> top > docs > PMC:7594251 > spans > 91484-103373 > annotations

PMC:7594251 / 91484-103373 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T6 2660-2667 https://glytoucan.org/Structures/Glycans/G15021LG denotes glucose
T7 2722-2729 https://glytoucan.org/Structures/Glycans/G15021LG denotes glucose

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 8558-8565 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T2 8676-8683 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 8903-8910 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T4 9165-9172 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T5 9282-9289 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T6 9748-9755 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T7 9807-9814 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T8 9921-9928 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T9 10052-10059 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T10 10099-10106 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T11 10360-10370 Body_part denotes intestinal http://purl.org/sig/ont/fma/fma7199
T12 10371-10381 Body_part denotes fatty acid http://purl.org/sig/ont/fma/fma82738
T13 10390-10397 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T14 10552-10559 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T15 10712-10719 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T16 10800-10818 Body_part denotes proteins complexes http://purl.org/sig/ont/fma/fma67906
T17 10861-10868 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T18 10951-10958 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T19 11239-11245 Body_part denotes serine http://purl.org/sig/ont/fma/fma82764
T183 501-504 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T184 714-721 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T185 964-971 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T186 1075-1077 Body_part denotes H4 http://purl.org/sig/ont/fma/fma84132
T187 1181-1183 Body_part denotes H3 http://purl.org/sig/ont/fma/fma84131
T188 1379-1382 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T189 1537-1544 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T190 1691-1694 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T191 1858-1865 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T192 2365-2372 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T193 2403-2411 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T194 2625-2630 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T195 2660-2667 Body_part denotes glucose http://purl.org/sig/ont/fma/fma82743
T196 2722-2729 Body_part denotes glucose http://purl.org/sig/ont/fma/fma82743
T197 3004-3011 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T198 3081-3091 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T199 3176-3186 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T200 3262-3269 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T201 3312-3319 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T202 3577-3588 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T203 3773-3784 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T204 4347-4354 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T205 4547-4556 Body_part denotes protein’s http://purl.org/sig/ont/fma/fma67257
T206 4701-4718 Body_part denotes protein complexes http://purl.org/sig/ont/fma/fma67906
T207 4701-4708 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T208 4956-4964 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T209 5185-5192 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T210 5250-5257 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T211 5964-5971 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T212 6825-6832 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T213 6954-6961 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T214 7041-7048 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T34 2625-2630 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T104 283-286 Disease denotes CSP http://purl.obolibrary.org/obo/MONDO_0005078
T105 549-552 Disease denotes STD http://purl.obolibrary.org/obo/MONDO_0021681
T106 2821-2824 Disease denotes SOS http://purl.obolibrary.org/obo/MONDO_0011604
T107 2923-2926 Disease denotes SOS http://purl.obolibrary.org/obo/MONDO_0011604
T108 2943-2946 Disease denotes STD http://purl.obolibrary.org/obo/MONDO_0021681
T109 3130-3133 Disease denotes SOS http://purl.obolibrary.org/obo/MONDO_0011604
T110 3875-3878 Disease denotes SOS http://purl.obolibrary.org/obo/MONDO_0011604
T111 3977-3980 Disease denotes SOS http://purl.obolibrary.org/obo/MONDO_0011604
T112 5291-5297 Disease denotes dengue http://purl.obolibrary.org/obo/MONDO_0005502
T113 5309-5312 Disease denotes NS3 http://purl.obolibrary.org/obo/MONDO_0012371
T114 9738-9741 Disease denotes CSP http://purl.obolibrary.org/obo/MONDO_0005078
T115 9757-9760 Disease denotes CSP http://purl.obolibrary.org/obo/MONDO_0005078
T116 9905-9908 Disease denotes CSP http://purl.obolibrary.org/obo/MONDO_0005078
T117 10270-10273 Disease denotes CSP http://purl.obolibrary.org/obo/MONDO_0005078
T118 10671-10674 Disease denotes CSP http://purl.obolibrary.org/obo/MONDO_0005078

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 8396-8397 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 8435-8436 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 8459-8460 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 8480-8481 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 8645-8646 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 8744-8751 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T7 8974-8976 http://purl.obolibrary.org/obo/CLO_0002960 denotes F1
T8 9024-9025 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 9148-9149 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 9280-9281 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 9746-9747 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 9805-9806 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 9912-9913 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 9944-9945 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 9981-9982 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 10043-10051 http://purl.obolibrary.org/obo/CLO_0007225 denotes labelled
