PMC:7571312 / 130659-132285 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T48","span":{"begin":179,"end":188},"obj":"Body_part"},{"id":"T49","span":{"begin":479,"end":486},"obj":"Body_part"},{"id":"T50","span":{"begin":1263,"end":1270},"obj":"Body_part"},{"id":"T51","span":{"begin":1513,"end":1517},"obj":"Body_part"}],"attributes":[{"id":"A48","pred":"fma_id","subj":"T48","obj":"http://purl.org/sig/ont/fma/fma82748"},{"id":"A49","pred":"fma_id","subj":"T49","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A50","pred":"fma_id","subj":"T50","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A51","pred":"fma_id","subj":"T51","obj":"http://purl.org/sig/ont/fma/fma256135"}],"text":"LJEC2522 + PF-00835231\nCrystals of PF-00835231 bound to SARS2/CoV-2 DC2 protease via soaking: Freshly prepared SARS2/CoV-2 DC2 protease at 25.8 mg/mL was passed through a 0.45 mM cellulose acetate spin filter and set up for crystallization using an NT-8 crystallization robot (Formulatrix). Using MRC-2 crystallization plates, wells containing 40 mL of 0.2 M potassium sodium tartrate tetrahydrate and 20% w/v PEG 3350 were dispensed, and then sitting drops consisting of 0.3 μL protein were set up in a 1:1 ratio with a well buffer. Crystallization plates were incubated at 13 °C, and large crystals shaped as beveled plates measuring 0.35 × 0.2 × 0.025 mm3 grew after 48 h. PF-00835231 (in 100% DMSO solution) was introduced to the drop (in situ), at a final concentration of 1 mM, and then incubated at 13 °C for 24 h. Soaked crystals were flash-frozen in liquid nitrogen after being passed through a cryo consisting of a well buffer containing 20% glycerol. Structure determination.\nX-ray diffraction data were collected at the IMCA-CAT 17-ID beamline of Advanced Photon Source at Argonne National Labs and processed using autoPROC. Structure of the SARS CoV main protease in complex with PF-835231 was determined by molecular replacement using the published protein structure (PDBID 1Q2W) as the starting model in program Phaser and refined iteratively using autoBUSTER followed by model building in Coot.\nStructure of the SARS CoV-2 main protease in complex with PF-835231 was determined similarly by rigid body refinement using the SARS CoV main protease structure in complex with the same ligand as the starting model."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T110","span":{"begin":1154,"end":1158},"obj":"Disease"},{"id":"T111","span":{"begin":1428,"end":1432},"obj":"Disease"},{"id":"T112","span":{"begin":1539,"end":1543},"obj":"Disease"}],"attributes":[{"id":"A110","pred":"mondo_id","subj":"T110","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A111","pred":"mondo_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A112","pred":"mondo_id","subj":"T112","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"LJEC2522 + PF-00835231\nCrystals of PF-00835231 bound to SARS2/CoV-2 DC2 protease via soaking: Freshly prepared SARS2/CoV-2 DC2 protease at 25.8 mg/mL was passed through a 0.45 mM cellulose acetate spin filter and set up for crystallization using an NT-8 crystallization robot (Formulatrix). Using MRC-2 crystallization plates, wells containing 40 mL of 0.2 M potassium sodium tartrate tetrahydrate and 20% w/v PEG 3350 were dispensed, and then sitting drops consisting of 0.3 μL protein were set up in a 1:1 ratio with a well buffer. Crystallization plates were incubated at 13 °C, and large crystals shaped as beveled plates measuring 0.35 × 0.2 × 0.025 mm3 grew after 48 h. PF-00835231 (in 100% DMSO solution) was introduced to the drop (in situ), at a final concentration of 1 mM, and then incubated at 13 °C for 24 h. Soaked crystals were flash-frozen in liquid nitrogen after being passed through a cryo consisting of a well buffer containing 20% glycerol. Structure determination.\nX-ray diffraction data were collected at the IMCA-CAT 17-ID beamline of Advanced Photon Source at Argonne National Labs and processed using autoPROC. Structure of the SARS CoV main protease in complex with PF-835231 was determined by molecular replacement using the published protein structure (PDBID 1Q2W) as the starting model in program Phaser and refined iteratively using autoBUSTER followed by model building in Coot.\nStructure of the SARS CoV-2 main protease in complex with PF-835231 was determined similarly by rigid body refinement using the SARS CoV main protease structure in complex with the same ligand as the starting model."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T211","span":{"begin":68,"end":71},"obj":"http://purl.obolibrary.org/obo/CL_0000784"},{"id":"T212","span":{"begin":123,"end":126},"obj":"http://purl.obolibrary.org/obo/CL_0000784"},{"id":"T213","span":{"begin":169,"end":170},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T214","span":{"begin":406,"end":409},"obj":"http://purl.obolibrary.org/obo/CLO_0050644"},{"id":"T215","span":{"begin":502,"end":503},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T216","span":{"begin":504,"end":507},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T217","span":{"begin":519,"end":520},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T218","span":{"begin":670,"end":672},"obj":"http://purl.obolibrary.org/obo/CLO_0001382"},{"id":"T219","span":{"begin":753,"end":754},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T220","span":{"begin":902,"end":903},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T221","span":{"begin":923,"end":924},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"LJEC2522 + PF-00835231\nCrystals of PF-00835231 bound to SARS2/CoV-2 DC2 protease via soaking: Freshly prepared SARS2/CoV-2 DC2 protease at 25.8 mg/mL was passed through a 0.45 mM cellulose acetate spin filter and set up for crystallization using an NT-8 crystallization robot (Formulatrix). Using MRC-2 crystallization plates, wells containing 40 mL of 0.2 M potassium sodium tartrate tetrahydrate and 20% w/v PEG 3350 were dispensed, and then sitting drops consisting of 0.3 μL protein were set up in a 1:1 ratio with a well buffer. Crystallization plates were incubated at 13 °C, and large crystals shaped as beveled plates measuring 0.35 × 0.2 × 0.025 mm3 grew after 48 h. PF-00835231 (in 100% DMSO solution) was introduced to the drop (in situ), at a final concentration of 1 mM, and then incubated at 13 °C for 24 h. Soaked crystals were flash-frozen in liquid nitrogen after being passed through a cryo consisting of a well buffer containing 20% glycerol. Structure determination.\nX-ray diffraction data were collected at the IMCA-CAT 17-ID beamline of Advanced Photon Source at Argonne National Labs and processed using autoPROC. Structure of the SARS CoV main protease in complex with PF-835231 was determined by molecular replacement using the published protein structure (PDBID 1Q2W) as the starting model in program Phaser and refined iteratively using autoBUSTER followed by model building in Coot.\nStructure of the SARS CoV-2 main protease in complex with PF-835231 was determined similarly by rigid body refinement using the SARS CoV main protease structure in complex with the same ligand as the starting model."}

