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PMC:7594251 / 56268-58653 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T83107 400-407 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T98493 544-551 Body_part denotes tubulin http://purl.org/sig/ont/fma/fma67116
T25827 699-714 Body_part denotes protein complex http://purl.org/sig/ont/fma/fma67906
T12583 1100-1107 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T393 278-279 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T394 523-524 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T395 567-568 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T396 690-691 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T397 699-714 http://purl.obolibrary.org/obo/GO_0043234 denotes protein complex
T398 843-844 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T399 1196-1197 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T400 1323-1324 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T401 1352-1353 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T402 1358-1359 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T403 1449-1450 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T404 1455-1456 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T405 1488-1489 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T406 1584-1585 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T407 1590-1591 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T408 1725-1726 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T409 1808-1810 http://purl.obolibrary.org/obo/CLO_0004265 denotes HT
T410 1943-1944 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T411 2050-2052 http://purl.obolibrary.org/obo/CLO_0004265 denotes HT
T412 2099-2101 http://purl.obolibrary.org/obo/CLO_0003622 denotes HB
T413 2106-2107 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T414 2150-2152 http://purl.obolibrary.org/obo/CLO_0003622 denotes HB
T415 2203-2204 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T62744 164-171 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T98062 236-242 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T40790 263-270 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T44712 358-365 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T28626 400-407 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T42404 476-482 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T71241 495-507 Chemical denotes baccatin III http://purl.obolibrary.org/obo/CHEBI_32898
T1136 512-524 Chemical denotes epothilone A http://purl.obolibrary.org/obo/CHEBI_31549
T86674 512-522 Chemical denotes epothilone http://purl.obolibrary.org/obo/CHEBI_60831
T56747 617-623 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T53977 692-698 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T12012 699-706 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T980 880-886 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T94020 1090-1096 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T54355 1100-1107 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T84899 1140-1146 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T31753 1325-1332 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T25990 1344-1351 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T53503 1576-1583 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T61929 1708-1714 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T55944 1718-1724 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T89000 1728-1730 Chemical denotes HA http://purl.obolibrary.org/obo/CHEBI_73924
T2221 1802-1804 Chemical denotes HA http://purl.obolibrary.org/obo/CHEBI_73924
T58953 1936-1942 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T66981 2092-2094 Chemical denotes HA http://purl.obolibrary.org/obo/CHEBI_73924
T75289 2147-2149 Chemical denotes HA http://purl.obolibrary.org/obo/CHEBI_73924
T33419 2356-2362 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
631 1652-1656 Gene denotes spin Gene:10927
632 495-507 Chemical denotes baccatin III MESH:C073950
633 512-524 Chemical denotes epothilone A MESH:C093787

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T16144 373-381 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange
T55554 1062-1070 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange
T99470 1495-1503 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T388 0-6 Sentence denotes 3.1.5.
T389 7-52 Sentence denotes The INPHARMA Method for Pharmacophore Mapping
T390 53-271 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 272-408 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 409-584 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 585-660 Sentence denotes Since the observation is on the ligand site, it provides unique advantages.
T394 661-752 Sentence denotes The detailed conformation of a ligand-protein complex can be addressed by conventional NMR.
T395 753-861 Sentence denotes However, it is time-consuming and demands full solving of the structure and there is also a size limitation.
T396 862-917 Sentence denotes From that aspect, ligand-based methods are more useful.
T397 918-1114 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 1115-1222 Sentence denotes Then, information on the ligand structure can be derived from tr-NOE build up as a function of mixing time.
T399 1223-1300 Sentence denotes This can be readily explained using the originally proposed schematics [284].
T400 1301-1415 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 1416-1667 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 1668-1811 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 1812-1996 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 1997-2102 Sentence denotes This results in the transfer of the magnetization of HT, which had been originally coming from HA, to HB.
T405 2103-2248 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 2249-2385 Sentence denotes The detailed analysis of such intermolecular NOE peaks helps in assessing the relative orientation of each ligand in the binding pocket.