Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 688
Aptamer sequence: CUGGACGACGGGGACGCCACUGGACUAGGUAAGCCAGGACCGUACGUCGGGAGCCGUCAGAAUA
Target unique ID: 6305
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_645 Trp70-727 Molecule Tryptophan 13 nM 50 mM HEPES (pH 7.0), 250 mM NaCl, 5 mM MgCl2, 5 mM CaCl2, 5 mM glycine 16186130
Structure information of aptamer
Aptamer Sequence: CUGGACGACGGGGACGCCACUGGACUAGGUAAGCCAGGACCGUACGUCGGGAGCCGUCAGAAUA
The optimal secondary structure in dot-bracket notation: ((.((((((((........((((.((.....))))))..)))).)))).)).............
The centroid secondary structure in dot-bracket notation: ((.((((((((........((((.((.....))))))..)))).)))).)).............
The MFE structure
The Centroid structure
The mountain plot representation
Aptamer information
Type Detail Type Detail
Aptamer ID Apta_645 Description Trp70-727
Aptamer chemistry RNA Length 64 nt
GC content 62.5% Molecular weight 20,782.47 Da
Molarity of 1 μg/μl solution 48.12 μM Number of G-quadruplexes 2
G-Score 18 Function Targeted binding
Sequence CUGGACGACGGGGACGCCACUGGACUAGGUAAGCCAGGACCGUACGUCGGGAGCCGUCAGAAUA
Applications Binding to L-tryptophan
Target information
Type Detail Type Detail
PubChem ID 6305 Molecular name Tryptophan
Molecular formula C11H12N2O2 Molecular weight 204.22
IUPAC name (2S)-2-amino-3-(1H-indol-3-yl)propanoic acid InChIKey QIVBCDIJIAJPQS-VIFPVBQESA-N
LogP 1.122 Topological polar surface area 79.11
Hydrogen bond acceptor 2 Hydrogen bond donor 3

