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PMC:7605337 / 49730-51701 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T68 969-976 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749
T69 1097-1104 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749
T70 1750-1757 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T71 1758-1765 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T334 188-197 Disease denotes nCOV-2019 http://purl.obolibrary.org/obo/MONDO_0100096
T335 791-795 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T292 84-87 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T293 150-152 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T294 481-482 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T295 1122-1123 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T296 1397-1402 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T297 1673-1674 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T298 1719-1720 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T26248 476-478 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T24077 969-976 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449
T53963 1097-1104 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449
T36380 1176-1178 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T17190 1475-1482 Chemical denotes solvent http://purl.obolibrary.org/obo/CHEBI_46787
T95994 1750-1757 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T7 1758-1765 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T337 0-206 Sentence denotes The total binding energy calculation of all the variants showed that mutation Y489A has the highest binding affinity among all systems which is about 11 kcal/mol stronger than that of the nCOV-2019 complex.
T338 207-305 Sentence denotes This residue is located in β6, which is part of the recognition region of RBD for binding to ACE2.
T339 306-480 Sentence denotes Removal of this bulky hydrophobic residue at the interface with ACE2 caused the extended loop to move closer to the ACE2 interface and make more H-bonds with ACE2 (Table S3).
T340 481-608 Sentence denotes A high electrostatic interaction energy is the reason for the higher binding energy of mutant Y489A than the wild-type complex.
T341 609-800 Sentence denotes It is interesting to note that among the five residues L455, F456, Y473, A475, and Y489 that make hydrophobic interactions with ACE2, Y489 is the only residue that is conserved from SARS-COV.
T342 801-962 Sentence denotes However, the experimental binding affinity measurements using deep mutational scanning showed that mutations at this position lower the binding affinity to ACE2.
T343 963-1044 Sentence denotes Other alanine substitutions that increase the binding energy are G446A and G447A.
T344 1045-1179 Sentence denotes Residues G446 and G447 reside in L1 and mutation to alanine can make L1 take a more rigid form as shown in the RMSF plot in Figure S3.
T345 1180-1513 Sentence denotes However, experiment showed that these mutations have similar or lower binding affinities to ACE2 than the wild-type RBD and care must be taken when interpreting these results.25 This discrepancy could be due to force-field inaccuracy and the deficiencies in the PBSA method for the treatment of solvent in binding energy calculation.
T346 1514-1623 Sentence denotes Further studies are needed to investigate whether these mutations will increase the binding affinity to ACE2.
T347 1624-1971 Sentence denotes Deep mutational scanning using flow cytometry is a qualitative method to measure the impact of a large number of mutations of protein–protein interactions and further experiments such as SPR or isothermal titration calorimetry which are conventional methods for measuring binding affinities needed to study the effect of these mutations in detail.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1292 300-304 Gene denotes ACE2 Gene:59272
1293 370-374 Gene denotes ACE2 Gene:59272
1294 422-426 Gene denotes ACE2 Gene:59272
1295 464-468 Gene denotes ACE2 Gene:59272
1296 737-741 Gene denotes ACE2 Gene:59272
1297 957-961 Gene denotes ACE2 Gene:59272
1298 1272-1276 Gene denotes ACE2 Gene:59272
1299 1618-1622 Gene denotes ACE2 Gene:59272
1300 234-236 Gene denotes β6 Gene:28873
1301 188-192 Species denotes nCOV Tax:2697049
1302 791-799 Species denotes SARS-COV Tax:694009
1303 664-668 Chemical denotes L455
1304 670-674 Chemical denotes F456
1305 676-680 Chemical denotes Y473
1306 682-686 Chemical denotes A475
1307 692-696 Chemical denotes Y489
1308 743-747 Chemical denotes Y489
1309 969-976 Chemical denotes alanine MESH:D000409
1310 1097-1104 Chemical denotes alanine MESH:D000409
1311 1442-1446 Chemical denotes PBSA MESH:C437084