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PMC:7441777 / 30994-31987 JSONTXT

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LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T195 568-571 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T196 583-585 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T197 583-585 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T198 950-951 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T422 204-214 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T423 221-225 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T424 232-235 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T425 511-520 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T427 527-540 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T428 547-557 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T429 583-585 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T430 845-856 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T431 868-878 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T12 776-785 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
744 199-203 Gene denotes RdRp Gene:43740578
745 216-220 Gene denotes RdRp Gene:43740578
746 227-231 Gene denotes RdRp Gene:43740578
747 241-245 Gene denotes RdRp Gene:43740578
748 246-250 Gene denotes TF2b Gene:2959
749 506-510 Gene denotes RdRp Gene:43740578
750 522-526 Gene denotes RdRp Gene:43740578
751 542-546 Gene denotes RdRp Gene:43740578
752 563-567 Gene denotes RdRp Gene:43740578
753 645-649 Gene denotes RdRp Gene:43740578
754 883-887 Gene denotes RdRp Gene:43740578
755 204-214 Chemical denotes remdesivir MESH:C000606551
756 845-856 Chemical denotes polyphenols MESH:D059808
757 868-878 Chemical denotes remdesivir MESH:C000606551

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T14 568-571 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T297 0-169 Sentence denotes It is evident from Table 4 that for all complexes, ΔEvdW varies between −22.55 kcal/mol and −37.82 kcal/mol while ΔEelec ranges from −47.18 kcal/mol to −123.63 kcal/mol.
T298 170-616 Sentence denotes Furthermore, in the cases of RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, and RdRp/TF2b, ΔEele is over-compensated by the desolvation energy (ΔGpol), indicating that the sum of these two components, ΔGpol + elec, is unfavorable to the binding and varies between 0.84 kcal/mol and 11.57 kcal/mol (see Table 4) and similar results are found for RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 (see Table S2 in Supplementary Information).
T299 617-735 Sentence denotes In contrast, in the case of RdRp/TF2a, ΔGpol + elec, is favorable to the complexation (ΔGpol + elec = −0.34 kcal/mol).
T300 736-888 Sentence denotes Overall, this suggests that the complex formation is mainly driven by the van der Waals interactions between polyphenols as well as remdesivir and RdRp.
T301 889-993 Sentence denotes Therefore, hydrophobic residues in the binding pocket played a crucial role in the complexation process.