T17 10168-10173 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T18 10354-10359 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T19 10360-10370 http://purl.obolibrary.org/obo/UBERON_0000160 denotes intestinal
T20 10360-10370 http://www.ebi.ac.uk/efo/EFO_0000834 denotes intestinal
T21 10732-10740 http://www.ebi.ac.uk/efo/EFO_0000876 denotes Extremes
T22 10800-10818 http://purl.obolibrary.org/obo/GO_0043234 denotes proteins complexes
T23 10949-10950 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 10999-11000 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 11044-11045 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 11095-11096 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 11180-11186 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T28 11663-11666 http://purl.obolibrary.org/obo/CLO_0001195 denotes 219
T646 84-87 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T647 109-114 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T648 944-945 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T649 954-963 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T650 1075-1077 http://purl.obolibrary.org/obo/CLO_0003599 denotes H4
T651 1079-1081 http://purl.obolibrary.org/obo/CLO_0003607 denotes H5
T652 1243-1244 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T653 1518-1519 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T654 1655-1656 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T655 1856-1857 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T656 1993-1994 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T657 2022-2028 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T658 2360-2361 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T659 2534-2536 http://purl.obolibrary.org/obo/CLO_0007874 denotes ms
T660 2625-2630 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T661 2625-2630 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T662 2625-2630 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T663 2625-2630 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T664 2777-2780 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T665 2829-2830 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T666 2913-2921 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeling
T667 3062-3063 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T668 3350-3353 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T669 3601-3604 http://purl.obolibrary.org/obo/CLO_0037067 denotes Val
T670 4042-4043 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T671 4104-4113 http://purl.obolibrary.org/obo/CLO_0007225 denotes Labelling
T672 4114-4115 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T673 4221-4229 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeling
T674 4259-4260 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T675 4564-4570 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T676 4587-4593 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T677 4701-4718 http://purl.obolibrary.org/obo/GO_0043234 denotes protein complexes
T678 5018-5024 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T679 5197-5198 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T680 5298-5303 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T681 5395-5396 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T682 5873-5879 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T683 5920-5926 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T684 6496-6497 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T685 6730-6731 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T686 6802-6803 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T687 7502-7503 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T688 7624-7625 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T689 7755-7756 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T526 195-199 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T527 639-645 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T528 714-721 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T529 809-816 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T530 946-953 Chemical denotes mitogen http://purl.obolibrary.org/obo/CHEBI_52290
T531 964-971 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T532 988-997 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T533 998-1006 Chemical denotes SB203580 http://purl.obolibrary.org/obo/CHEBI_90705
T534 1093-1101 Chemical denotes SB203580 http://purl.obolibrary.org/obo/CHEBI_90705
T535 1177-1179 Chemical denotes H2 http://purl.obolibrary.org/obo/CHEBI_18276
T536 1189-1195 Chemical denotes methyl http://purl.obolibrary.org/obo/CHEBI_32875|http://purl.obolibrary.org/obo/CHEBI_29309
T538 1245-1258 Chemical denotes pyridine ring http://purl.obolibrary.org/obo/CHEBI_52884
T539 1245-1253 Chemical denotes pyridine http://purl.obolibrary.org/obo/CHEBI_16227
T540 1285-1293 Chemical denotes SB203580 http://purl.obolibrary.org/obo/CHEBI_90705
T541 1364-1370 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T542 1400-1406 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T543 1442-1450 Chemical denotes SB203580 http://purl.obolibrary.org/obo/CHEBI_90705
T544 1537-1544 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T545 1545-1551 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T546 1726-1732 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T547 1807-1814 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T548 1858-1865 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T549 1895-1902 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T550 2004-2010 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T551 2011-2017 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T552 2050-2057 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T553 2104-2111 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T554 2233-2239 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T555 2365-2372 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T556 2403-2411 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T557 2583-2592 Chemical denotes glycolate http://purl.obolibrary.org/obo/CHEBI_29805
