> top > docs > PMC:7571312 > spans > 6194-8004 > annotations

PMC:7571312 / 6194-8004 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T55817 1391-1400 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T4591 1593-1601 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T6474 1718-1725 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T1473 1726-1734 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T34 120-124 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T35 295-299 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T36 521-525 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T37 736-740 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T38 1089-1093 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T39 1416-1420 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T24689 11-12 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30229 34-40 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T25588 216-222 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T99633 223-225 http://purl.obolibrary.org/obo/CLO_0008285 denotes P1
T58385 226-228 http://purl.obolibrary.org/obo/CLO_0008307 denotes P2
T89484 266-268 http://purl.obolibrary.org/obo/CLO_0008337 denotes P4
T40961 334-338 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2, a
T60248 391-393 http://purl.obolibrary.org/obo/CLO_0008307 denotes P2
T5489 462-464 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T9645 465-468 http://purl.obolibrary.org/obo/CLO_0007437 denotes M–1
T53142 465-468 http://purl.obolibrary.org/obo/CLO_0007448 denotes M–1
T23219 465-468 http://purl.obolibrary.org/obo/CLO_0007449 denotes M–1
T80219 465-468 http://purl.obolibrary.org/obo/CLO_0050175 denotes M–1
T91123 465-468 http://purl.obolibrary.org/obo/CLO_0052399 denotes M–1
T26503 469-472 http://purl.obolibrary.org/obo/CLO_0050050 denotes s–1
T80373 1122-1123 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T21360 1175-1176 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T91275 1201-1202 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T85006 1318-1320 http://purl.obolibrary.org/obo/CLO_0008285 denotes P1
T17731 1388-1390 http://purl.obolibrary.org/obo/CLO_0008285 denotes P1
T91390 1463-1465 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T31378 1480-1481 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58086 1669-1671 http://purl.obolibrary.org/obo/CLO_0008307 denotes P2
T31518 1693-1694 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T63 68-78 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T64 176-184 Chemical denotes acceptor http://purl.obolibrary.org/obo/CHEBI_15339
T65 223-225 Chemical denotes P1 http://purl.obolibrary.org/obo/CHEBI_60949
T66 226-228 Chemical denotes P2 http://purl.obolibrary.org/obo/CHEBI_33472
T67 266-268 Chemical denotes P4 http://purl.obolibrary.org/obo/CHEBI_35895
T68 367-373 Chemical denotes indole http://purl.obolibrary.org/obo/CHEBI_16881|http://purl.obolibrary.org/obo/CHEBI_35581
T70 382-387 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T71 391-393 Chemical denotes P2 http://purl.obolibrary.org/obo/CHEBI_33472
T72 844-852 Chemical denotes acceptor http://purl.obolibrary.org/obo/CHEBI_15339
T73 882-890 Chemical denotes carbonyl http://purl.obolibrary.org/obo/CHEBI_23019
T74 891-897 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T75 962-970 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T76 976-981 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T77 1022-1030 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T78 1048-1056 Chemical denotes carbonyl http://purl.obolibrary.org/obo/CHEBI_23019
T79 1057-1063 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T80 1079-1081 Chemical denotes NH http://purl.obolibrary.org/obo/CHEBI_29339|http://purl.obolibrary.org/obo/CHEBI_73424
T82 1149-1157 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T83 1318-1320 Chemical denotes P1 http://purl.obolibrary.org/obo/CHEBI_60949
T84 1388-1390 Chemical denotes P1 http://purl.obolibrary.org/obo/CHEBI_60949
T85 1391-1400 Chemical denotes glutamine http://purl.obolibrary.org/obo/CHEBI_28300
T86 1492-1500 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T87 1521-1523 Chemical denotes NH http://purl.obolibrary.org/obo/CHEBI_29339|http://purl.obolibrary.org/obo/CHEBI_73424
