrogen bond analysis revealed a higher number of hydrogen bonds with the surrounding water molecules in case of spike protein (2300 hydrogen bonds) than in complex with rutin (approximately, 2200 hydrogen bonds). Similarly, in case of main protease, 700 hydrogen bonds were formed while 560 hydrogen bonds in case of main protease complex with rutin (Figure 6(A,B)). In addition, the hydrogen bond landscape assessed against the inhibitor revealed the dynamic equilibration of the complex trajectories with a high number of hydrogen bonds, as shown in Figure 6(C,D). The average number of hydrogen bonds within spike-rutin and main protease-rutin are 3.72 and 2.29, respectively. The consistent numbers of hydrogen bonds were observed which contributed significantly to the proximal binding of the potent drug rutin with the spike and main protease receptor. The superimposed structures of spike protein and main protease both in complex with rutin before and after simulations is shown in Figure 7(A,B). Further, these results were strengthened by the vital contribution of the complex binding energies throughout the simulation run. These calculations with consistent high binding energies and large hydrogen bonds involvement demonstrated the stable binding of rutin with both spike and main protease proteins.","tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"431","span":{"begin":123,"end":128},"obj":"Gene"},{"id":"432","span":{"begin":901,"end":906},"obj":"Gene"},{"id":"433","span":{"begin":622,"end":627},"obj":"Gene"},{"id":"434","span":{"begin":1291,"end":1296},"obj":"Gene"},{"id":"435","span":{"begin":836,"end":841},"obj":"Gene"},{"id":"436","span":{"begin":9,"end":17},"obj":"Chemical"},{"id":"437","span":{"begin":60,"end":68},"obj":"Chemical"},{"id":"438","span":{"begin":96,"end":101},"obj":"Chemical"},{"id":"439","span":{"begin":143,"end":151},"obj":"Chemical"},{"id":"440","span":{"begin":207,"end":215},"obj":"Chemical"},{"id":"441","span":{"begin":265,"end":273},"obj":"Chemical"},{"id":"442","span":{"begin":302,"end":310},"obj":"Chemical"},{"id":"443","span":{"begin":395,"end":403},"obj":"Chemical"},{"id":"444","span":{"begin":535,"end":543},"obj":"Chemical"},{"id":"445","span":{"begin":600,"end":608},"obj":"Chemical"},{"id":"446","span":{"begin":717,"end":725},"obj":"Chemical"},{"id":"447","span":{"begin":1213,"end":1221},"obj":"Chemical"}],"attributes":[{"id":"A431","pred":"tao:has_database_id","subj":"431","obj":"Gene:43740568"},{"id":"A432","pred":"tao:has_database_id","subj":"432","obj":"Gene:43740568"},{"id":"A433","pred":"tao:has_database_id","subj":"433","obj":"Gene:43740568"},{"id":"A434","pred":"tao:has_database_id","subj":"434","obj":"Gene:43740568"},{"id":"A435","pred":"tao:has_database_id","subj":"435","obj":"Gene:43740568"},{"id":"A436","pred":"tao:has_database_id","subj":"436","obj":"MESH:D006859"},{"id":"A437","pred":"tao:has_database_id","subj":"437","obj":"MESH:D006859"},{"id":"A438","pred":"tao:has_database_id","subj":"438","obj":"MESH:D014867"},{"id":"A439","pred":"tao:has_database_id","subj":"439","obj":"MESH:D006859"},{"id":"A440","pred":"tao:has_database_id","subj":"440","obj":"MESH:D006859"},{"id":"A441","pred":"tao:has_database_id","subj":"441","obj":"MESH:D006859"},{"id":"A442","pred":"tao:has_database_id","subj":"442","obj":"MESH:D006859"},{"id":"A443","pred":"tao:has_database_id","subj":"443","obj":"MESH:D006859"},{"id":"A444","pred":"tao:has_database_id","subj":"444","obj":"MESH:D006859"},{"id":"A445","pred":"tao:has_database_id","subj":"445","obj":"MESH:D006859"},{"id":"A446","pred":"tao:has_database_id","subj":"446","obj":"MESH:D006859"},{"id":"A447","pred":"tao:has_database_id","subj":"447","obj":"MESH:D006859"},{"subj":"431","pred":"source","obj":"LitCovid-PubTator"},{"subj":"432","pred":"source","obj":"LitCovid-PubTator"},{"subj":"433","pred":"source","obj":"LitCovid-PubTator"},{"subj":"434","pred":"source","obj":"LitCovid-PubTator"},{"subj":"435","pred":"source","obj":"LitCovid-PubTator"},{"subj":"436","pred":"source","obj":"LitCovid-PubTator"},{"subj":"437","pred":"source","obj":"LitCovid-PubTator"},{"subj":"438","pred":"source","obj":"LitCovid-PubTator"},{"subj":"439","pred":"source","obj":"LitCovid-PubTator"},{"subj":"440","pred":"source","obj":"LitCovid-PubTator"},{"subj":"441","pred":"source","obj":"LitCovid-PubTator"},{"subj":"442","pred":"source","obj":"LitCovid-PubTator"},{"subj":"443","pred":"source","obj":"LitCovid-PubTator"},{"subj":"444","pred":"source","obj":"LitCovid-PubTator"},{"subj":"445","pred":"source","obj":"LitCovid-PubTator"},{"subj":"446","pred":"source","obj":"LitCovid-PubTator"},{"subj":"447","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T221","span":{"begin":0,"end":223},"obj":"Sentence"},{"id":"T222","span":{"begin":224,"end":377},"obj":"Sentence"},{"id":"T223","span":{"begin":378,"end":577},"obj":"Sentence"},{"id":"T224","span":{"begin":578,"end":690},"obj":"Sentence"},{"id":"T225","span":{"begin":691,"end":869},"obj":"Sentence"},{"id":"T226","span":{"begin":870,"end":1015},"obj":"Sentence"},{"id":"T227","span":{"begin":1016,"end":1145},"obj":"Sentence"},{"id":"T228","span":{"begin":1146,"end":1324},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T221","pred":"source","obj":"LitCovid-sentences"},{"subj":"T222","pred":"source","obj":"LitCovid-sentences"},{"subj":"T223","pred":"source","obj":"LitCovid-sentences"},{"subj":"T224","pred":"source","obj":"LitCovid-sentences"},{"subj":"T225","pred":"source","obj":"LitCovid-sentences"},{"subj":"T226","pred":"source","obj":"LitCovid-sentences"},{"subj":"T227","pred":"source","obj":"LitCovid-sentences"},{"subj":"T228","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#9693ec","default":true},{"id":"LitCovid-sentences","color":"#a9ec93"}]}]}}