T558 2593-2596 Chemical denotes NAD http://purl.obolibrary.org/obo/CHEBI_13389|http://purl.obolibrary.org/obo/CHEBI_15846
T560 2660-2667 Chemical denotes glucose http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167
T562 2670-2679 Chemical denotes phosphate http://purl.obolibrary.org/obo/CHEBI_18367|http://purl.obolibrary.org/obo/CHEBI_26020|http://purl.obolibrary.org/obo/CHEBI_35780|http://purl.obolibrary.org/obo/CHEBI_43474
T566 2680-2685 Chemical denotes NADPH http://purl.obolibrary.org/obo/CHEBI_16474|http://purl.obolibrary.org/obo/CHEBI_57783
T17092 2722-2729 Chemical denotes glucose http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167
T570 2972-2978 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T571 3004-3011 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T572 3081-3091 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T573 3081-3086 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T574 3087-3091 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T575 3161-3167 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T576 3176-3186 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T577 3176-3181 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T578 3182-3186 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T579 3262-3269 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T580 3312-3319 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T581 3320-3326 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T582 3425-3438 Chemical denotes benzimidazole http://purl.obolibrary.org/obo/CHEBI_36622|http://purl.obolibrary.org/obo/CHEBI_41275
T584 3461-3468 Chemical denotes uridine http://purl.obolibrary.org/obo/CHEBI_16704
T585 3501-3511 Chemical denotes UDP-GlcNAc http://purl.obolibrary.org/obo/CHEBI_16264
T586 3501-3504 Chemical denotes UDP http://purl.obolibrary.org/obo/CHEBI_17659|http://purl.obolibrary.org/obo/CHEBI_58223
T588 3505-3511 Chemical denotes GlcNAc http://purl.obolibrary.org/obo/CHEBI_506227|http://purl.obolibrary.org/obo/CHEBI_73685
T590 3577-3588 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T591 3577-3582 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T592 3583-3588 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T593 3596-3599 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T595 3601-3604 Chemical denotes Val http://purl.obolibrary.org/obo/CHEBI_16414|http://purl.obolibrary.org/obo/CHEBI_30015
T597 3606-3609 Chemical denotes Leu http://purl.obolibrary.org/obo/CHEBI_15603|http://purl.obolibrary.org/obo/CHEBI_25017|http://purl.obolibrary.org/obo/CHEBI_30006
T600 3611-3614 Chemical denotes Met http://purl.obolibrary.org/obo/CHEBI_16044|http://purl.obolibrary.org/obo/CHEBI_16643|http://purl.obolibrary.org/obo/CHEBI_16811
T603 3622-3625 Chemical denotes Trp http://purl.obolibrary.org/obo/CHEBI_16828|http://purl.obolibrary.org/obo/CHEBI_27897|http://purl.obolibrary.org/obo/CHEBI_29954
T606 3627-3630 Chemical denotes Phe http://purl.obolibrary.org/obo/CHEBI_17295|http://purl.obolibrary.org/obo/CHEBI_29997
T608 3720-3726 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T609 3773-3784 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T610 3773-3778 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T611 3779-3784 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T612 3830-3836 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T613 3927-3931 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T614 4098-4103 Chemical denotes butyl http://purl.obolibrary.org/obo/CHEBI_41264
T615 4238-4243 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T616 4261-4277 Chemical denotes tert-butyl group http://purl.obolibrary.org/obo/CHEBI_30355
T617 4266-4271 Chemical denotes butyl http://purl.obolibrary.org/obo/CHEBI_41264
T618 4272-4277 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T619 4295-4301 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T620 4347-4354 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T621 4355-4361 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T622 4381-4397 Chemical denotes tert-butyl group http://purl.obolibrary.org/obo/CHEBI_30355
T623 4386-4391 Chemical denotes butyl http://purl.obolibrary.org/obo/CHEBI_41264
T624 4392-4397 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T625 4464-4470 Chemical denotes methyl http://purl.obolibrary.org/obo/CHEBI_32875|http://purl.obolibrary.org/obo/CHEBI_29309
T627 4484-4490 Chemical denotes methyl http://purl.obolibrary.org/obo/CHEBI_32875|http://purl.obolibrary.org/obo/CHEBI_29309
T629 4517-4522 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T630 4557-4559 Chemical denotes 1H http://purl.obolibrary.org/obo/CHEBI_49637
T631 4576-4586 Chemical denotes tert-butyl http://purl.obolibrary.org/obo/CHEBI_30355
T632 4581-4586 Chemical denotes butyl http://purl.obolibrary.org/obo/CHEBI_41264
T633 4701-4708 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T634 4826-4842 Chemical denotes tert-butyl group http://purl.obolibrary.org/obo/CHEBI_30355
T635 4831-4836 Chemical denotes butyl http://purl.obolibrary.org/obo/CHEBI_41264
T636 4837-4842 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T637 4956-4964 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T638 5061-5077 Chemical denotes tert-butyl group http://purl.obolibrary.org/obo/CHEBI_30355
T639 5066-5071 Chemical denotes butyl http://purl.obolibrary.org/obo/CHEBI_41264
T640 5072-5077 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T641 5185-5192 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T642 5236-5242 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T643 5250-5257 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T644 5377-5383 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T645 5397-5413 Chemical denotes tert-butyl group http://purl.obolibrary.org/obo/CHEBI_30355
T646 5402-5407 Chemical denotes butyl http://purl.obolibrary.org/obo/CHEBI_41264
