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PMC:7219429 / 13501-17583 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T76 57-64 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T77 130-137 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T78 211-218 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T79 456-463 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T80 767-777 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T81 1441-1448 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T82 1560-1570 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T83 1717-1724 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T84 1807-1814 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T85 2000-2007 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T86 2181-2188 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T87 2633-2640 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T88 2674-2681 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T89 2728-2735 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T90 2955-2962 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T91 3161-3171 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T92 3355-3362 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T93 3625-3632 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T94 3687-3697 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T95 3904-3909 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T96 3915-3930 Body_part denotes plasma membrane http://purl.org/sig/ont/fma/fma63841
T97 3972-3982 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T98 4023-4027 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T8 123-126 Body_part denotes tip http://purl.obolibrary.org/obo/UBERON_2001840
T9 1783-1786 Body_part denotes tip http://purl.obolibrary.org/obo/UBERON_2001840
T10 1921-1924 Body_part denotes tip http://purl.obolibrary.org/obo/UBERON_2001840
T11 2278-2281 Body_part denotes tip http://purl.obolibrary.org/obo/UBERON_2001840
T12 3338-3341 Body_part denotes tip http://purl.obolibrary.org/obo/UBERON_2001840

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T49 40-48 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 183-186 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T52 1700-1708 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 1779-1782 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T55 1790-1798 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T56 1917-1920 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T58 2114-2122 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 2289-2292 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T131 76-77 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 245-247 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T133 245-247 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T134 424-426 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T135 424-426 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T136 524-525 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 596-597 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T138 605-607 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T139 622-624 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T140 702-703 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T141 767-786 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T142 767-786 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T143 962-963 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T144 1090-1091 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T145 1254-1255 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T146 1336-1338 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T147 1358-1360 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T148 1560-1579 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T149 1560-1579 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T150 1647-1649 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T151 1742-1743 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T152 1821-1822 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T153 1934-1935 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T154 2081-2082 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T155 2195-2196 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T156 2198-2199 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T157 2307-2308 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T158 2371-2372 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T159 2467-2468 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T160 2497-2498 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T161 2643-2644 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T162 2929-2930 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T163 2969-2971 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T164 3022-3025 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T165 3047-3048 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T166 3380-3386 http://purl.obolibrary.org/obo/UBERON_0002553 denotes cavity
T167 3530-3531 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T168 3687-3705 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residue
T169 3687-3705 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residue
T170 3737-3739 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T171 3902-3903 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T172 3915-3921 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T173 3922-3930 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T174 3963-3964 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T175 3972-3990 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residue
T176 3972-3990 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residue
T177 4079-4081 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T231 5-8 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T232 9-18 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T233 57-64 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T234 130-137 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T235 211-218 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T236 245-247 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T237 387-390 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T238 424-426 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T239 456-463 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T240 554-558 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T241 605-607 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T242 622-624 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T243 697-699 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T244 767-777 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T245 767-772 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T246 773-777 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T247 1336-1338 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T248 1441-1448 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T249 1560-1570 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T250 1560-1565 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T251 1566-1570 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T252 1717-1724 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T253 1736-1739 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T254 1762-1765 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T255 1807-1814 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T256 1970-1973 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T257 2000-2007 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T258 2181-2188 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T259 2440-2443 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T260 2516-2519 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T261 2616-2619 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T262 2633-2640 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T263 2657-2660 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T264 2674-2681 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T265 2694-2697 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T266 2728-2735 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T267 2805-2808 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T268 2809-2817 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T269 2932-2935 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T270 2955-2962 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T271 2969-2971 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T272 3097-3100 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T273 3161-3171 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T274 3161-3166 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T275 3167-3171 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T276 3215-3218 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T277 3315-3318 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T278 3355-3362 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T279 3409-3417 Chemical denotes Hydrogen http://purl.obolibrary.org/obo/CHEBI_18276
T280 3487-3490 Chemical denotes Gln http://purl.obolibrary.org/obo/CHEBI_30011
T281 3507-3510 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T283 3532-3540 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T284 3568-3571 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T285 3625-3632 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T286 3633-3636 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T287 3647-3650 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T290 3687-3705 Chemical denotes amino acid residue http://purl.obolibrary.org/obo/CHEBI_33708
T291 3687-3697 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T292 3687-3692 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T293 3693-3697 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T294 3716-3718 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T295 3737-3739 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T296 3818-3821 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T299 3863-3876 Chemical denotes sphingomyelin http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583
T301 3881-3892 Chemical denotes cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T302 3904-3909 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T303 3972-3990 Chemical denotes amino acid residue http://purl.obolibrary.org/obo/CHEBI_33708
T304 3972-3982 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T305 3972-3977 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T306 3978-3982 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T16 3647-3650 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T17 3818-3821 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T98 0-148 Sentence denotes When ATM molecules were merged with the SARS-CoV-2 spike protein, there was a very good fit for one particular pose at the tip of protein (Fig. 2 ).
