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PMC:7605337 / 36031-37624 JSONTXT

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LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T235 38-42 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T236 50-59 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T237 123-132 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T238 209-213 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T239 274-283 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T240 371-375 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T241 454-458 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T242 466-475 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T243 511-515 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T244 596-600 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T245 687-696 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T246 801-805 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T247 988-997 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T248 1111-1115 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T249 1150-1159 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T250 1258-1267 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T251 1400-1404 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T252 1421-1430 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T253 1489-1493 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T254 1521-1530 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T237 60-63 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T238 133-136 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T239 137-138 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T240 645-646 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T241 898-900 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T242 906-907 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T243 1034-1035 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T110 89-97 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T111 647-651 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T113 840-844 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T115 1036-1040 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T117 1184-1188 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T239 0-114 Sentence denotes The evolution of the coronavirus from SARS-COV to nCOV-2019 has reshaped the interfacial hydrogen bonds with ACE2.
T240 115-183 Sentence denotes G502 in nCOV-2019 has a persistent H-bond with residue K353 on ACE2.
T241 184-265 Sentence denotes This residue was G488 in SARS-COV, which also makes the H-bond with K353 on ACE2.
T242 266-342 Sentence denotes Q493 in nCOV-2019 makes H-bond with E35 and another H-bond with K31 on ACE2.
T243 343-426 Sentence denotes This residue was an N479 in SARS-COV, which only makes one H-bond with K31 on ACE2.
T244 427-520 Sentence denotes An important mutation from SARS-COV to nCOV-2019 is residue Q498, which was Y484 in SARS-COV.
T245 521-631 Sentence denotes Q498 makes two H-bonds with residues D38 and K353 on ACE2, whereas Y484 in SARS-COV does not make any H-bonds.
T246 632-776 Sentence denotes Importantly, a salt bridge between K417 and D30 in the nCOV-2019/ACE2 complex contributes to the total binding energy by −12.34 ± 0.23 kcal/mol.
T247 777-887 Sentence denotes This residue is V404 in SARS-COV which is not able to make any salt-bridge and does not make H-bond with ACE2.
T248 888-1033 Sentence denotes Gao et al.27 used a FEP approach and showed that mutation V404 to K417 lowers the binding energy of nCOV-2019 RBD to ACE2 by −2.2 ± 0.9 kcal/mol.
T249 1034-1125 Sentence denotes A salt bridge between R426 on RBD and E329 on ACE2 stabilizes the complex in SARS-COV/ACE2.
T250 1126-1219 Sentence denotes This residue is N439 in nCOV-2019 which is unable to make salt-bridge with ACE2 residue E329.
T251 1220-1391 Sentence denotes One of the most observed mutations in nCOV-2019 according to the GISAID database is N439K which recovers some of the electrostatic interactions with ACE2 at this position.
T252 1392-1466 Sentence denotes Y436 in SARS-COV and Y449 in nCOV-2019 both make H-bonds with D38 on ACE2.
T253 1467-1593 Sentence denotes The unchanged T486 in SARS-COV corresponds to T500 in nCOV-2019, both of which make consistent H-bonds with ACE2 residue D355.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
850 109-113 Gene denotes ACE2 Gene:59272
851 178-182 Gene denotes ACE2 Gene:59272
852 260-264 Gene denotes ACE2 Gene:59272
853 337-341 Gene denotes ACE2 Gene:59272
854 421-425 Gene denotes ACE2 Gene:59272
855 574-578 Gene denotes ACE2 Gene:59272
856 697-701 Gene denotes ACE2 Gene:59272
857 882-886 Gene denotes ACE2 Gene:59272
858 1005-1009 Gene denotes ACE2 Gene:59272
859 1080-1084 Gene denotes ACE2 Gene:59272
860 1120-1124 Gene denotes ACE2 Gene:59272
861 1201-1205 Gene denotes ACE2 Gene:59272
862 1369-1373 Gene denotes ACE2 Gene:59272
863 1461-1465 Gene denotes ACE2 Gene:59272
864 1575-1579 Gene denotes ACE2 Gene:59272
865 414-417 Gene denotes K31 Gene:3881
866 330-333 Gene denotes K31 Gene:3881
867 21-32 Species denotes coronavirus Tax:11118
868 38-46 Species denotes SARS-COV Tax:694009
869 50-54 Species denotes nCOV Tax:2697049
870 123-127 Species denotes nCOV Tax:2697049
871 209-217 Species denotes SARS-COV Tax:694009
872 274-278 Species denotes nCOV Tax:2697049
873 371-379 Species denotes SARS-COV Tax:694009
874 454-462 Species denotes SARS-COV Tax:694009
875 466-470 Species denotes nCOV Tax:2697049
876 511-519 Species denotes SARS-COV Tax:694009
877 596-604 Species denotes SARS-COV Tax:694009
878 687-691 Species denotes nCOV Tax:2697049
879 801-809 Species denotes SARS-COV Tax:694009
880 988-992 Species denotes nCOV Tax:2697049
881 1111-1119 Species denotes SARS-COV Tax:694009
882 1150-1154 Species denotes nCOV Tax:2697049
883 1258-1262 Species denotes nCOV Tax:2697049
884 1400-1408 Species denotes SARS-COV Tax:694009
885 1421-1425 Species denotes nCOV Tax:2697049
886 1489-1497 Species denotes SARS-COV Tax:694009
887 1521-1525 Species denotes nCOV Tax:2697049
888 89-97 Chemical denotes hydrogen MESH:D006859
889 115-119 Chemical denotes G502
890 170-174 Chemical denotes K353
891 201-205 Chemical denotes G488
892 252-256 Chemical denotes K353
893 363-367 Chemical denotes N479
894 487-491 Chemical denotes Q498
895 503-507 Chemical denotes Y484
896 521-525 Chemical denotes Q498
897 588-592 Chemical denotes Y484
898 667-671 Chemical denotes K417
899 793-797 Chemical denotes V404
900 954-958 Chemical denotes K417
901 1056-1060 Chemical denotes R426
902 1072-1076 Chemical denotes E329
903 1142-1146 Chemical denotes N439
904 1214-1218 Chemical denotes E329
905 1392-1396 Chemical denotes Y436
906 1413-1417 Chemical denotes Y449
907 1588-1592 Chemical denotes D355