T647 5408-5413 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T648 5469-5485 Chemical denotes tert-butyl group http://purl.obolibrary.org/obo/CHEBI_30355
T649 5474-5479 Chemical denotes butyl http://purl.obolibrary.org/obo/CHEBI_41264
T650 5480-5485 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T651 5489-5495 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T652 5574-5580 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T653 5605-5611 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T654 5770-5775 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T655 5780-5787 Chemical denotes solvent http://purl.obolibrary.org/obo/CHEBI_46787
T656 5809-5815 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T657 5853-5859 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T658 5940-5946 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T659 5964-5971 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T660 5978-5985 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T661 6047-6054 Chemical denotes prodrug http://purl.obolibrary.org/obo/CHEBI_50266
T662 6140-6147 Chemical denotes quinone http://purl.obolibrary.org/obo/CHEBI_36141
T663 6462-6472 Chemical denotes asparagine http://purl.obolibrary.org/obo/CHEBI_22653
T664 6498-6506 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T665 6558-6567 Chemical denotes aziridine http://purl.obolibrary.org/obo/CHEBI_30969
T666 6608-6615 Chemical denotes solvent http://purl.obolibrary.org/obo/CHEBI_46787
T23797 6743-6750 Chemical denotes solvent http://purl.obolibrary.org/obo/CHEBI_46787
T25837 6825-6832 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T75648 6908-6914 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T96730 6954-6961 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T53890 7041-7048 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T32855 7089-7096 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T55729 7138-7145 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T47776 7184-7202 Chemical denotes triazolopyridazine http://purl.obolibrary.org/obo/CHEBI_48384
T84009 7218-7225 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T62193 7336-7342 Chemical denotes methyl http://purl.obolibrary.org/obo/CHEBI_32875|http://purl.obolibrary.org/obo/CHEBI_29309
T44312 7343-7348 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T25777 7354-7360 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T26250 7373-7379 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T88957 7385-7391 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T85582 7407-7413 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T46490 7419-7425 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T38398 7443-7448 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T94756 7552-7557 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T55063 7558-7567 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T3389 7612-7618 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T5082 7636-7643 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T39367 7659-7677 Chemical denotes triazolopyridazine http://purl.obolibrary.org/obo/CHEBI_48384
T28009 7720-7725 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T17318 7795-7802 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T1462 7884-7891 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T73744 7956-7974 Chemical denotes triazolopyridazine http://purl.obolibrary.org/obo/CHEBI_48384
T45570 7983-7989 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T6158 7998-8010 Chemical denotes methyl group http://purl.obolibrary.org/obo/CHEBI_32875
T85158 7998-8004 Chemical denotes methyl http://purl.obolibrary.org/obo/CHEBI_29309
T13480 8005-8010 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T97666 8052-8057 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T70994 8058-8063 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T86094 8084-8092 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T60748 8336-8344 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T70776 8558-8565 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T46909 8676-8683 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T58074 8687-8693 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T32483 8787-8793 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T32375 8819-8821 Chemical denotes 1H http://purl.obolibrary.org/obo/CHEBI_49637
T80174 8834-8836 Chemical denotes 1H http://purl.obolibrary.org/obo/CHEBI_49637
T35438 8878-8884 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T25554 8896-8902 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T34470 8903-8910 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T57878 8994-8996 Chemical denotes 1H http://purl.obolibrary.org/obo/CHEBI_49637
T38614 8997-8999 Chemical denotes 1H http://purl.obolibrary.org/obo/CHEBI_49637
T60908 9137-9143 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T47768 9165-9172 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T66836 9263-9269 Chemical denotes methyl http://purl.obolibrary.org/obo/CHEBI_32875|http://purl.obolibrary.org/obo/CHEBI_29309
T46479 9282-9289 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T85952 9462-9469 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T21306 9598-9602 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T85693 9621-9623 Chemical denotes 1H http://purl.obolibrary.org/obo/CHEBI_49637
T57200 9748-9755 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T43008 9807-9814 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T28259 9884-9890 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T70946 9921-9928 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T39339 9990-9996 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T77983 10052-10059 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T24857 10080-10082 Chemical denotes 1H http://purl.obolibrary.org/obo/CHEBI_49637
T79343 10099-10106 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T60641 10178-10186 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T37117 10324-10340 Chemical denotes naphthoate ester http://purl.obolibrary.org/obo/CHEBI_46831