T99 149-300 Sentence denotes All other docking attempts on the NTD or the RBD of the spike protein were unsuccessful (Figure S2) as they did not satisfy the minimum cut-off values.
T100 301-373 Sentence denotes Not surprisingly, their trajectories started destabilizing before 10 ns.
T101 374-508 Sentence denotes In contrast, ATM #1 (coloured in yellow in Figure S2) remained bound to the spike protein throughout the simulation process (Fig. 3 ).
T102 509-701 Sentence denotes Interestingly, a significant movement of the drug was observed from its docked pose to a stable MD pose (dock-to-MD transition), particularly during the first 10-ns of simulations (Figure S3).
T103 702-760 Sentence denotes A stable complex association was then reached after 10 ns.
T104 761-931 Sentence denotes Three amino acid residues, referred to as the “QFN triad”, exhibited significant conformational rearrangement during the binding process: Q-134, F-135 and N-137 (Fig. 3).
T105 932-1139 Sentence denotes The principal moves comprised a significant reorientation of the aromatic ring of F-135, from suboptimal stacking to stabilized T-shape CH-π interaction, and a concomitant retraction of the Q-134 side chain.
T106 1140-1362 Sentence denotes Fluctuations during the 10 to 50 ns period did not affect the overall geometry of the complex, which converged to a mean energy of interaction of 92.4 ± 5.8 kJ.mol−1 as determined from triplicate MD simulations (Table S1).
T107 1363-1547 Sentence denotes Schematically, the binding site is formed by two discontinuous regions of the protein, including the QFN triad with additional C-136, D-138, R-158 and S-161 residues (Fig. 4, Fig. 5 ).
T108 1548-1662 Sentence denotes These seven amino acid residues accounted for almost 90% of the whole energy of interaction (Table S1 and Fig. 5).
T109 1663-1902 Sentence denotes Fig. 2 Molecular complex between the SARS-CoV-2 spike protein trimer and ATM. (a) Detailed view of ATM bound to the NTD tip of SARS-CoV-2 spike protein chain A, shown at two distinct magnifications and orientations (left and right panels).
T110 1903-1995 Sentence denotes Note that the NTD tip displays a complementary landing surface for ATM (highlighted in red).
T111 1996-2248 Sentence denotes The protein stretch 134-138, which contains the QFN triad, is highlighted in green. (b) The trimeric structure of the SARS-CoV-2 spike is represented in surface rendition with subunit (protein chain A, B and C) in cyan, yellow and purple, respectively.
T112 2249-2330 Sentence denotes AMT (in red) is bound to the tip of the NTD domain of the A subunit (left panel).
T113 2331-2452 Sentence denotes The ribbon structure of the cyan (chain A) subunit is shown in the right panel. (c) Above views of the spike-ATM complex.
T114 2453-2548 Sentence denotes Note that the B and C subunits also display a fully accessible ATM binding site (red asterisk).
T115 2549-2693 Sentence denotes Fig. 3 Induced-fit conformational rearrangements during binding of ATM on the spike protein. (a) Docking of ATM on the spike protein (time = 0).
