Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 623
Aptamer sequence: GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG
Target unique ID: 30323
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_589 10.1 Molecule Daunorubicin 20 nM 20 mM Tris-HCl (pH 7.4), 140 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2, and 0.05% v/v Tween-20 25248985
Structure information of aptamer
Aptamer Sequence: GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG
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_589 Description 10.1
Aptamer chemistry DNA Length 80 nt
GC content 58.8% Molecular weight 25,063.98 Da
Molarity of 1 μg/μl solution 39.90 μM Number of G-quadruplexes 3
G-Score 63 Function Target recognition
Sequence GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG
Applications Recognition and targeting therapy of gastric cancer
Target information
Type Detail Type Detail
PubChem ID 30323 Molecular name Daunorubicin
Molecular formula C27H29NO10 Molecular weight 527.5
IUPAC name (7S,9S)-9-acetyl-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy-6,9,11-trihydroxy-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione InChIKey STQGQHZAVUOBTE-VGBVRHCVSA-N
LogP 1.029 Topological polar surface area 185.84
Hydrogen bond acceptor 11 Hydrogen bond donor 5

Synonym(s):
daunorubicin; Daunomycin; 20830-81-3; Cerubidine; Acetyladriamycin; Leukaemomycin C; Rubidomycin; (+)-Daunomycin; DaunoXome; Daunorubicinum; Daunorubicine; Rubomycin C; RP 13057; C27H29NO10; NSC-82151; Daunarubicinum; Daunorrubicina; DaunoXome (TN); Daunamycin; FI 6339; UNII-ZS7284E0ZP; ZS7284E0ZP; (7S,9S)-9-acetyl-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy-6,9,11-trihydroxy-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione; (8S-cis)-8-Acetyl-10-((3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyrannosyl)oxy)-7,8,9,10-tetrahydro-6,8,11-trihydroxy-1-methoxy-5,12-napthacenedione; CHEBI:41977; FI6339; FI-6339; NCGC00024246-05; Anthracyline; NDC-0082-4155; DSSTox_CID_2883; DSSTox_RID_76773; DSSTox_GSID_22883; 5,12-Naphthacenedione,8-acetyl-10-[(3-amino-2,3,6-trideoxy-a-L-lyxo-hexopyranosyl)oxy]-7,8,9,10-tetrahydro-6,8,11-trihydroxy-1-methoxy-, (8S,10S)-; RP-13057; Daunorubicinum [INN-Latin]; MLS000069508; Daunorubicin [INN:BAN]; RCRA waste no. U059; (1S,3S)-3-acetyl-3,5,12-trihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside; CAS-20830-81-3; Daunorubicin (INN); NSC82151; SMR000058559; NDC 0082-4155; CCRIS 914; SR-01000000033; SR-05000001600; NSC-83142; HSDB 5095; NCI-C04693; EINECS 244-069-7; NSC 83142; VS-103; BRN 1445583; Tocris-1467; Daunorubicin(Daunomycin); AI3-52942; (7S,9S)-9-acetyl-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy-6,9,11-trihydroxy-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione;hydrochloride; Prestwick3_000487; CHEMBL178; SCHEMBL3041; BSPBio_000353; 5,12-Naphthacenedione, 8-acetyl-10-((3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranosyl)oxy)-7,8,9,10-tetrahydro-6,8,11-trihydroxy-1-methoxy-, (8S-cis)-; cid_62770; BPBio1_000389; GTPL7063; DTXSID7022883; BDBM32017; Valrubicin