T41675 10324-10334 Chemical denotes naphthoate http://purl.obolibrary.org/obo/CHEBI_25482
T79793 10335-10340 Chemical denotes ester http://purl.obolibrary.org/obo/CHEBI_35701
T85096 10371-10381 Chemical denotes fatty acid http://purl.obolibrary.org/obo/CHEBI_35366
T48890 10377-10381 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T92250 10390-10397 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T53375 10407-10416 Chemical denotes ketorolac http://purl.obolibrary.org/obo/CHEBI_6129
T64655 10417-10420 Chemical denotes ANS http://purl.obolibrary.org/obo/CHEBI_39708
T63906 10509-10515 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T65279 10552-10559 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T23599 10560-10566 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T79552 10712-10719 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T41635 10800-10808 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T4092 10861-10868 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T35786 10951-10958 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T89568 11239-11245 Chemical denotes serine http://purl.obolibrary.org/obo/CHEBI_17822
T81502 11275-11284 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T93491 11285-11307 Chemical denotes chymotrypsin inhibitor http://purl.obolibrary.org/obo/CHEBI_64943
T66488 11298-11307 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T88221 11368-11390 Chemical denotes chymotrypsin inhibitor http://purl.obolibrary.org/obo/CHEBI_64943
T34199 11381-11390 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
950 940-943 Gene denotes p38 Gene:1432
951 998-1006 Chemical denotes SB203580 MESH:C093642
952 1093-1101 Chemical denotes SB203580 MESH:C093642
953 1245-1253 Chemical denotes pyridine MESH:C023666
954 1285-1293 Chemical denotes SB203580 MESH:C093642
955 1442-1450 Chemical denotes SB203580 MESH:C093642
963 2360-2364 Gene denotes a 3D Gene:140564
964 2705-2721 Species denotes L. mesenteroides Tax:1245
965 2583-2592 Chemical denotes glycolate MESH:C031149
966 2593-2597 Chemical denotes NAD+ MESH:D009243
967 2660-2667 Chemical denotes glucose MESH:D005947
968 2680-2685 Chemical denotes NADPH MESH:D009249
969 2722-2729 Chemical denotes glucose MESH:D005947
979 3410-3438 Chemical denotes 2-(3′-pyridyl)-benzimidazole
980 3461-3499 Chemical denotes uridine diphosphateN-acetylglucosamine
981 3501-3511 Chemical denotes UDP-GlcNAc
982 3596-3599 Chemical denotes Ile MESH:D007532
983 3601-3604 Chemical denotes Val MESH:D014633
984 3606-3609 Chemical denotes Leu MESH:D007930
985 3622-3625 Chemical denotes Trp MESH:D014364
986 3627-3630 Chemical denotes Phe MESH:D010649
987 3632-3635 Chemical denotes His MESH:D006639
990 4093-4097 Gene denotes Tert Gene:7015
991 4104-4113 Disease denotes Labelling
1006 5309-5312 Gene denotes NS3 Gene:3845
1007 5469-5473 Gene denotes tert Gene:7015
1008 5397-5401 Gene denotes tert Gene:7015
1009 5061-5065 Gene denotes tert Gene:7015
1010 4826-4830 Gene denotes tert Gene:7015
1011 4576-4580 Gene denotes tert Gene:7015
1012 4381-4385 Gene denotes tert Gene:7015
1013 4261-4265 Gene denotes tert Gene:7015
1014 4722-4726 Gene denotes high Gene:104137
1015 4750-4777 Species denotes Bacillus stearothermophilus Tax:1422
1016 5291-5303 Species denotes dengue virus Tax:12637
1017 4557-4559 Chemical denotes 1H
1018 5510-5516 Chemical denotes Val155
1019 5522-5528 Chemical denotes DENpro
1032 6134-6138 Gene denotes NQO2 Gene:4835
1033 6263-6267 Gene denotes NQO2 Gene:4835
1034 6062-6072 Chemical denotes tretazicar MESH:C100099
1035 6074-6113 Chemical denotes (5-(aziridin-1-yl)-2,4-dinitrobenzamide MESH:C100099
1036 6124-6130 Chemical denotes CB1954 MESH:C100099
1037 6241-6251 Chemical denotes tretazicar MESH:C100099
1038 6366-6376 Chemical denotes tretazicar MESH:C100099
1039 6462-6472 Chemical denotes asparagine MESH:D001216
1040 6498-6506 Chemical denotes hydrogen MESH:D006859
1041 6533-6543 Chemical denotes tretazicar MESH:C100099
1042 6558-6567 Chemical denotes aziridine MESH:C033132
1043 6578-6588 Chemical denotes tretazicar MESH:C100099
1058 7052-7056 Gene denotes Brd4 Gene:23476
1059 7114-7118 Gene denotes Brd4 Gene:23476
1060 7271-7275 Gene denotes Brd4 Gene:23476
1061 8129-8133 Gene denotes Brd4 Gene:23476
1062 8134-8137 Gene denotes BD1 Gene:1672
1063 7119-7122 Gene denotes BD1 Gene:1672
1064 7057-7060 Gene denotes BD1 Gene:1672
1065 7184-7202 Chemical denotes triazolopyridazine
1066 7443-7448 Chemical denotes water MESH:D014867
1067 7552-7557 Chemical denotes water MESH:D014867
1068 7659-7677 Chemical denotes triazolopyridazine
1069 7956-7974 Chemical denotes triazolopyridazine
1070 8084-8092 Chemical denotes hydrogen MESH:D006859
1071 8119-8125 Chemical denotes Asn140
1082 8732-8735 Chemical denotes 13C MESH:C000615229
1083 8740-8743 Chemical denotes 15N
1084 8815-8818 Chemical denotes 13C MESH:C000615229
1085 8819-8821 Chemical denotes 1H
1086 8830-8833 Chemical denotes 13C MESH:C000615229
1087 8834-8836 Chemical denotes 1H
1088 8977-8980 Chemical denotes 15N
1089 8981-8984 Chemical denotes 13C MESH:C000615229
1090 8994-8996 Chemical denotes 1H
1091 8997-8999 Chemical denotes 1H
1101 10399-10405 Gene denotes hIFABP Gene:2169
1102 10354-10359 Species denotes human Tax:9606
1103 9621-9623 Chemical denotes 1H
1104 10039-10042 Chemical denotes 15N
1105 10080-10082 Chemical denotes 1H
1106 10178-10186 Chemical denotes hydrogen MESH:D006859
1107 10324-10340 Chemical denotes naphthoate ester
1108 10407-10416 Chemical denotes ketorolac MESH:D020910
1109 10417-10420 Chemical denotes ANS MESH:C027132
1111 11239-11245 Chemical denotes serine MESH:D012694

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 9453-9461 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange
T3606 934-938 http://purl.obolibrary.org/obo/GO_0004707 denotes MAPK
T66733 1153-1157 http://purl.obolibrary.org/obo/GO_0004707 denotes MAPK
T42258 1320-1324 http://purl.obolibrary.org/obo/GO_0004707 denotes MAPK
T6077 1455-1459 http://purl.obolibrary.org/obo/GO_0004707 denotes MAPK

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T589 0-4 Sentence denotes 3.6.
