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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T57","span":{"begin":54,"end":61},"obj":"Body_part"},{"id":"T58","span":{"begin":89,"end":94},"obj":"Body_part"},{"id":"T59","span":{"begin":351,"end":362},"obj":"Body_part"},{"id":"T60","span":{"begin":603,"end":605},"obj":"Body_part"},{"id":"T61","span":{"begin":681,"end":688},"obj":"Body_part"},{"id":"T62","span":{"begin":811,"end":822},"obj":"Body_part"},{"id":"T63","span":{"begin":915,"end":926},"obj":"Body_part"}],"attributes":[{"id":"A57","pred":"fma_id","subj":"T57","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A58","pred":"fma_id","subj":"T58","obj":"http://purl.org/sig/ont/fma/fma82737"},{"id":"A59","pred":"fma_id","subj":"T59","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A60","pred":"fma_id","subj":"T60","obj":"http://purl.org/sig/ont/fma/fma66599"},{"id":"A61","pred":"fma_id","subj":"T61","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A62","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma82816"},{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma82816"}],"text":"Structures of azithromycin (ATM) and SARS-CoV-2 spike protein trimer. (a) ATM, with both sugar-like pyranyl groups N-pyr and Ac-pyr indicated. The molecules are shown in chemical, tube and sphere rendering (carbon in green, nitrogen in blue, oxygen in red, hydrogen in white). (b) Molecular structure similarity between ATM and the saccharide part of ganglioside GM1. Both structures can adopt a globular shape the surface of which is covered with a patchwork of OH (arrows 1 and 2) and CH groups (arrow 3). The volume occupied by ATM and the saccharide part of GM1 can be estimated to be 2082 and 2293 Å3, respectively. (c) front and above views of the trimeric spike, each spike protein subunit with a distinct surface colour (cyan for chain A, yellow for chain B, purple for chain C). Atoms belonging to the ganglioside-binding domain of each subunit are visible underneath the slightly transparent surface. The ganglioside-binding domains, the NTD and the RBD are indicated."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T3","span":{"begin":180,"end":184},"obj":"Body_part"}],"attributes":[{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"}],"text":"Structures of azithromycin (ATM) and SARS-CoV-2 spike protein trimer. (a) ATM, with both sugar-like pyranyl groups N-pyr and Ac-pyr indicated. The molecules are shown in chemical, tube and sphere rendering (carbon in green, nitrogen in blue, oxygen in red, hydrogen in white). (b) Molecular structure similarity between ATM and the saccharide part of ganglioside GM1. Both structures can adopt a globular shape the surface of which is covered with a patchwork of OH (arrows 1 and 2) and CH groups (arrow 3). The volume occupied by ATM and the saccharide part of GM1 can be estimated to be 2082 and 2293 Å3, respectively. (c) front and above views of the trimeric spike, each spike protein subunit with a distinct surface colour (cyan for chain A, yellow for chain B, purple for chain C). Atoms belonging to the ganglioside-binding domain of each subunit are visible underneath the slightly transparent surface. The ganglioside-binding domains, the NTD and the RBD are indicated."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T37","span":{"begin":37,"end":45},"obj":"Disease"},{"id":"T38","span":{"begin":948,"end":951},"obj":"Disease"}],"attributes":[{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A38","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0008449"},{"id":"A39","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0018075"}],"text":"Structures of azithromycin (ATM) and SARS-CoV-2 spike protein trimer. (a) ATM, with both sugar-like pyranyl groups N-pyr and Ac-pyr indicated. The molecules are shown in chemical, tube and sphere rendering (carbon in green, nitrogen in blue, oxygen in red, hydrogen in white). (b) Molecular structure similarity between ATM and the saccharide part of ganglioside GM1. Both structures can adopt a globular shape the surface of which is covered with a patchwork of OH (arrows 1 and 2) and CH groups (arrow 3). The volume occupied by ATM and the saccharide part of GM1 can be estimated to be 2082 and 2293 Å3, respectively. (c) front and above views of the trimeric spike, each spike protein subunit with a distinct surface colour (cyan for chain A, yellow for chain B, purple for chain C). Atoms belonging to the ganglioside-binding domain of each subunit are visible underneath the slightly transparent surface. The ganglioside-binding domains, the NTD and the RBD are indicated."