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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1139-1149 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 39-47 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 135-143 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T3 172-180 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 312-313 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T2 339-344 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T3 345-348 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T4 433-439 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T5 445-451 http://purl.obolibrary.org/obo/UBERON_0002553 denotes cavity
T6 597-602 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T7 834-835 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1139-1158 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T9 1139-1158 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T10 1215-1221 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T11 1227-1233 http://purl.obolibrary.org/obo/UBERON_0002553 denotes cavity

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 76-83 Chemical denotes neutron http://purl.obolibrary.org/obo/CHEBI_30222
T2 556-560 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T3 642-649 Chemical denotes neutron http://purl.obolibrary.org/obo/CHEBI_30222
T4 711-724 Chemical denotes hydrogen atom http://purl.obolibrary.org/obo/CHEBI_29305|http://purl.obolibrary.org/obo/CHEBI_49637
T6 720-724 Chemical denotes atom http://purl.obolibrary.org/obo/CHEBI_33250
T7 905-913 Chemical denotes thiolate http://purl.obolibrary.org/obo/CHEBI_50539
T8 1039-1046 Chemical denotes neutron http://purl.obolibrary.org/obo/CHEBI_30222
T9 1139-1149 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T10 1139-1144 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T11 1145-1149 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T12 1182-1190 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T13 1374-1381 Chemical denotes neutron http://purl.obolibrary.org/obo/CHEBI_30222
T14 1401-1406 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T15 1420-1428 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T16 1611-1615 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T17 1654-1664 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 209-226 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T2 209-226 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 39-49 Species denotes SARS-CoV-2 Tax:2697049
17 124-128 Gene denotes Mpro Gene:8673700
18 135-145 Species denotes SARS-CoV-2 Tax:2697049
19 172-180 Disease denotes COVID-19 MESH:C000657245
20 228-231 Chemical denotes 3CL
21 232-236 Gene denotes Mpro Gene:8673700
22 285-291 Chemical denotes Cys145
23 296-301 Chemical denotes His41
24 663-666 Chemical denotes 3CL
25 667-671 Gene denotes Mpro Gene:8673700
26 711-719 Chemical denotes hydrogen MESH:D006859
27 869-875 Chemical denotes Cys145
28 905-913 Chemical denotes thiolate
29 925-930 Chemical denotes His41
30 1182-1190 Chemical denotes hydrogen MESH:D006859
31 1420-1428 Chemical denotes hydrogen MESH:D006859

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-100 Sentence denotes Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography.
T2 101-227 Sentence denotes The main protease (3CL Mpro) from SARS-CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication.
T3 228-311 Sentence denotes 3CL Mpro possesses an unusual catalytic dyad composed of Cys145 and His41 residues.
T4 312-603 Sentence denotes A critical question in the field has been what the protonation states of the ionizable residues in the substrate-binding active site cavity are; resolving this point would help understand the catalytic details of the enzyme and inform rational drug development against this pernicious virus.
T5 604-782 Sentence denotes Here, we present the room-temperature neutron structure of 3CL Mpro, which allowed direct determination of hydrogen atom positions and, hence, protonation states in the protease.
T6 783-1034 Sentence denotes We observe that the catalytic site natively adopts a zwitterionic reactive form where Cys145 is in the negatively charged thiolate state, and His41 is doubly protonated and positively charged, instead of the neutral unreactive state usually envisaged.
T7 1035-1261 Sentence denotes The neutron structure also identified the protonation states, and thus electrical charges, of all other amino acid residues and revealed intricate hydrogen bonding networks in the active site cavity and at the dimer interface.
T8 1262-1523 Sentence denotes The fine atomic details present in this structure were made possible by the unique scattering properties of the neutron, which is an ideal probe for locating hydrogen positions and experimentally determining protonation states at near-physiological temperature.
T9 1524-1707 Sentence denotes Our observations provide critical information for structure-assisted and computational drug design, allowing precise tailoring of inhibitors to the enzyme's electrostatic environment.

sentences

Id Subject Object Predicate Lexical cue
T1 0-100 Sentence denotes Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography.
T2 101-227 Sentence denotes The main protease (3CL Mpro) from SARS-CoV-2, the etiological agent of COVID-19, is an essential enzyme for viral replication.
T3 228-311 Sentence denotes 3CL Mpro possesses an unusual catalytic dyad composed of Cys145 and His41 residues.
T4 312-603 Sentence denotes A critical question in the field has been what the protonation states of the ionizable residues in the substrate-binding active site cavity are; resolving this point would help understand the catalytic details of the enzyme and inform rational drug development against this pernicious virus.
T5 604-782 Sentence denotes Here, we present the room-temperature neutron structure of 3CL Mpro, which allowed direct determination of hydrogen atom positions and, hence, protonation states in the protease.
T6 783-1034 Sentence denotes We observe that the catalytic site natively adopts a zwitterionic reactive form where Cys145 is in the negatively charged thiolate state, and His41 is doubly protonated and positively charged, instead of the neutral unreactive state usually envisaged.
T7 1035-1261 Sentence denotes The neutron structure also identified the protonation states, and thus electrical charges, of all other amino acid residues and revealed intricate hydrogen bonding networks in the active site cavity and at the dimer interface.
T8 1262-1523 Sentence denotes The fine atomic details present in this structure were made possible by the unique scattering properties of the neutron, which is an ideal probe for locating hydrogen positions and experimentally determining protonation states at near-physiological temperature.
T9 1524-1707 Sentence denotes Our observations provide critical information for structure-assisted and computational drug design, allowing precise tailoring of inhibitors to the enzyme's electrostatic environment.

mondo_disease

Id Subject Object Predicate Lexical cue mondo_id
T1 39-49 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T2 135-145 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T3 172-180 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 39-47 OrganismTaxon denotes SARS-CoV 694009
T2 135-143 OrganismTaxon denotes SARS-CoV 694009

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 445-451 Body_part denotes cavity http://purl.obolibrary.org/obo/UBERON_0002553
T2 1227-1233 Body_part denotes cavity http://purl.obolibrary.org/obo/UBERON_0002553