LitCovid-PD-CHEBI

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T719","span":{"begin":0,"end":22},"obj":"Sentence"},{"id":"T720","span":{"begin":23,"end":93},"obj":"Sentence"},{"id":"T721","span":{"begin":94,"end":290},"obj":"Sentence"},{"id":"T722","span":{"begin":291,"end":533},"obj":"Sentence"},{"id":"T723","span":{"begin":534,"end":675},"obj":"Sentence"},{"id":"T724","span":{"begin":676,"end":821},"obj":"Sentence"},{"id":"T725","span":{"begin":822,"end":961},"obj":"Sentence"},{"id":"T726","span":{"begin":962,"end":986},"obj":"Sentence"},{"id":"T727","span":{"begin":987,"end":1136},"obj":"Sentence"},{"id":"T728","span":{"begin":1137,"end":1410},"obj":"Sentence"},{"id":"T729","span":{"begin":1411,"end":1626},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"LJEC2522 + PF-00835231\nCrystals of PF-00835231 bound to SARS2/CoV-2 DC2 protease via soaking: Freshly prepared SARS2/CoV-2 DC2 protease at 25.8 mg/mL was passed through a 0.45 mM cellulose acetate spin filter and set up for crystallization using an NT-8 crystallization robot (Formulatrix). Using MRC-2 crystallization plates, wells containing 40 mL of 0.2 M potassium sodium tartrate tetrahydrate and 20% w/v PEG 3350 were dispensed, and then sitting drops consisting of 0.3 μL protein were set up in a 1:1 ratio with a well buffer. Crystallization plates were incubated at 13 °C, and large crystals shaped as beveled plates measuring 0.35 × 0.2 × 0.025 mm3 grew after 48 h. PF-00835231 (in 100% DMSO solution) was introduced to the drop (in situ), at a final concentration of 1 mM, and then incubated at 13 °C for 24 h. Soaked crystals were flash-frozen in liquid nitrogen after being passed through a cryo consisting of a well buffer containing 20% glycerol. Structure determination.\nX-ray diffraction data were collected at the IMCA-CAT 17-ID beamline of Advanced Photon Source at Argonne National Labs and processed using autoPROC. Structure of the SARS CoV main protease in complex with PF-835231 was determined by molecular replacement using the published protein structure (PDBID 1Q2W) as the starting model in program Phaser and refined iteratively using autoBUSTER followed by model building in Coot.\nStructure of the SARS CoV-2 main protease in complex with PF-835231 was determined similarly by rigid body refinement using the SARS CoV main protease structure in complex with the same ligand as the starting model."}

LitCovid-PubTator