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T110","span":{"begin":71,"end":72},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T111","span":{"begin":180,"end":184},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T112","span":{"begin":278,"end":279},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T113","span":{"begin":394,"end":395},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T114","span":{"begin":448,"end":449},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T115","span":{"begin":603,"end":605},"obj":"http://purl.obolibrary.org/obo/CLO_0001577"},{"id":"T116","span":{"begin":702,"end":703},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T117","span":{"begin":744,"end":745},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T118","span":{"begin":764,"end":765},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"}],"text":"Structures of azithromycin (ATM) and SARS-CoV-2 spike protein trimer. (a) ATM, with both sugar-like pyranyl groups N-pyr and Ac-pyr indicated. The molecules are shown in chemical, tube and sphere rendering (carbon in green, nitrogen in blue, oxygen in red, hydrogen in white). (b) Molecular structure similarity between ATM and the saccharide part of ganglioside GM1. Both structures can adopt a globular shape the surface of which is covered with a patchwork of OH (arrows 1 and 2) and CH groups (arrow 3). The volume occupied by ATM and the saccharide part of GM1 can be estimated to be 2082 and 2293 Å3, respectively. (c) front and above views of the trimeric spike, each spike protein subunit with a distinct surface colour (cyan for chain A, yellow for chain B, purple for chain C). Atoms belonging to the ganglioside-binding domain of each subunit are visible underneath the slightly transparent surface. The ganglioside-binding domains, the NTD and the RBD are indicated."}

LitCovid-PD-CHEBI

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T14","span":{"begin":363,"end":366},"obj":"GlycoEpitope"},{"id":"T15","span":{"begin":562,"end":565},"obj":"GlycoEpitope"}],"attributes":[{"id":"A14","pred":"glyco_epitope_db_id","subj":"T14","obj":"http://www.glycoepitope.jp/epitopes/EP0050"},{"id":"A15","pred":"glyco_epitope_db_id","subj":"T15","obj":"http://www.glycoepitope.jp/epitopes/EP0050"}],"text":"Structures of azithromycin (ATM) and SARS-CoV-2 spike protein trimer. (a) ATM, with both sugar-like pyranyl groups N-pyr and Ac-pyr indicated. The molecules are shown in chemical, tube and sphere rendering (carbon in green, nitrogen in blue, oxygen in red, hydrogen in white). (b) Molecular structure similarity between ATM and the saccharide part of ganglioside GM1. Both structures can adopt a globular shape the surface of which is covered with a patchwork of OH (arrows 1 and 2) and CH groups (arrow 3). The volume occupied by ATM and the saccharide part of GM1 can be estimated to be 2082 and 2293 Å3, respectively. (c) front and above views of the trimeric spike, each spike protein subunit with a distinct surface colour (cyan for chain A, yellow for chain B, purple for chain C). Atoms belonging to the ganglioside-binding domain of each subunit are visible underneath the slightly transparent surface. The ganglioside-binding domains, the NTD and the RBD are indicated."