T89 1531-1537 Chemical denotes lactam http://purl.obolibrary.org/obo/CHEBI_24995
T90 1552-1560 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T91 1602-1608 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T92 1652-1654 Chemical denotes NH http://purl.obolibrary.org/obo/CHEBI_29339|http://purl.obolibrary.org/obo/CHEBI_73424
T94 1662-1668 Chemical denotes indole http://purl.obolibrary.org/obo/CHEBI_16881|http://purl.obolibrary.org/obo/CHEBI_35581
T96 1669-1671 Chemical denotes P2 http://purl.obolibrary.org/obo/CHEBI_33472
T97 1695-1703 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T98 1718-1725 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T28 0-149 Sentence denotes Performing a similar analysis, we tested 1 and additional HRV 3Cpro inhibitors that displayed very weak to unmeasurable SARS CoV-1 3CLpro inhibition.
T29 150-324 Sentence denotes Concurrently, new Michael acceptor derivatives were designed that tested P1/P2 alterations and truncation of the P3/P4 binding motif to optimize SARS CoV-1 3CLpro inhibition.
T30 325-714 Sentence denotes Compound 2, a derivative that contains an indole capping group at P2, displayed modest levels of irreversible inhibition (kobs/I = 586 ± 11 M–1 s–1) that enabled cocrystallization in complex with SARS CoV-1 3CLpro (PDB code 6XHO).29 Comparison of this structure with the complex of 1 in HRV 3Cpro helped to rationalize the poor performance of the warhead, which had been successful in HRV.
T31 715-864 Sentence denotes The structure of the SARS CoV-1 3CLpro complex revealed an eclipsed torsion about the resulting sp3 α,β-carbons from the Michael acceptor (Figure 3).
T32 865-1003 Sentence denotes Furthermore, the carbonyl oxygen sp2 lone pair electrons are not aligned well with either 3CLpro hydrogen bond donor of the oxyanion hole.
T33 1004-1238 Sentence denotes Specifically, the hydrogen bond between the carbonyl oxygen and the Gly143 NH in the SARS CoV-1 3CLpro complex is 3.4 Å, while the corresponding hydrogen bond distance is a much more favorable 2.8 Å in the complex of 1 with HRV 3Cpro.
T34 1239-1516 Sentence denotes In contrast to these unfavorable interactions, the constrained lactam30 at the P1 site, which was designed to be isosteric with the highly conserved P1 glutamine present in all SARS CoV substrates, is well positioned in the S1 pocket making a favorable hydrogen bond to His163.
T35 1517-1633 Sentence denotes The NH of the lactam is within the hydrogen bond distance to Glu166 and the backbone oxygen of Phe140 in the 3CLpro.
T36 1634-1810 Sentence denotes Additionally, the NH of the indole P2 capping moiety makes a hydrogen bond with the protein backbone while it extends across an otherwise lipophilic surface over the P3 pocket.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
192 120-128 Species denotes SARS CoV Tax:694009
193 295-303 Species denotes SARS CoV Tax:694009
194 447-451 Species denotes kobs Tax:59530
195 521-529 Species denotes SARS CoV Tax:694009
196 736-744 Species denotes SARS CoV Tax:694009
197 1089-1097 Species denotes SARS CoV Tax:694009
198 1416-1424 Species denotes SARS CoV Tax:694009
199 58-61 Species denotes HRV Tax:169066
200 612-615 Species denotes HRV Tax:169066
201 710-713 Species denotes HRV Tax:169066
202 1228-1231 Species denotes HRV Tax:169066
203 811-826 Chemical denotes sp3 α,β-carbons
204 891-901 Chemical denotes oxygen sp2
205 962-970 Chemical denotes hydrogen MESH:D006859
206 1022-1030 Chemical denotes hydrogen MESH:D006859
207 1057-1063 Chemical denotes oxygen MESH:D010100
208 1072-1078 Chemical denotes Gly143
209 1149-1157 Chemical denotes hydrogen MESH:D006859
210 1302-1308 Chemical denotes lactam MESH:D007769
211 1391-1400 Chemical denotes glutamine MESH:D005973
212 1492-1500 Chemical denotes hydrogen MESH:D006859
213 1509-1515 Chemical denotes His163
214 1531-1537 Chemical denotes lactam MESH:D007769
215 1552-1560 Chemical denotes hydrogen MESH:D006859
216 1578-1584 Chemical denotes Glu166
217 1602-1608 Chemical denotes oxygen MESH:D010100
218 1612-1618 Chemical denotes Phe140
219 1695-1703 Chemical denotes hydrogen MESH:D006859

2_test

Id Subject Object Predicate Lexical cue
33054210-10197965-61913454 1308-1310 10197965 denotes 30