Table 1.
Top 10 RNA secondary motifs and chemicals predicted by the RNALigands database.
| Name | Sequence, secondary structure | Binding sites | Motif | PDB (score) | Chemical |
|---|---|---|---|---|---|
| 1 |
AUUAAAGGUUUAUACCUUCCCAGGUAACAAACCAACCAACUUUCGAUCUCUUGUAGAUCUGUUCUCUAAACGAACUUUAAAAUCUGUGUGGCUGUCACUCGGCUG ……(((((.(((((….))))).)))))……….(((((….))))).((((…….))))………….(((((….))))). (− 19.50) |
5′UTR | I: (U, A) A (U, A) AC, H: (G, C) UCACU | FMN(106), B1Z(49) | Riboflavin 5'-monophosphate sodium salt hydrate |
| 2 |
AUGCUUAGUGCACUCACGCAGUAUAAUUAAUAACUAAUUACUGUCGUUGACAGGACACGAGUAACUCGUCUAUCUUCUGCAGGCUGCUUACGGUUUCGUCCGUGUUGCAGCCGAUCAUCAGCACAUCUAGGUUU .(((((((((….((((((((……………))))).)))((.(((((.(((((…)))))….)))))))((((((.(((((……))))).))))))…….))))…))))). (− 38.30) |
5′UTR | B: (G, C) U (C, G), B: (G, C) A (C, G), H: (G, C) UAA, I: (U, A) CUAUC (U, A) C, I: (C, G) U (U, G) UU, H: (G, C) UUUCGU, B: (C, G) AUC (U, A), M: (C, G) ACUC (A, U) (U, A) (G, C) GAUCAUCA | GLY(86), TOA(92), 4PQ(23), SAH(39), SAM(32), HPA(99), C2E(38), SAM(54) |
3-Ammonio-3-deoxy-alpha-D-glucopyranose S-Adenosyl-l-homocysteine Hypoxanthine 5-Hydroxy-l-tryptophan |
| 3 |
GUCCGGGUGUGACCGAAAGGUAA …(((……)))……. (− 4.30) |
5′UTR | H: (G, C) GUGUGA | ARG(25) | |
| 4 |
CGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUAUACAGGGC .((((((((.((….))))))))))(((((((((((………))).))))))))……. (− 24.00) |
FSE | B: (G, C) U (G, U), B: (G, C) A (U, A) | LYS(48), TOA(58) | Kanosamine hydrochloride |
| 5 |
UGUGCAGAAUGAAUU …………… (0.00) |
FSE | – | – | |
| 6 |
UCGUAACUACAUAGCACAAGUA …………………. (0.00) |
FSE | – | – | |
| 7 |
CAAUCUUUAAUCAGUGUGUAA ………………… (0.00) |
3′UTR | – | – | |
| 8 |
AUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGA ….((.((.(((….))))).))…………. (− 5.60) |
3′UTR | I: (G, C) GA (G, C) A, B: (G, C) A (C, G), H: (U, G) GAAA | GES(60), TOA(92), AMZ(60) | 3-Ammonio-3-deoxy-alpha-D-glucopyranose |
| 9 |
AGUGUACAGUGAACAAUGCUAGG …………………. (0.00) |
3′UTR | – | – | |
| 10 |
AGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA .((((((.(((((((…(((.(((.((………….)).))).)))….)))))))…….))))))………………………………………. (− 12.10) |
3′UTR | I: (C, G) C (C, G) U, I: (A, U) A (U, A) G | GES(71), HPA(89) | Hypoxanthine |
FMN, FLAVIN MONONUCLEOTIDE; B1Z, adenosylcobalamin; GLY, GLYCINE; TOA, 3-ammonio-3-deoxy-alpha-D-glucopyranose; 4PQ, 5-hydroxy-L-tryptophan; SAH, S-ADENOSYL HOMOCYSTEINE; SAM, S-ADENOSYL METHIONINE; HPA, HYPOXANTHINE; C2E, 9,9′-[(2R,3R,3aS,5 S,7aR,9R,10R,10aS,12 S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2 H,7 H-difuro[3,2-d:3′,2′j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6 H-purin-6-one); ARG, ARGININE; LYS, LYSINE; GES, 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranose; AMZ, AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE. The compounds highlighted in bold represent candidates selected based on our screening criteria.