impurity, daunorubicin; HMS2089H04; HMS2091K06; Pharmakon1600-01500223; ZINC3917708; Tox21_110896; BDBM50368352; GR-318; HY-13062A; LMPK13050002; MFCD00866340; NSC756717; Tox21_110896_1; CCG-212559; CS-2004; DB00694; NSC-756717; NCGC00024246-06; NCGC00024246-07; NCGC00024246-09; NCGC00024246-10; NCGC00024246-15; NCGC00024246-18; NCGC00025173-01; (1S,3S)-3-acetyl-3,5,12-trihydroxy-10-(methyloxy)-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside; (1S,3S)-3-acetyl-3,5,12-trihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-a-L-lyxo-hexopyranoside; (7S,9R)-9-Acetyl-7-[(2S,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-oxan-2-yl]oxy-6,9,11-trihydroxy-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione; (7S,9S)-9-acetyl-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-tetrahydropyran-2-yl]oxy-6,9,11-trihydroxy-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione; 5,12-Naphthacenedione, 8-acetyl-10-((3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranosyl)oxy)-7,8,9,10-tetrahydro-6,8,11-trihydroxy-1-methoxy-, (8S,10S)-; SBI-0206677.P002; AB00514669; 30D813; C01907; D07776; Epirubicin hydrochloride impurity, daunorubicin-; 15159-EP2270008A1; 15159-EP2272827A1; 15159-EP2277565A2; 15159-EP2277566A2; 15159-EP2277567A1; 15159-EP2277568A2; 15159-EP2277569A2; 15159-EP2277570A2; 15159-EP2289892A1; 15159-EP2292280A1; 15159-EP2292617A1; 15159-EP2295416A2; 15159-EP2295426A1; 15159-EP2295427A1; 15159-EP2298748A2; 15159-EP2298778A1; 15159-EP2301928A1; 15159-EP2305642A2; 15159-EP2305679A1; 15159-EP2308833A2; 15159-EP2308861A1; 15159-EP2311808A1; 15159-EP2311829A1; 15159-EP2311842A2; 15159-EP2316832A1; 15159-EP2316833A1; 16803-EP2272832A1; 16803-EP2277565A2; 16803-EP2277566A2; 16803-EP2277567A1; 16803-EP2277568A2; 16803-EP2277569A2; 16803-EP2277570A2; 16803-EP2280012A2; 16803-EP2281815A1; 16803-EP2286812A1; 16803-EP2292280A1; 16803-EP2292615A1; 16803-EP2298768A1; 16803-EP2301928A1; 16803-EP2301933A1; 16803-EP2305640A2; 16803-EP2305671A1; 16803-EP2311825A1; 16803-EP2311827A1; 16803-EP2311840A1; 16803-EP2316937A1; AB00514669-09; AB01644616_09; AB01644616_10; A814957; Q411659; SR-01000000033-4; SR-05000001600-1; SR-05000001600-2; BRD-K43389675-001-01-3; BRD-K43389675-003-02-7; BRD-K43389675-003-03-5; BRD-K43389675-003-20-9; 2-HYDROXY-5-(4-NITRO-PHENYLSULFAMOYL)-BENZOICACID; (7S,9S)-7-[(2R,4S,5S,6S)-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-9-ethanoyl-4-methoxy-6,9,11-tris(oxidanyl)-8,10-dihydro-7H-tetracene-5,12-dione;hydrochloride; (7S,9S)-9-acetyl-7-(4-amino-5-hydroxy-6-methyl-tetrahydropyran-2-yl)oxy-6,9,11-trihydroxy-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione chloride; (7S,9S)-9-acetyl-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-tetrahydropyran-2-yl]oxy-6,9,11-trihydroxy-4-methoxy-8,10-dihydro-7H-tetracene-5,12-quinone;hydrochloride; (7S,9S)-9-acetyl-7-[[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-2-oxanyl]oxy]-6,9,11-trihydroxy-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione;hydrochloride; (8S,10S)-8-acetyl-10-(((2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl)oxy)-6,8,11-trihydroxy-1-methoxy-7,8,9,10-tetrahydrotetracene-5,12-dione; (8S,10S)-8-acetyl-10-{[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-6,8,11-trihydroxy-1-methoxy-5,7,8,9,10,12-hexahydrotetracene-5,12-dione; (8S-cis)-8-Acetyl-10-[(3-amino-2,3,6-trideoxy-.alpha.-L-lyxo-hexopyranosyl)oxy]-7,8,9,10-tetrahydro--6,8,11-trihydroxy-1-methoxy-5,12-naphthacenedione

Activity data

No relevant experimental diagram

 Interaction ID 623
Target type Molecule
Target unique ID 30323
Activity 20 nM
Binding Conditions/Buffer

20 mM Tris-HCl (pH 7.4), 140 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2, and 0.05% v/v Tween-20
Assay

N/A
PubMed ID 25248985

No relevant experimental diagram

 Interaction ID 1211
Target type Molecule
Target unique ID 30323
Activity 20 nM
Binding Conditions/Buffer

