PMC:7279430 / 27954-28753 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"1620","span":{"begin":43,"end":47},"obj":"Species"},{"id":"1621","span":{"begin":115,"end":125},"obj":"Species"},{"id":"1622","span":{"begin":198,"end":202},"obj":"Species"},{"id":"1623","span":{"begin":345,"end":349},"obj":"Species"},{"id":"1624","span":{"begin":504,"end":508},"obj":"Species"},{"id":"1625","span":{"begin":59,"end":74},"obj":"Chemical"},{"id":"1626","span":{"begin":76,"end":90},"obj":"Chemical"},{"id":"1627","span":{"begin":96,"end":109},"obj":"Chemical"},{"id":"1628","span":{"begin":222,"end":237},"obj":"Chemical"},{"id":"1629","span":{"begin":239,"end":243},"obj":"Chemical"},{"id":"1630","span":{"begin":246,"end":260},"obj":"Chemical"},{"id":"1631","span":{"begin":262,"end":269},"obj":"Chemical"},{"id":"1632","span":{"begin":276,"end":289},"obj":"Chemical"},{"id":"1633","span":{"begin":369,"end":384},"obj":"Chemical"},{"id":"1634","span":{"begin":386,"end":390},"obj":"Chemical"},{"id":"1635","span":{"begin":393,"end":407},"obj":"Chemical"},{"id":"1636","span":{"begin":409,"end":416},"obj":"Chemical"},{"id":"1637","span":{"begin":423,"end":436},"obj":"Chemical"},{"id":"1638","span":{"begin":573,"end":588},"obj":"Chemical"},{"id":"1639","span":{"begin":643,"end":657},"obj":"Chemical"},{"id":"1640","span":{"begin":712,"end":725},"obj":"Chemical"},{"id":"1641","span":{"begin":747,"end":755},"obj":"Chemical"}],"attributes":[{"id":"A1620","pred":"tao:has_database_id","subj":"1620","obj":"Tax:114629"},{"id":"A1621","pred":"tao:has_database_id","subj":"1621","obj":"Tax:2697049"},{"id":"A1622","pred":"tao:has_database_id","subj":"1622","obj":"Tax:114629"},{"id":"A1623","pred":"tao:has_database_id","subj":"1623","obj":"Tax:114629"},{"id":"A1624","pred":"tao:has_database_id","subj":"1624","obj":"Tax:114629"},{"id":"A1629","pred":"tao:has_database_id","subj":"1629","obj":"MESH:D014867"},{"id":"A1631","pred":"tao:has_database_id","subj":"1631","obj":"MESH:D012394"},{"id":"A1634","pred":"tao:has_database_id","subj":"1634","obj":"MESH:D014867"},{"id":"A1636","pred":"tao:has_database_id","subj":"1636","obj":"MESH:D012394"},{"id":"A1641","pred":"tao:has_database_id","subj":"1641","obj":"MESH:D006859"}],"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":"Figure 3 Lowest-energy docked poses of (E,E)-α-farnesene, (E)-β-farnesene, (E,E)-farnesol, and (E)-nerolidol with SARS-CoV-2 endoribonuclease (PDB: 6VWW). (A) Ribbon structure of the enzyme and (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange). (B) Solid structure of the enzyme showing (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange) in the binding cleft. (C) Lowest-energy docked pose of (E,E)-α-farnesene in the binding site. (D) Lowest-energy docked pose of (E)-β-farnesene in the binding site. (E) Lowest-energy docked pose of (E,E)-farnesol in the binding site. (F) Lowest-energy docked pose of (E)-nerolidol in the binding site. Hydrogen bonds are indicated with blue dashed lines."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T161","span":{"begin":115,"end":123},"obj":"Disease"}],"attributes":[{"id":"A161","pred":"mondo_id","subj":"T161","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Figure 3 Lowest-energy docked poses of (E,E)-α-farnesene, (E)-β-farnesene, (E,E)-farnesol, and (E)-nerolidol with SARS-CoV-2 endoribonuclease (PDB: 6VWW). (A) Ribbon structure of the enzyme and (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange). (B) Solid structure of the enzyme showing (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange) in the binding cleft. (C) Lowest-energy docked pose of (E,E)-α-farnesene in the binding site. (D) Lowest-energy docked pose of (E)-β-farnesene in the binding site. (E) Lowest-energy docked pose of (E,E)-farnesol in the binding site. (F) Lowest-energy docked pose of (E)-nerolidol in the binding site. Hydrogen bonds are indicated with blue dashed lines."