T116 2694-2785 Sentence denotes ATM is in yellow spheres, and the protein segment 134-137 is in balls and sticks rendition.
T117 2786-2844 Sentence denotes Three parts of the ATM molecule are marked with asterisks.
T118 2845-2999 Sentence denotes The orientation of the side chains of residues 134-137 is shown under the complex. (b) ATM bound to the spike protein after MD simulations (time = 50 ns).
T119 3000-3079 Sentence denotes Note that the complex has evolved according to a typical induced-fit mechanism.
T120 3080-3143 Sentence denotes The asterisks on ATM help visualize its conformational changes.
T121 3144-3294 Sentence denotes Reorientation of amino acid side chains is also clearly visible in the ATM-spike complex and in the isolated 134-137 fragment shown under the complex.
T122 3295-3363 Sentence denotes Fig. 4 Schematic of ATM interaction at the tip of the spike protein.
T123 3364-3408 Sentence denotes Residues lining cavity under 3.5Å are shown.
T124 3409-3469 Sentence denotes Hydrogen bonds and CH-π stacking interactions are indicated.
T125 3470-3586 Sentence denotes Note that Q-134 (Gln-134) and S-161 (Ser-161) are linked by a hydrogen bond, which stabilizes the ATM-spike complex.
T126 3587-3661 Sentence denotes Fig. 5 Energy of interaction of spike protein-ATM and spike-GM1 complexes.
T127 3662-3802 Sentence denotes Results are expressed by amino acid residue as mean ± SD of three distinct MD simulations (50 ns) with the same starting docking conditions.
T128 3803-3938 Sentence denotes In the case of GM1, the simulations are done in presence of sphingomyelin and cholesterol to mimic a lipid raft plasma membrane domain.
T129 3939-4028 Sentence denotes Each bar corresponds to a single amino acid residue, as indicated in the horizontal axis.
T130 4029-4082 Sentence denotes Detailed values and statistics are shown in Table S1.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
379 1801-1806 Gene denotes spike Gene:43740568
380 2434-2439 Gene denotes spike Gene:43740568
381 1711-1716 Gene denotes spike Gene:43740568
382 2467-2474 Gene denotes B and C
383 2125-2130 Gene denotes spike Gene:43740568
384 2198-2205 Gene denotes B and C
385 1700-1710 Species denotes SARS-CoV-2 Tax:2697049
386 1790-1800 Species denotes SARS-CoV-2 Tax:2697049
387 2114-2124 Species denotes SARS-CoV-2 Tax:2697049
392 2627-2632 Gene denotes spike Gene:43740568
393 2668-2673 Gene denotes spike Gene:43740568
394 2949-2954 Gene denotes spike Gene:43740568
395 3219-3224 Gene denotes spike Gene:43740568
402 3349-3354 Gene denotes spike Gene:43740568
403 3572-3577 Gene denotes spike Gene:43740568
404 3409-3417 Chemical denotes Hydrogen MESH:D006859
405 3487-3490 Chemical denotes Gln MESH:D005973
406 3507-3510 Chemical denotes Ser MESH:D012694
407 3532-3540 Chemical denotes hydrogen MESH:D006859
414 3619-3624 Gene denotes spike Gene:43740568
415 3641-3646 Gene denotes spike Gene:43740568
416 3818-3821 Chemical denotes GM1 MESH:D005677
417 3863-3876 Chemical denotes sphingomyelin MESH:D013109
418 3881-3892 Chemical denotes cholesterol MESH:D002784
419 3904-3909 Chemical denotes lipid MESH:D008055
427 51-56 Gene denotes spike Gene:43740568
428 205-210 Gene denotes spike Gene:43740568
429 450-455 Gene denotes spike Gene:43740568
430 40-50 Species denotes SARS-CoV-2 Tax:2697049
431 808-811 Chemical denotes QFN
432 916-917 Chemical denotes N MESH:D009584
433 1490-1491 Chemical denotes C MESH:D002244