PMC:7571312 / 130659-132285 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T48 179-188 Body_part denotes cellulose http://purl.org/sig/ont/fma/fma82748
T49 479-486 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T50 1263-1270 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T51 1513-1517 Body_part denotes body http://purl.org/sig/ont/fma/fma256135

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T110 1154-1158 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T111 1428-1432 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T112 1539-1543 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T211 68-71 http://purl.obolibrary.org/obo/CL_0000784 denotes DC2
T212 123-126 http://purl.obolibrary.org/obo/CL_0000784 denotes DC2
T213 169-170 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T214 406-409 http://purl.obolibrary.org/obo/CLO_0050644 denotes w/v
T215 502-503 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T216 504-507 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T217 519-520 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T218 670-672 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T219 753-754 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T220 902-903 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T221 923-924 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T94315 11-13 Chemical denotes PF http://purl.obolibrary.org/obo/CHEBI_74795|http://purl.obolibrary.org/obo/CHEBI_90284
T35035 35-37 Chemical denotes PF http://purl.obolibrary.org/obo/CHEBI_74795|http://purl.obolibrary.org/obo/CHEBI_90284
T35251 179-196 Chemical denotes cellulose acetate http://purl.obolibrary.org/obo/CHEBI_145232
T19137 189-196 Chemical denotes acetate http://purl.obolibrary.org/obo/CHEBI_30089|http://purl.obolibrary.org/obo/CHEBI_47622
T67659 359-368 Chemical denotes potassium http://purl.obolibrary.org/obo/CHEBI_26216
T82330 369-375 Chemical denotes sodium http://purl.obolibrary.org/obo/CHEBI_26708
T33318 376-384 Chemical denotes tartrate http://purl.obolibrary.org/obo/CHEBI_132950|http://purl.obolibrary.org/obo/CHEBI_30929|http://purl.obolibrary.org/obo/CHEBI_50562
T22599 410-413 Chemical denotes PEG http://purl.obolibrary.org/obo/CHEBI_46793
T31946 479-486 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T26094 526-532 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T77705 676-678 Chemical denotes PF http://purl.obolibrary.org/obo/CHEBI_74795|http://purl.obolibrary.org/obo/CHEBI_90284
T76569 697-701 Chemical denotes DMSO http://purl.obolibrary.org/obo/CHEBI_28262
T55351 702-710 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T99825 866-874 Chemical denotes nitrogen http://purl.obolibrary.org/obo/CHEBI_25555
T70082 930-936 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T1062 952-960 Chemical denotes glycerol http://purl.obolibrary.org/obo/CHEBI_17754
T984 1044-1046 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_17754|http://purl.obolibrary.org/obo/CHEBI_141439
T19989 1193-1195 Chemical denotes PF http://purl.obolibrary.org/obo/CHEBI_74795|http://purl.obolibrary.org/obo/CHEBI_90284
T25872 1263-1270 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T1067 1469-1471 Chemical denotes PF http://purl.obolibrary.org/obo/CHEBI_74795|http://purl.obolibrary.org/obo/CHEBI_90284
T57084 1597-1603 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T719 0-22 Sentence denotes LJEC2522 + PF-00835231
T720 23-93 Sentence denotes Crystals of PF-00835231 bound to SARS2/CoV-2 DC2 protease via soaking:
T721 94-290 Sentence denotes 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).
T722 291-533 Sentence denotes 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.
T723 534-675 Sentence denotes 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.
T724 676-821 Sentence denotes 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.
T725 822-961 Sentence denotes Soaked crystals were flash-frozen in liquid nitrogen after being passed through a cryo consisting of a well buffer containing 20% glycerol.
T726 962-986 Sentence denotes Structure determination.
T727 987-1136 Sentence denotes X-ray diffraction data were collected at the IMCA-CAT 17-ID beamline of Advanced Photon Source at Argonne National Labs and processed using autoPROC.
T728 1137-1410 Sentence denotes 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.
T729 1411-1626 Sentence denotes Structure 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

Id Subject Object Predicate Lexical cue tao:has_database_id
2323 123-126 Gene denotes DC2 Gene:58505
2324 68-71 Gene denotes DC2 Gene:58505
2325 56-61 Species denotes SARS2 Tax:2697049
2326 62-67 Species denotes CoV-2 Tax:2697049
2327 111-116 Species denotes SARS2 Tax:2697049
2328 117-122 Species denotes CoV-2 Tax:2697049
2329 179-196 Chemical denotes cellulose acetate MESH:C005062
2330 359-397 Chemical denotes potassium sodium tartrate tetrahydrate MESH:C029768
2331 410-413 Chemical denotes PEG
2332 697-701 Chemical denotes DMSO MESH:D004121
2333 866-874 Chemical denotes nitrogen MESH:D009584
2334 952-960 Chemical denotes glycerol MESH:D005990
2335 297-302 CellLine denotes MRC-2 CVCL:0440
2337 1154-1162 Species denotes SARS CoV Tax:694009
2341 1428-1438 Species denotes SARS CoV-2 Tax:2697049
2342 1539-1547 Species denotes SARS CoV Tax:694009
2343 1469-1478 Chemical denotes PF-835231