Synonym(s):
L-tryptophan; tryptophan; 73-22-3; L-Tryptophane; h-Trp-oh; (S)-Tryptophan; Tryptophane; Optimax; trofan; tryptacin; Ardeytropin; (2S)-2-amino-3-(1H-indol-3-yl)propanoic acid; Pacitron; Indole-3-alanine; Kalma; L-beta-3-Indolylalanine; L-Tryptofan; L-Trp; L-(-)-Tryptophan; 3-Indol-3-ylalanine; Tryptan; Lyphan; Tryptophan (VAN); 1-beta-3-Indolylalanine; Tryptophan (H-3); Triptofano [Spanish]; Tryptophanum [Latin]; 1H-Indole-3-alanine; 1beta-3-Indolylalanine; 2-Amino-3-indolylpropanoic acid; L(-)-Tryptophan; triptofano; Tryptophanum; (S)-alpha-Amino-1H-indole-3-propanoic acid; Tryptophane [French]; Tryptophan, L-; (L)-TRYPTOPHAN; (-)-Tryptophan; alpha'-Amino-3-indolepropionic acid; Tryptophan [USAN:INN]; L-alpha-amino-3-indolepropionic acid; L-alpha-Aminoindole-3-propionic acid; Sedanoct; (S)-alpha-Aminoindole-3-propionic acid; 1H-Indole-3-alanine (VAN); EH 121; trp; Alanine, 3-indol-3-yl-; (S)-2-Amino-3-(3-indolyl)propionic acid; CCRIS 617; L-Alanine, 3-(1H-indol-3-yl)-; 1H-Indole-3-alanine, (S)-; alpha-Amino-3-indolepropionic acid, L-; HSDB 4142; (S)-alpha-amino-beta-(3-indolyl)-propionic acid; NCI-C01729; AI3-18478; UNII-8DUH1N11BX; Indole-3-propionic acid, alpha-amino-; 1H-Indole-3-propanoic acid, alpha-amino-, (S)-; Propionic acid, 2-amino-3-indol-3-yl-; CHEBI:16828; Lopac-T-0254; MFCD00064340; 8DUH1N11BX; (S)-alpha-Amino-beta-indolepropionic acid; CHEMBL54976; (S)-2-Amino-3-(1H-indol-3-yl)propanoic acid; DSSTox_CID_1419; DSSTox_RID_76152; DSSTox_GSID_21419; l-b-3-Indolylalanine; D-Trp-OH; CAS-73-22-3; Propionic acid, 2-amino-3-indol-3-yl; L-Tryptophan (9CI); Tryptophan (USP/INN); (S)-a-Amino-b-indolepropionic acid; (S)-a-Aminoindole-3-propionic acid; Alanine, 3-indol-3-yl; EINECS 200-795-6; NSC 13119; (2S)-2-amino-3-(1H-indol-3-yl)propanoate; trytophan; (S)-a-Amino-1H-indole-3-propanoic acid; TRP-01; 2-amino-3-indol-3-ylpropanoic acid; L-Trytophan; NSC-13119; 1qaw; L-Tryptophan,(S); L-Trp-OH; 2a4m; H-L-Trp-OH; L-Tryptophan (JP17); S(-)-1-alpha-Aminoindole-3-propionic acid; Tryptophan (L-Tryptophan); Tryptophan, L- (8CI); bmse000050; bmse000868; bmse001017; Epitope ID:136043; EC 200-795-6; T 0254; SCHEMBL7328; 2-Amino-3-indolylpropanoate; (S)-(-)-2-Amino-3-(3-indolyl)propionic Acid; (S)-1H-Indole-3-alanine; Lopac0_001183; GTPL717; MLS001056750; DivK1c_000457; (s)-a-amino-b-indolepropionate; 151A3008-4CFE-40C9-AC0B-467EF0CB50EA; DTXSID5021419; (S)-a-Aminoindole-3-propionate; BDBM21974; HMS501G19; KBio1_000457; ZINC83315; 3-(1H-indol-3-yl)-L-Alanine; L-a-Amino-3-indolepropionic acid; NINDS_000457; alpha-Aminoindole-3-propionic acid; HMS3263N07; Pharmakon1600-01500600; ACT08662; HY-N0623; L-Tryptophan, Cell Culture Reagent; STR02722; (S)-alpha-Aminoindole-3-propionate; Tox21_201246; Tox21_300359; Tox21_501183; HTS001390; NSC757373; s3987; (s)-alpha-amino-beta-indolepropionate; L-Tryptophan, Vetec(TM), 98.5%; (S)-a-Amino-1H-indole-3-propanoate; AKOS015854052; Indoe-3-propionic acid, alpha-amino-; 2-Chloro-5-(methylsulfonyl)benzoicacid; AM82273; CCG-205257; CS-W020011; DB00150; LP01183; MCULE-8004234494; NSC-757373; SDCCGSBI-0051150.P002; IDI1_000457; NCGC00015994-01; NCGC00094437-01; NCGC00094437-02; NCGC00094437-03; NCGC00094437-04; NCGC00094437-08; NCGC00254424-01; NCGC00258798-01; NCGC00261868-01; (S)-alpha-Amino-1H-indole-3-propanoate; AC-17050; BP-13286; SMR000326686; TS-04426; DB-029986; L-Tryptophan, BioUltra, >=99.5% (NT); A7403; EU-0101183; T0541; (S)-Tryptophan 1H-Indole-3-alanine, (S)-; 73T223; C00078; D00020; L-Tryptophan, reagent grade, >=98% (HPLC); M02943; P16427; AB00373874_05; L-Tryptophan, Vetec(TM) reagent grade, >=98%; (S)-2-amino-3-(1H-Indol-3-yl)-propionic acid; A837752; Q181003; SR-01000075590; 4-(3-METHOXYANILINO)-4-OXOBUT-2-ENOICACID; SR-01000075590-1; F0001-2364; Z1245635763; L-Tryptophan, certified reference material, TraceCERT(R); Tryptophan, European Pharmacopoeia (EP) Reference Standard; UNII-0O72R8RF8A component QIVBCDIJIAJPQS-VIFPVBQESA-N; UNII-N7U7BXP2OI component QIVBCDIJIAJPQS-VIFPVBQESA-N; UNII-X9U7434L7A component QIVBCDIJIAJPQS-VIFPVBQESA-N; L-Tryptophan, United States Pharmacopeia (USP) Reference Standard; 80206-30-0; L-Tryptophan, from non-animal source, meets EP, JP, USP testing specifications, suitable for cell culture, 99.0-101.0%; L-Tryptophan, PharmaGrade, Ajinomoto, EP, JP, USP, Manufactured under appropriate GMP controls for pharma or biopharmaceutical production, suitable for cell culture