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T223","span":{"begin":157,"end":158},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T224","span":{"begin":301,"end":302},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"}],"text":"Figure 3 Lowest-energy docked poses of (E,E)-α-farnesene, (E)-β-farnesene, (E,E)-farnesol, and (E)-nerolidol with SARS-CoV-2 endoribonuclease (PDB: 6VWW). (A) Ribbon structure of the enzyme and (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange). (B) Solid structure of the enzyme showing (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange) in the binding cleft. (C) Lowest-energy docked pose of (E,E)-α-farnesene in the binding site. (D) Lowest-energy docked pose of (E)-β-farnesene in the binding site. (E) Lowest-energy docked pose of (E,E)-farnesol in the binding site. (F) Lowest-energy docked pose of (E)-nerolidol in the binding site. Hydrogen bonds are indicated with blue dashed lines."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T442","span":{"begin":48,"end":57},"obj":"Chemical"},{"id":"T443","span":{"begin":65,"end":74},"obj":"Chemical"},{"id":"T444","span":{"begin":76,"end":90},"obj":"Chemical"},{"id":"T445","span":{"begin":82,"end":90},"obj":"Chemical"},{"id":"T446","span":{"begin":100,"end":109},"obj":"Chemical"},{"id":"T447","span":{"begin":203,"end":212},"obj":"Chemical"},{"id":"T448","span":{"begin":228,"end":237},"obj":"Chemical"},{"id":"T449","span":{"begin":239,"end":243},"obj":"Chemical"},{"id":"T450","span":{"begin":246,"end":260},"obj":"Chemical"},{"id":"T451","span":{"begin":252,"end":260},"obj":"Chemical"},{"id":"T452","span":{"begin":262,"end":269},"obj":"Chemical"},{"id":"T453","span":{"begin":280,"end":289},"obj":"Chemical"},{"id":"T454","span":{"begin":350,"end":359},"obj":"Chemical"},{"id":"T455","span":{"begin":375,"end":384},"obj":"Chemical"},{"id":"T456","span":{"begin":386,"end":390},"obj":"Chemical"},{"id":"T457","span":{"begin":393,"end":407},"obj":"Chemical"},{"id":"T458","span":{"begin":399,"end":407},"obj":"Chemical"},{"id":"T459","span":{"begin":409,"end":416},"obj":"Chemical"},{"id":"T460","span":{"begin":427,"end":436},"obj":"Chemical"},{"id":"T461","span":{"begin":509,"end":518},"obj":"Chemical"},{"id":"T462","span":{"begin":579,"end":588},"obj":"Chemical"},{"id":"T463","span":{"begin":643,"end":657},"obj":"Chemical"},{"id":"T464","span":{"begin":649,"end":657},"obj":"Chemical"},{"id":"T465","span":{"begin":716,"end":725},"obj":"Chemical"},{"id":"T466","span":{"begin":747,"end":755},"obj":"Chemical"}],"attributes":[{"id":"A442","pred":"chebi_id","subj":"T442","obj":"http://purl.obolibrary.org/obo/CHEBI_39237"},{"id":"A443","pred":"chebi_id","subj":"T443","obj":"http://purl.obolibrary.org/obo/CHEBI_39237"},{"id":"A444","pred":"chebi_id","subj":"T444","obj":"http://purl.obolibrary.org/obo/CHEBI_16619"},{"id":"A445","pred":"chebi_id","subj":"T445","obj":"http://purl.obolibrary.org/obo/CHEBI_28600"},{"id":"A446","pred":"chebi_id","subj":"T446","obj":"http://purl.obolibrary.org/obo/CHEBI_7524"},{"id":"A447","pred":"chebi_id","subj":"T447","obj":"http://purl.obolibrary.org/obo/CHEBI_39237"},{"id":"A448","pred":"chebi_id