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T83","span":{"begin":143,"end":367},"obj":"Sentence"},{"id":"T84","span":{"begin":368,"end":507},"obj":"Sentence"},{"id":"T85","span":{"begin":508,"end":787},"obj":"Sentence"},{"id":"T86","span":{"begin":788,"end":910},"obj":"Sentence"},{"id":"T87","span":{"begin":911,"end":978},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Structures of azithromycin (ATM) and SARS-CoV-2 spike protein trimer. (a) ATM, with both sugar-like pyranyl groups N-pyr and Ac-pyr indicated. The molecules are shown in chemical, tube and sphere rendering (carbon in green, nitrogen in blue, oxygen in red, hydrogen in white). (b) Molecular structure similarity between ATM and the saccharide part of ganglioside GM1. Both structures can adopt a globular shape the surface of which is covered with a patchwork of OH (arrows 1 and 2) and CH groups (arrow 3). The volume occupied by ATM and the saccharide part of GM1 can be estimated to be 2082 and 2293 Å3, respectively. (c) front and above views of the trimeric spike, each spike protein subunit with a distinct surface colour (cyan for chain A, yellow for chain B, purple for chain C). Atoms belonging to the ganglioside-binding domain of each subunit are visible underneath the slightly transparent surface. The ganglioside-binding domains, the NTD and the RBD are indicated."}

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"294","span":{"begin":467,"end":481},"obj":"Gene"},{"id":"295","span":{"begin":675,"end":680},"obj":"Gene"},{"id":"296","span":{"begin":663,"end":668},"obj":"Gene"},{"id":"297","span":{"begin":48,"end":53},"obj":"Gene"},{"id":"298","span":{"begin":37,"end":47},"obj":"Species"},{"id":"299","span":{"begin":14,"end":26},"obj":"Chemical"},{"id":"300","span":{"begin":115,"end":120},"obj":"Chemical"},{"id":"301","span":{"begin":125,"end":131},"obj":"Chemical"},{"id":"302","span":{"begin":207,"end":213},"obj":"Chemical"},{"id":"303","span":{"begin":224,"end":232},"obj":"Chemical"},{"id":"304","span":{"begin":242,"end":248},"obj":"Chemical"},{"id":"305","span":{"begin":257,"end":265},"obj":"Chemical"},{"id":"306","span":{"begin":332,"end":342},"obj":"Chemical"},{"id":"307","span":{"begin":351,"end":362},"obj":"Chemical"},{"id":"308","span":{"begin":363,"end":366},"obj":"Chemical"},{"id":"309","span":{"begin":562,"end":565},"obj":"Chemical"},{"id":"310","span":{"begin":811,"end":822},"obj":"Chemical"},{"id":"311","span":{"begin":915,"end":926},"obj":"Chemical"}],"attributes":[{"id":"A295","pred":"tao:has_database_id","subj":"295","obj":"Gene:43740568"},{"id":"A296","pred":"tao:has_database_id","subj":"296","obj":"Gene:43740568"},{"id":"A297","pred":"tao:has_database_id","subj":"297","obj":"Gene:43740568"},{"id":"A298","pred":"tao:has_database_id","subj":"298","obj":"Tax:2697049"},{"id":"A299","pred":"tao:has_database_id","subj":"299","obj":"MESH:D017963"},{"id":"A300","pred":"tao:has_database_id","subj":"300","obj":"MESH:D009242"},{"id":"A302","pred":"tao:has_database_id","subj":"302","obj":"MESH:D002244"},{"id":"A303","pred":"tao:has_database_id","subj":"303","obj":"MESH:D009584"},{"id":"A304","pred":"tao:has_database_id","subj":"304","obj":"MESH:D010100"},{"id":"A305","pred":"tao:has_database_id","subj":"305","obj":"MESH:D006859"},{"id":"A306","pred":"tao:has_database_id","subj":"306","obj":"MESH:D002241"},{"id":"A307","pred":"tao:has_database_id","subj":"307","obj":"MESH:D005732"},{"id":"A308","pred":"tao:has_database_id","subj":"308","obj":"MESH:D005677"},{"id":"A309","pred":"tao:has_database_id","subj":"309","obj":"MESH:D005677"},{"id":"A310","pred":"tao:has_database_id","subj":"310","obj":"MESH:D005732"},{"id":"A311","pred":"tao:has_database_id","subj":"311","obj":"MESH:D005732"}],"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":"Structures of azithromycin (ATM) and SARS-CoV-2 spike protein trimer. (a) ATM, with both sugar-like pyranyl groups N-pyr and Ac-pyr indicated. The molecules are shown in chemical, tube and sphere rendering (carbon in green, nitrogen in blue, oxygen in red, hydrogen in white). (b) Molecular structure similarity between ATM and the saccharide part of ganglioside GM1. Both structures can adopt a globular shape the surface of which is covered with a patchwork of OH (arrows 1 and 2) and CH groups (arrow 3). The volume occupied by ATM and the saccharide part of GM1 can be estimated to be 2082 and 2293 Å3, respectively. (c) front and above views of the trimeric spike, each spike protein subunit with a distinct surface colour (cyan for chain A, yellow for chain B, purple for chain C). Atoms belonging to the ganglioside-binding domain of each subunit are visible underneath the slightly transparent surface. The ganglioside-binding domains, the NTD and the RBD are indicated."}

PMC:7219429 / 11105-12083 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7219429 / 11105-12083 JSON TXT