Activity data
Interaction ID 688
Target type Molecule
Target unique ID 6305
Activity 13 nM
Binding Conditions/Buffer

50 mM HEPES (pH 7.0), 250 mM NaCl, 5 mM MgCl2, 5 mM CaCl2, 5 mM glycine
Assay

Affinity chromatography and specificity of tryptophan aptamers
PubMed ID 16186130
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1068 DNA CGGGACAAGACAACGAACGAACAGGAAGAGAACCGGAATGCAGACGTCAGGG 56.25%
Apta_312 RNA GGGAAAAGAGACGGCCGGCGCCAUAGCCGAGAUCCGAGGUGUUGCCGAGAA 54.69%
Apta_305 RNA GGGAGGACGAUGCGGAUCGCCCUGAACCGGCCCAGCAGACUGCUGACGGCACGAUCCGCAUCGUCCUCCC 54.29%
Apta_271 RNA CUGUCGAGCAUGCUCAGGGUAACGUAUAGUCAAGACACCUCAAGUGUAACU 53.12%
Apta_1143 RNA ACGAGUUGUCGCAUGUGCGGUUCAGUCUGGUCCUUCAGCACCGUACAACAA 53.12%
Apta_499 RNA GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC 53.09%
Apta_1057 RNA UCUGAGGGGUUGGGGCCGCAGUCUCGUCGCCAUGGCUAACGAGGCCGGAACUAGUUUUAGCCGAAAUGAUCGAUGC 52.63%
Apta_396 RNA GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA 52.50%
Apta_397 RNA GGGAGGACGAUGCGGAUACCAGGAUCACAUCCUGAGGAACCCCGGCUCCCAACCUCAGACGACUCGCUGAGGAUCCGAGA 52.50%
Apta_415 RNA GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA 52.50%
Apta_416 RNA GGACCUCGGCGAAAGCCGGUAACGCCACAAGUCGGAGGGUAAGAUCUGACAGGAACUGGGUGACGGAGGUUAGGUGC 51.95%
Apta_353 RNA GAAUUCCGCGUGUGCCAGCGAAAGUUGCGUAUGGGUCACAUCGCAGGCACAUGUCAUCUGGGCGGUCCGUUCGGGAUCC 51.90%
Apta_399 RNA GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA 51.90%
Apta_276 RNA GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC 51.76%
Apta_129 RNA GGGAGGACGAUGCGGACACCGUUAAUCUGAGGCCCUGUCCUAUUCCUUCACGCCUCAGA 51.56%
Apta_155 RNA GACCCAGGGCCGGGACGCAAAGCAGCCAAAACAGACGGCCCCAGUCAGGGAGUU 51.56%
Apta_394 RNA GGGCGAAUUCAACUGCCAUCUAGGCAGUAACCAGGAGUUAGUAGGACAAGUUUCGUCC 51.56%
Apta_856 RNA UGGGCCGGAGGUUAGCUUGCCCAUGGCAAGCAGGGCGCCACGGACCCA 51.56%
Apta_413 RNA GUGAGACCAGCCGAGUGGUGUCUGGCUAUUCACUGGAGCGUGGGUGGAACCCCUGCGCACUCGUUUGGCUGUCCGGGCCUUCGGGCCGGGAUUAUCUCU 51.52%
Apta_414 RNA GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA 51.25%

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AptaDB is an online database we developed to integrate comprehensive information about aptamer.
The detail of this database is described here:

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