","subj":"T448","obj":"http://purl.obolibrary.org/obo/CHEBI_39237"},{"id":"A449","pred":"chebi_id","subj":"T449","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A450","pred":"chebi_id","subj":"T450","obj":"http://purl.obolibrary.org/obo/CHEBI_16619"},{"id":"A451","pred":"chebi_id","subj":"T451","obj":"http://purl.obolibrary.org/obo/CHEBI_28600"},{"id":"A452","pred":"chebi_id","subj":"T452","obj":"http://purl.obolibrary.org/obo/CHEBI_87661"},{"id":"A453","pred":"chebi_id","subj":"T453","obj":"http://purl.obolibrary.org/obo/CHEBI_7524"},{"id":"A454","pred":"chebi_id","subj":"T454","obj":"http://purl.obolibrary.org/obo/CHEBI_39237"},{"id":"A455","pred":"chebi_id","subj":"T455","obj":"http://purl.obolibrary.org/obo/CHEBI_39237"},{"id":"A456","pred":"chebi_id","subj":"T456","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A457","pred":"chebi_id","subj":"T457","obj":"http://purl.obolibrary.org/obo/CHEBI_16619"},{"id":"A458","pred":"chebi_id","subj":"T458","obj":"http://purl.obolibrary.org/obo/CHEBI_28600"},{"id":"A459","pred":"chebi_id","subj":"T459","obj":"http://purl.obolibrary.org/obo/CHEBI_87661"},{"id":"A460","pred":"chebi_id","subj":"T460","obj":"http://purl.obolibrary.org/obo/CHEBI_7524"},{"id":"A461","pred":"chebi_id","subj":"T461","obj":"http://purl.obolibrary.org/obo/CHEBI_39237"},{"id":"A462","pred":"chebi_id","subj":"T462","obj":"http://purl.obolibrary.org/obo/CHEBI_39237"},{"id":"A463","pred":"chebi_id","subj":"T463","obj":"http://purl.obolibrary.org/obo/CHEBI_16619"},{"id":"A464","pred":"chebi_id","subj":"T464","obj":"http://purl.obolibrary.org/obo/CHEBI_28600"},{"id":"A465","pred":"chebi_id","subj":"T465","obj":"http://purl.obolibrary.org/obo/CHEBI_7524"},{"id":"A466","pred":"chebi_id","subj":"T466","obj":"http://purl.obolibrary.org/obo/CHEBI_18276"}],"text":"Figure 3 Lowest-energy docked poses of (E,E)-α-farnesene, (E)-β-farnesene, (E,E)-farnesol, and (E)-nerolidol with SARS-CoV-2 endoribonuclease (PDB: 6VWW). (A) Ribbon structure of the enzyme and (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange). (B) Solid structure of the enzyme showing (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange) in the binding cleft. (C) Lowest-energy docked pose of (E,E)-α-farnesene in the binding site. (D) Lowest-energy docked pose of (E)-β-farnesene in the binding site. (E) Lowest-energy docked pose of (E,E)-farnesol in the binding site. (F) Lowest-energy docked pose of (E)-nerolidol in the binding site. Hydrogen bonds are indicated with blue dashed lines."}

{"project":"LitCovid-sentences","denotations":[{"id":"T227","span":{"begin":0,"end":148},"obj":"Sentence"},{"id":"T228","span":{"begin":149,"end":746},"obj":"Sentence"},{"id":"T229","span":{"begin":747,"end":799},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Figure 3 Lowest-energy docked poses of (E,E)-α-farnesene, (E)-β-farnesene, (E,E)-farnesol, and (E)-nerolidol with SARS-CoV-2 endoribonuclease (PDB: 6VWW). (A) Ribbon structure of the enzyme and (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange). (B) Solid structure of the enzyme showing (E,E)-α-farnesene (green), (E)-β-farnesene (aqua), (E,E)-farnesol (magenta), and (E)-nerolidol (orange) in the binding cleft. (C) Lowest-energy docked pose of (E,E)-α-farnesene in the binding site. (D) Lowest-energy docked pose of (E)-β-farnesene in the binding site. (E) Lowest-energy docked pose of (E,E)-farnesol in the binding site. (F) Lowest-energy docked pose of (E)-nerolidol in the binding site. Hydrogen bonds are indicated with blue dashed lines."}