PMC:7219429 / 5605-6415 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T35","span":{"begin":36,"end":43},"obj":"Body_part"}],"attributes":[{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"2.1 Pdb files\nThe SARS-CoV-2 spike protein trimer in the prefusion conformation was obtained from pdb file # 6VSB [20]. Hydroxychloroquine (CLQ-OH) is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. CLQ-OH was generated by hydroxylation of chloroquine (CLQ) and validated as previously described [10]. CLQ was retrieved from pdb file # 4V2O (CLQ co-crystallized with saposin B) [21].\nAzithromycin (ATM) is (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-11-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-2-ethyl-3,4,10-trihydroxy-13-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-1-oxa-6-azacyclopentadecan-15-one. The 3D structure of ATM was obtained from pdb file # 5UXD (ATM co-crystallized with macrolide 2′-phosphotransferase) [22]."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T29","span":{"begin":19,"end":27},"obj":"Disease"},{"id":"T30","span":{"begin":153,"end":155},"obj":"Disease"}],"attributes":[{"id":"A29","pred":"mondo_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A30","pred":"mondo_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/MONDO_0010725"}],"text":"2.1 Pdb files\nThe SARS-CoV-2 spike protein trimer in the prefusion conformation was obtained from pdb file # 6VSB [20]. Hydroxychloroquine (CLQ-OH) is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. CLQ-OH was generated by hydroxylation of chloroquine (CLQ) and validated as previously described [10]. CLQ was retrieved from pdb file # 4V2O (CLQ co-crystallized with saposin B) [21].\nAzithromycin (ATM) is (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-11-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-2-ethyl-3,4,10-trihydroxy-13-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-1-oxa-6-azacyclopentadecan-15-one. The 3D structure of ATM was obtained from pdb file # 5UXD (ATM co-crystallized with macrolide 2′-phosphotransferase) [22]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T62","span":{"begin":153,"end":155},"obj":"http://purl.obolibrary.org/obo/CLO_0008882"},{"id":"T63","span":{"begin":398,"end":399},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T64","span":{"begin":466,"end":468},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T65","span":{"begin":806,"end":808},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"}],"text":"2.1 Pdb files\nThe SARS-CoV-2 spike protein trimer in the prefusion conformation was obtained from pdb file # 6VSB [20]. Hydroxychloroquine (CLQ-OH) is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. CLQ-OH was generated by hydroxylation of chloroquine (CLQ) and validated as previously described [10]. CLQ was retrieved from pdb file # 4V2O (CLQ co-crystallized with saposin B) [21].\nAzithromycin (ATM) is (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-11-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-2-ethyl-3,4,10-trihydroxy-13-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-1-oxa-6-azacyclopentadecan-15-one. The 3D structure of ATM was obtained from pdb file # 5UXD (ATM co-crystallized with macrolide 2′-phosphotransferase) [22]."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T76","span":{"begin":36,"end":43},"obj":"Chemical"},{"id":"T77","span":{"begin":153,"end":155},"obj":"Chemical"},{"id":"T78","span":{"begin":187,"end":192},"obj":"Chemical"},{"id":"T79","span":{"begin":193,"end":199},"obj":"Chemical"},{"id":"T80","span":{"begin":201,"end":206},"obj":"Chemical"},{"id":"T82","span":{"begin":207,"end":212},"obj":"Chemical"},{"id":"T83","span":{"begin":213,"end":220},"obj":"Chemical"},{"id":"T84","span":{"begin":263,"end":274},"obj":"Chemical"},{"id":"T85","span":{"begin":421,"end":424},"obj":"Chemical"},{"id":"T86","span":{"begin":504,"end":511},"obj":"Chemical"},{"id":"T87","span":{"begin":530,"end":533},"obj":"Chemical"},{"id":"T88","span":{"begin":536,"end":541},"obj":"Chemical"},{"id":"T90","span":{"begin":580,"end":587},"obj":"Chemical"},{"id":"T91","span":{"begin":590,"end":597},"obj":"Chemical"},{"id":"T93","span":{"begin":620,"end":623},"obj":"Chemical"},{"id":"T94","span":{"begin