T590 5-62 Sentence denotes Other Methods Used to Determine the Drug-Target Complexes
T591 63-217 Sentence denotes Substantial progress has been made in the NMR field over the past 5–10 years, and various methods were established to determine the drug-target complexes.
T592 218-359 Sentence denotes Most of them utilize either NOE or chemical shift perturbations (CSP) although in silico models/programs, using NMR-derivate data also exist.
T593 361-367 Sentence denotes 3.6.1.
T594 368-377 Sentence denotes DIRECTION
T595 378-565 Sentence denotes One of the methods called difference of inversion recovery rate with and without target irradiation (DIRECTION) is used to map pharmacophores and can be an alternative to STD experiments.
T596 566-722 Sentence denotes This method uses the difference between longitudinal relaxation rates of ligand protons with- and with-out irradiation of the protons of the target protein.
T597 723-817 Sentence denotes The DIRECTION approach, however cannot be used for slowly exchanging (strong binding) ligands.
T598 818-1017 Sentence denotes The practical approach of this method was demonstrated on the experiment when analyzed the interactions between p38 MAPK (p38 a mitogen-activated protein kinase) and its inhibitor-SB203580 [389,390].
T599 1018-1204 Sentence denotes The results from this experiment showed that protons H1, H4, H5, and H6 of SB203580, are in close neighborhood with the protons of p38 MAPK when compared with H2, H3, and methyl protons.
T600 1205-1325 Sentence denotes It indicates that two aromatic rings (a pyridine ring and fluorophenyl ring) of SB203580 interact tightly with p38 MAPK.
T601 1326-1474 Sentence denotes The results were later confirmed with proton density map of each ligand’s proton, based on the crystal structure of SB203580–p38 MAPK complex [391].
T602 1475-1641 Sentence denotes Moreover, the same authors already created a new and improved protein–ligand docking method by combining the DIRECTION obtained NMR data with docking software. [392].
T603 1643-1649 Sentence denotes 3.6.2.
T604 1650-1654 Sentence denotes ILOE
T605 1655-1766 Sentence denotes A second method that can be used to map pharmacophores is called inter-ligand nuclear Overhauser effect (ILOE).
T606 1767-1992 Sentence denotes This 2D NMR experiment detects when two ligands bind simultaneously to adjacent sites on a protein surface although both of the ligands do not have to bind to the same binding pocket (opposite to INPHARMA, see above) [5,393].
T607 1993-2193 Sentence denotes A negative ligand−ligand NOE signal will be created when ligands bind in close proximity to each other whereas ligands that do not bind will show no NOEs, or at most very weak positive ones [372,394].
T608 2194-2287 Sentence denotes ILOE also enables determination of the ligand orientations with respect to one another [393].
T609 2288-2412 Sentence denotes As in the case of INPHARMA, ILOE can be utilized even in the absence of a 3D protein structure and used with large proteins.
T610 2413-2543 Sentence denotes Additionally, ILOE differs from INPHARMA in mixing times—for ILOE the mixing times are typically in the range of 600–800 ms [345].
T611 2544-2812 Sentence denotes Application of ILOE was first shown on glycolate+NAD+ in the presence of porcine heart lactatedehydrogenase, and by glucose-6-phosphate+NADPH in the presence of L. mesenteroides glucose-6-phosphatedehydrogenase and from that time it has been widely used [393,395,396].
T612 2814-2820 Sentence denotes 3.6.3.
T613 2821-2828 Sentence denotes SOS-NMR
T614 2829-3092 Sentence denotes A third method called structural information using Overhauser effects and selective labeling (SOS-NMR), relies of STD experiments performed on ligand complexes with different protein samples that have been fully deuterated excluding a specific type of amino acid.
T615 3093-3335 Sentence denotes In other words, the data obtained by SOS-NMR gives insight into the ligand-binding amino acid composition and when taken into consideration the 3D structure of targeted protein can be used to establish the structure of protein-ligand complex.
T616 3336-3513 Sentence denotes This approach has been demonstrated using two complexes—FKBP complexed to 2-(3′-pyridyl)-benzimidazole and MurA complexed to uridine diphosphateN-acetylglucosamine (UDP-GlcNAc).
T617 3514-3595 Sentence denotes The results showed that for FKBP and MurA, only four and three amino acids (FKBP:
T618 3596-3621 Sentence denotes Ile, Val, Leu, Met; MurA:
T619 3622-3740 Sentence denotes Trp, Phe, His) were needed to be selectively protonated in perdeuterated samples to establish the ligand-binding site.
