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PMC:7594251 / 56321-58653 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T83107 347-354 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T98493 491-498 Body_part denotes tubulin http://purl.org/sig/ont/fma/fma67116
T25827 646-661 Body_part denotes protein complex http://purl.org/sig/ont/fma/fma67906
T12583 1047-1054 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T393 225-226 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T394 470-471 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T395 514-515 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T396 637-638 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T397 646-661 http://purl.obolibrary.org/obo/GO_0043234 denotes protein complex
T398 790-791 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T399 1143-1144 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T400 1270-1271 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T401 1299-1300 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T402 1305-1306 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T403 1396-1397 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T404 1402-1403 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T405 1435-1436 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T406 1531-1532 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T407 1537-1538 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T408 1672-1673 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T409 1755-1757 http://purl.obolibrary.org/obo/CLO_0004265 denotes HT
T410 1890-1891 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T411 1997-1999 http://purl.obolibrary.org/obo/CLO_0004265 denotes HT
T412 2046-2048 http://purl.obolibrary.org/obo/CLO_0003622 denotes HB
T413 2053-2054 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T414 2097-2099 http://purl.obolibrary.org/obo/CLO_0003622 denotes HB
T415 2150-2151 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T62744 111-118 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T98062 183-189 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T40790 210-217 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T44712 305-312 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T28626 347-354 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T42404 423-429 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T71241 442-454 Chemical denotes baccatin III http://purl.obolibrary.org/obo/CHEBI_32898
T1136 459-471 Chemical denotes epothilone A http://purl.obolibrary.org/obo/CHEBI_31549
T86674 459-469 Chemical denotes epothilone http://purl.obolibrary.org/obo/CHEBI_60831
T56747 564-570 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T53977 639-645 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T12012 646-653 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T980 827-833 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T94020 1037-1043 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T54355 1047-1054 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T84899 1087-1093 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T31753 1272-1279 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T25990 1291-1298 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T53503 1523-1530 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T61929 1655-1661 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T55944 1665-1671 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T89000 1675-1677 Chemical denotes HA http://purl.obolibrary.org/obo/CHEBI_73924
T2221 1749-1751 Chemical denotes HA http://purl.obolibrary.org/obo/CHEBI_73924
T58953 1883-1889 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T66981 2039-2041 Chemical denotes HA http://purl.obolibrary.org/obo/CHEBI_73924
T75289 2094-2096 Chemical denotes HA http://purl.obolibrary.org/obo/CHEBI_73924
T33419 2303-2309 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
631 1599-1603 Gene denotes spin Gene:10927
632 442-454 Chemical denotes baccatin III MESH:C073950
633 459-471 Chemical denotes epothilone A MESH:C093787

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T16144 320-328 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange
T55554 1009-1017 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange
T99470 1442-1450 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T390 0-218 Sentence denotes The INPHARMA method (see Figure 10) was designed to determine the relative orientation between two competitive ligands in the receptor-binding pocket through the observation of inter-ligand NOE between the two ligands.
T391 219-355 Sentence denotes It is a tr-NOE in nature as it is mediated by the bound conformation of the competing ligands and in exchange with the receptor protein.
T392 356-531 Sentence denotes The first example was competitive binding and observation of inter-ligand NOE between baccatin III and epothilone A in the presence of tubulin, which acts as a receptor [284].
T393 532-607 Sentence denotes Since the observation is on the ligand site, it provides unique advantages.
T394 608-699 Sentence denotes The detailed conformation of a ligand-protein complex can be addressed by conventional NMR.
T395 700-808 Sentence denotes However, it is time-consuming and demands full solving of the structure and there is also a size limitation.
T396 809-864 Sentence denotes From that aspect, ligand-based methods are more useful.
T397 865-1061 Sentence denotes The only limiting fact is that it should fulfill all the conditions of tr-NOE explained previously in terms of dissociation constant (Kd), fast exchange regime, and proper ligand to protein ratio.
T398 1062-1169 Sentence denotes Then, information on the ligand structure can be derived from tr-NOE build up as a function of mixing time.
T399 1170-1247 Sentence denotes This can be readily explained using the originally proposed schematics [284].
T400 1248-1362 Sentence denotes The NOESY spectrum of a mixture of the two ligands A and B in the presence of the common receptor (T) is recorded.
T401 1363-1614 Sentence denotes Under the situation that each of A and B exhibit competitive binding in a fast exchange regime with the receptor T, intermolecular tr-NOE peaks between the two ligands A and B can then be observed in the NOESY spectrum due to extensive spin diffusion.
T402 1615-1758 Sentence denotes During the NOESY mixing time, the first proton of ligand A (HA) binds to receptor T, which results in transfers of magnetization from HA to HT.
T403 1759-1943 Sentence denotes Subsequently, the complex AT dissociates as they fulfill the dissociation constant range, which creates the opportunity for ligand B to bind to the receptor T at the same binding site.
T404 1944-2049 Sentence denotes This results in the transfer of the magnetization of HT, which had been originally coming from HA, to HB.
T405 2050-2195 Sentence denotes As a result, an inter-molecular correlation HA–HB can be seen, and this inter-molecular NOE will be a function of mixing time as described above.
T406 2196-2332 Sentence denotes The detailed analysis of such intermolecular NOE peaks helps in assessing the relative orientation of each ligand in the binding pocket.