":708,"end":711},"obj":"Chemical"},{"id":"T95","span":{"begin":747,"end":750},"obj":"Chemical"},{"id":"T96","span":{"begin":772,"end":781},"obj":"Chemical"}],"attributes":[{"id":"A76","pred":"chebi_id","subj":"T76","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A77","pred":"chebi_id","subj":"T77","obj":"http://purl.obolibrary.org/obo/CHEBI_73819"},{"id":"A78","pred":"chebi_id","subj":"T78","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A79","pred":"chebi_id","subj":"T79","obj":"http://purl.obolibrary.org/obo/CHEBI_25902"},{"id":"A80","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_37807"},{"id":"A81","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_62801"},{"id":"A82","pred":"chebi_id","subj":"T82","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A83","pred":"chebi_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/CHEBI_16236"},{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_3638"},{"id":"A85","pred":"chebi_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A86","pred":"chebi_id","subj":"T86","obj":"http://purl.obolibrary.org/obo/CHEBI_43176"},{"id":"A87","pred":"chebi_id","subj":"T87","obj":"http://purl.obolibrary.org/obo/CHEBI_29354"},{"id":"A88","pred":"chebi_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/CHEBI_37807"},{"id":"A89","pred":"chebi_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/CHEBI_62801"},{"id":"A90","pred":"chebi_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/CHEBI_43176"},{"id":"A91","pred":"chebi_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/CHEBI_32772"},{"id":"A92","pred":"chebi_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/CHEBI_44520"},{"id":"A93","pred":"chebi_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/CHEBI_29354"},{"id":"A94","pred":"chebi_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A95","pred":"chebi_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A96","pred":"chebi_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/CHEBI_25106"}],"text":"2.1 Pdb files\nThe SARS-CoV-2 spike protein trimer in the prefusion conformation was obtained from pdb file # 6VSB [20]. Hydroxychloroquine (CLQ-OH) is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. CLQ-OH was generated by hydroxylation of chloroquine (CLQ) and validated as previously described [10]. CLQ was retrieved from pdb file # 4V2O (CLQ co-crystallized with saposin B) [21].\nAzithromycin (ATM) is (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-11-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-2-ethyl-3,4,10-trihydroxy-13-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-1-oxa-6-azacyclopentadecan-15-one. The 3D structure of ATM was obtained from pdb file # 5UXD (ATM co-crystallized with macrolide 2′-phosphotransferase) [22]."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T2","span":{"begin":390,"end":397},"obj":"http://purl.obolibrary.org/obo/GO_0030290"}],"text":"2.1 Pdb files\nThe SARS-CoV-2 spike protein trimer in the prefusion conformation was obtained from pdb file # 6VSB [20]. Hydroxychloroquine (CLQ-OH) is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. CLQ-OH was generated by hydroxylation of chloroquine (CLQ) and validated as previously described [10]. CLQ was retrieved from pdb file # 4V2O (CLQ co-crystallized with saposin B) [21].\nAzithromycin (ATM) is (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-11-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-2-ethyl-3,4,10-trihydroxy-13-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-1-oxa-6-azacyclopentadecan-15-one. The 3D structure of ATM was obtained from pdb file # 5UXD (ATM co-crystallized with macrolide 2′-phosphotransferase) [22]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T44","span":{"begin":0,"end":14},"obj":"Sentence"},{"id":"T45","span":{"begin":15,"end":120},"obj":"Sentence"},{"id":"T46","span":{"begin":121,"end":221},"obj":"Sentence"},{"id":"T47","span":{"begin":222,"end":324},"obj":"Sentence"},{"id":"T48","span":{"begin":325,"end":406},"obj":"Sentence"},{"id":"T49","span":{"begin":407,"end":687},"obj":"Sentence"},{"id":"T50","span":{"begin":688,"end":810},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.1 Pdb files\nThe SARS-CoV-2 spike protein trimer in the prefusion conformation was obtained from pdb file # 6VSB [20]. Hydroxychloroquine (CLQ-OH) is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. CLQ-OH was generated by hydroxylation of chloroquine (CLQ) and validated as previously described [10]. CLQ was retrieved from pdb file # 4V2O (CLQ co-crystallized with saposin B) [21].