T620 3741-3853 Sentence denotes Additionally, on average only 6 amino acids were required for accurate identification of ligand-binding surface.
T621 3854-3956 Sentence denotes According to authors SOS-NMR can greatly improve the early stages of the drug discovery process [397].
T622 3957-4084 Sentence denotes Moreover, combining SOS-NMR with other methods can even further increase chances for a positive outcome of an experiment [398].
T623 4086-4092 Sentence denotes 3.6.4.
T624 4093-4113 Sentence denotes Tert-butyl Labelling
T625 4114-4195 Sentence denotes A completely different approach to this topic was taken by Chen et al. [399,400].
T626 4196-4376 Sentence denotes Instead of using isotope labeling, Chen’s group decided to use a tert-butyl group contained within ligand-1 to obtain structural information about the protein-ligand complex [400].
T627 4377-4523 Sentence denotes The tert-butyl group formed an intense singlet in 1.0 to 1.5 ppm range thanks to rapid methyl rotation and methyl reorientation within that group.
T628 4524-4807 Sentence denotes When compared with the protein’s 1H-NMR signal, the tert-butyl signal tended to be much narrower and resulted in easy detection without the need for isotopic enrichment even in protein complexes of high molecular mass such as Bacillus stearothermophilus DnaB hexamer (320 kDa) [399].
T629 4808-4987 Sentence denotes Additionally, the tert-butyl group produces intense NOESY cross peaks that can be observed even in the situations where normally cross-peaks of the proteins are barely detectable.
T630 4988-5078 Sentence denotes This is partially because the signal corresponded to nine protons within tert-butyl group.
T631 5079-5193 Sentence denotes Those aspects enable measurements of pseudo-contact shifts generated by paramagnetic tags attached to the protein.
T632 5194-5258 Sentence denotes As a result, it allows positioning of the ligand on the protein.
T633 5259-5414 Sentence denotes An example of this approach, is dengue virus NS2B-NS3 protease from serotype 2 (referred as DENpro) in complexed with ligand containing a tert-butyl group.
T634 5415-5535 Sentence denotes The result of this experiment showed NOEs between the tert-butyl group of ligand-1 and residue Val155 from DENpro [400].
T635 5537-5543 Sentence denotes 3.6.5.
T636 5544-5550 Sentence denotes SALMON
T637 5551-5728 Sentence denotes Solvent accessibility, ligand binding, and mapping of ligand orientation by NMR spectroscopy (SALMON) is another method based on the data obtained via nuclear Overhauser effect.
T638 5729-5987 Sentence denotes This method utilizes WaterLOGSY [401] to probe for solvent accessibility to the ligand and determine the orientation of the ligand by analyzing signal changes in WaterLOGSY spectra (positive signal from unbound ligand vs. negative for protein-bound ligands).
T639 5988-6179 Sentence denotes This method was first used to determine the orientation of prodrug called tretazicar ((5-(aziridin-1-yl)-2,4-dinitrobenzamide) known as CB1954 in NQO2 (quinone oxidoreductase 2) binding site.
T640 6180-6395 Sentence denotes Previous attempts had been made to obtain the orientation of tretazicar bounded to NQO2, however the results obtained from X-ray crystallography were inconclusive as two orientations of tretazicar could be possible.
T641 6396-6622 Sentence denotes The information obtained via SALMON showed that the side chain of asparagine at position 161 formed a hydrogen bond with 2-nitrogroup of tretazicar, and that the aziridine moiety of tretazicar pointed toward the solvent [401].
T642 6624-6630 Sentence denotes 3.6.6.
T643 6631-6646 Sentence denotes LOGSY Titration
T644 6647-6765 Sentence denotes Another variant of WaterLOGSY method called LOGSY utilizes the titration slopes as a measure of solvent accessibility.
T645 6766-6848 Sentence denotes The titration slopes are created by a constant increase of protein concentrations.
T646 6849-6993 Sentence denotes This method also provides more insight into the process of ligand solvation by checking the influence of protein concentration onto the process.
T647 6994-7155 Sentence denotes This approach was used on the bromodomain 1 of protein 4 (Brd4-BD1) by mapping epitopes of two ligands interacting with Brd4-BD1 and predicting ligands position.
T648 7156-7276 Sentence denotes The results showed that the triazolopyridazine moiety of both ligands was implanted into the binding pocket of the Brd4.
T649 7277-7453 Sentence denotes Additionally, the results from LOGSY titration showed that methyl-group 1 of ligand 1, aromatic proton 8 of ligand 2 and aromatic proton 8 of ligand 1 exhibit strong water NOE.
T650 7454-7683 Sentence denotes This information enabled researchers to utilize a chemical replacement strategy (substitute bound water molecules by suitable functional groups) for aromatic proton 8 in a series of ligands containing the triazolopyridazine ring.
T651 7684-7822 Sentence denotes Those protons were replaced with an amino or aminomethyl groups and as a result, the binding affinity of those ligands increased 100-fold.