2 M MgCl2 and 0.5 M NaCl
Assay

N/A
PubMed ID 17931589
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_589 DNA GGGAATTCGAGCTCGGTACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCTAGCTGCAGGCATGCAAGCTTGG
100.00%
Apta_68 DNA AGATGCCTGTCGAGCATGCTGTGAATAGGTAGGGTCGGATGGGCTACGGTGTAGCTAAACTGCTTTGTCGACGGG 58.75%
Apta_1119 DNA GGGAATGGATCCACATCTACGAATTCGGTTGTGAAGATTGGGAGCGTCGTGGCTACTTCACTGCAGACTTGACGAAGCTT 57.50%
Apta_951 DNA CACCTAATACGACTCACTATAGCGGATCCGAGGGGGTAGCGGGTGGGCCGGTGGATGCGGGGCGCCGGCGCCTGGCTCGAACAAGCTTGC 56.67%
Apta_773 DNA GAATTCAGTCGGACAGCGGTGGTGCTTGTGTATGGGGGTGGTTGGTGGGTTTTATGCTGCTGGATGGACGAATATCGTCTCCC 56.63%
Apta_769 DNA GAATTCAGTCGGACAGCGAGTTGTTGTTAGGGTGTTGGGTTGGGGTTTTAGGGTCCCTGTCGTCGATGGACGAATATCGTCTCCC 56.47%
Apta_1131 DNA GCCGAGATTGCACTTACTATCTCAAGAAGGGTAGTAAGAGGAGTGGGTGATTATGGGTAAGTTGTATGAGGTAATTGAATAAGCTGGTATGCGC 56.38%
Apta_67 DNA AGATGCCTGTCGAGCATGCTGTTGTGGTAGGGTTAGGGATGGTAGCGGTTGTAGCTAAACTGCTTTGTCGACGGG 56.25%
Apta_759 DNA GAGGCATACCAGCTTATTATTGGGGCCGGGGCAAGGGGGGGGTACCGTGGTAGGACAGATAGTAAGTGCAATCTGCGAA 56.25%
Apta_891 DNA GGAGACCGTACCATCTGTTCGTGGAAGCGCTTTGCTCGTCCATTAGCCTTGTGCTCGTGC 56.25%
Apta_1118 DNA GGGAATGGATCCACATCTACGAATTCATCAGGGCTAAAGAGTGCAGAGTTACTTAGTTCACTGCAGACTTGACGAAGCTT 56.25%
Apta_950 DNA CACCTAATACGACTCACTATAGCGGATCCGAAGGGGGCGCGAGGTGTAAGGGTGTGGGGTGGTGGGTGGGCCTGGCTCGAACAAGCTTGC 55.56%
Apta_1133 DNA GCCGAGATTGCACTTACTATCTAAAGAAGAGTAGTAAGAGGCGTGGGTGATTATGGGTAAGTTGTATGAGGTAATTGAATAAGCTGGTATGCGC 55.32%
Apta_1137 DNA GCCGAGATTGCACTTACTATCTCAAGAAGAGTAGTAAGAGGAGTGGGTGGTTATGAGTAAGTTGTATGTGGTAATTGAATAAGCTGGTATGCGC 55.32%
Apta_495 DNA GGGAATGGATCCACATCTACGTATTACTGCTGGTGACGAGGGCTAGACGACGTACCTTCACTGCAGACTTGACGAAGCTT 55.00%
Apta_832 DNA CCGGAGGTGGGTGAGGTCTGCGGCAGGCTGTGTGGGTGGACCGGAGGGGGGTGAGGTCTGCGGCAGGCTGTGTGGGTGGA 55.00%
Apta_1071 DNA TTGAAGTGACTCCGCACTGGGTGGGTGGGAGGGTCGTGCGGCTGGTCATAGCAGGGT 55.00%
Apta_1136 DNA GCCGAGATTGCACTTACTATCTAAAGAAAGGTAGTAAGAGTGGGTGATTATGGGTAAGTTGTATGAGGTAATTGAATAAGCTGGTATGCGC 54.95%
Apta_771 DNA GAATTCCGTCGGACAGCGGTATGCATGGGAGGTTCTGGAGGGGGTGGGTTGGCGTGCGTTCCAGATGGACGAATATCGTCTCCC 54.76%
Apta_772 DNA GAATTCAGTCGGACAGCGCGGTGTTGGTGGTGGGGTGGTTTGGGAATCTGTTCGGCTGGAGATGGACGAATATCGTCTCCC 54.32%

ABOUT

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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