\nAzithromycin (ATM) is (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-11-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-2-ethyl-3,4,10-trihydroxy-13-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-1-oxa-6-azacyclopentadecan-15-one. The 3D structure of ATM was obtained from pdb file # 5UXD (ATM co-crystallized with macrolide 2′-phosphotransferase) [22]."}

{"project":"LitCovid-PubTator","denotations":[{"id":"189","span":{"begin":5,"end":8},"obj":"Gene"},{"id":"200","span":{"begin":30,"end":35},"obj":"Gene"},{"id":"201","span":{"begin":348,"end":351},"obj":"Gene"},{"id":"202","span":{"begin":99,"end":102},"obj":"Gene"},{"id":"203","span":{"begin":19,"end":29},"obj":"Species"},{"id":"204","span":{"begin":121,"end":139},"obj":"Chemical"},{"id":"205","span":{"begin":141,"end":147},"obj":"Chemical"},{"id":"206","span":{"begin":152,"end":220},"obj":"Chemical"},{"id":"207","span":{"begin":222,"end":228},"obj":"Chemical"},{"id":"208","span":{"begin":263,"end":274},"obj":"Chemical"},{"id":"209","span":{"begin":276,"end":279},"obj":"Chemical"},{"id":"212","span":{"begin":730,"end":733},"obj":"Gene"},{"id":"213","span":{"begin":772,"end":781},"obj":"Chemical"}],"attributes":[{"id":"A189","pred":"tao:has_database_id","subj":"189","obj":"Gene:5131"},{"id":"A200","pred":"tao:has_database_id","subj":"200","obj":"Gene:43740568"},{"id":"A201","pred":"tao:has_database_id","subj":"201","obj":"Gene:5131"},{"id":"A202","pred":"tao:has_database_id","subj":"202","obj":"Gene:5131"},{"id":"A203","pred":"tao:has_database_id","subj":"203","obj":"Tax:2697049"},{"id":"A204","pred":"tao:has_database_id","subj":"204","obj":"MESH:D006886"},{"id":"A208","pred":"tao:has_database_id","subj":"208","obj":"MESH:D002738"},{"id":"A209","pred":"tao:has_database_id","subj":"209","obj":"MESH:D002738"},{"id":"A212","pred":"tao:has_database_id","subj":"212","obj":"Gene:5131"},{"id":"A213","pred":"tao:has_database_id","subj":"213","obj":"MESH:D018942"}],"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":"2.1 Pdb files\nThe SARS-CoV-2 spike protein trimer in the prefusion conformation was obtained from pdb file # 6VSB [20]. Hydroxychloroquine (CLQ-OH) is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. CLQ-OH was generated by hydroxylation of chloroquine (CLQ) and validated as previously described [10]. CLQ was retrieved from pdb file # 4V2O (CLQ co-crystallized with saposin B) [21].\nAzithromycin (ATM) is (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-11-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-2-ethyl-3,4,10-trihydroxy-13-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-1-oxa-6-azacyclopentadecan-15-one. The 3D structure of ATM was obtained from pdb file # 5UXD (ATM co-crystallized with macrolide 2′-phosphotransferase) [22]."}

{"project":"2_test","denotations":[{"id":"32405156-32075877-48151011","span":{"begin":116,"end":118},"obj":"32075877"},{"id":"32405156-26616259-48151012","span":{"begin":402,"end":404},"obj":"26616259"},{"id":"T51455","span":{"begin":116,"end":118},"obj":"32075877"},{"id":"T56339","span":{"begin":402,"end":404},"obj":"26616259"}],"text":"2.1 Pdb files\nThe SARS-CoV-2 spike protein trimer in the prefusion conformation was obtained from pdb file # 6VSB [20]. Hydroxychloroquine (CLQ-OH) is (RS)-2-[{4-[(7-chloroquinolin-4-yl)amino]pentyl}(ethyl)amino]ethanol. CLQ-OH was generated by hydroxylation of chloroquine (CLQ) and validated as previously described [10]. CLQ was retrieved from pdb file # 4V2O (CLQ co-crystallized with saposin B) [21].\nAzithromycin (ATM) is (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-11-[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy-2-ethyl-3,4,10-trihydroxy-13-[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy-3,5,6,8,10,12,14-heptamethyl-1-oxa-6-azacyclopentadecan-15-one. The 3D structure of ATM was obtained from pdb file # 5UXD (ATM co-crystallized with macrolide 2′-phosphotransferase) [22]."}