T652 7823-8144 Sentence denotes Finally, the results obtained from X-ray crystallography for ligands with such modifications allowed to find the binding mode of the triazolopyridazine ring of ligand 1 (with methyl group pointing internally) and the substituted amino group was found to create hydrogen bond to the side chain of Asn140 of Brd4-BD1 [402].
T653 8146-8152 Sentence denotes 3.6.7.
T654 8153-8208 Sentence denotes Nuclear Magnetic Resonance Molecular Replacement (NMR2)
T655 8209-8416 Sentence denotes The most recent approach called Nuclear Magnetic Resonance Molecular Replacement (NMR2) utilizes spatial data obtained through solution-state NMR in order to locate the binding pocket of a complex structure.
T656 8417-8587 Sentence denotes For that, it uses a receptor model, e.g., a X-ray structure of a homolog, to conduct an analysis and at the same time excluding the need for protein resonance assignment.
T657 8588-8657 Sentence denotes To conduct an experiment using such an approach requires a few steps.
T658 8658-8752 Sentence denotes First, either the protein or ligand used in the complex must be uniformly 13C and 15N labeled.
T659 8753-8842 Sentence denotes Then, an experiment to assign the ligand is needed such as 2D 13C,1H-HMQC or 13C,1H-HMBC.
T660 8843-9006 Sentence denotes The next step is the evaluation of ligand intra- and ligand–protein intermolecular distances through NOE cross peaks obtained from F1-15N,13C-filtered 1H,1H-NOESY.
T661 9007-9185 Sentence denotes Lastly, choosing a proper input structure is required which can be either X-ray or NMR structures in apo form, with another bound ligand, or a homolog to the protein of interest.
T662 9186-9355 Sentence denotes Then the NMR2 program analyzes for all possible partial assignments (such as methyl groups of a protein) and calculates the complex structures for all options [403,404].
T663 9356-9488 Sentence denotes This method was already successfully used to resolve complex structures in case of slow and fast exchange ligands [403,404,405,406].
T664 9490-9496 Sentence denotes 3.6.8.
T665 9497-9502 Sentence denotes HECSP
T666 9503-9620 Sentence denotes In silico methods combined with NMR derived information can also be used to determine accurate drug-target complexes.
T667 9621-9756 Sentence denotes 1H empirical chemical shift perturbation (HECSP) is an empirical model that is based on chemical shift perturbation (CSP) of a protein.
T668 9757-9900 Sentence denotes CSP represents the change in chemical shifts in a protein due to alteration of its chemical environment (which can happen upon ligand binding).
T669 9901-10060 Sentence denotes The CSP of a target protein is obtained by a series of 2D HSQC experiments with a set of ligand titrations involving samples that contain 15N-labelled protein.
T670 10061-10138 Sentence denotes The calculation of 1H-CSPs inside the protein are based on four contributors:
T671 10139-10228 Sentence denotes 1) ring current, 2) electric field, 3) hydrogen bonding, and last 4) magnetic anisotropy.
T672 10229-10429 Sentence denotes To show the value of the HECSP model two CSP examples were used: apo-neocarzinostatin (apoNCS)-naphthoate ester complex, and human intestinal fatty acid binding protein (hIFABP)-ketorolac-ANS complex.
T673 10430-10621 Sentence denotes The results from the experiment showed that HECSP model can distinguish native ligand from decoys and more clearly define protein-ligand complex structures with NMR derived information [407].
T674 10623-10629 Sentence denotes 3.6.9.
T675 10630-10637 Sentence denotes SAMPLEX
T676 10638-10819 Sentence denotes Another program that can utilize CSP called Smoothed Automatic Mapping of Protein from Listed Extremes (SAMPLEX) can help to determine the interaction surface of proteins complexes.
T677 10820-10977 Sentence denotes SAMPLEX takes the chemical shifts of the protein of interests in both the free and bound state and corresponding 3D structure of a protein in the free state.
T678 10978-11161 Sentence denotes The programs returns a confidence value for each residue to be in a perturbed or unperturbed state (0.05 as being in a perturbed state, −0.05 as remaining in their unperturbed state).
T679 11162-11310 Sentence denotes This approach was tested on five examples, one of which was Subtilisin BPN’ (serine protease) complexed with its inhibitor–chymotrypsin inhibitor 2.
T680 11311-11449 Sentence denotes The results showed that residue 2, and residues 56–62 of chymotrypsin inhibitor-2 were perturbed and residue 63 was in an ambiguous state.
T681 11450-11556 Sentence denotes To compare, the X-ray crystallography data showed residues 50 and 54–61 to be involved in the interaction.
T682 11557-11733 Sentence denotes For subtilisin BPN’ the program predicted residues 33, 97, 99–109, 126-128, 141, 154–156, 167–171 and 218–219 to perturbed and residues 65, 98 and 220 to be in ambiguous state.
T683 11734-11889 Sentence denotes That information was also confronted with the X-ray crystallography data which shown residues 99–104, 125–128, 154–157, 167, 218–221 to be perturbed [408].