Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 624
Aptamer sequence: ACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCT
Target unique ID: 30323
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_590 10.10V Molecule Daunorubicin 272 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: ACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCT
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_590 Description 10.10V
Aptamer chemistry DNA Length 41 nt
GC content 58.5% Molecular weight 12,873.24 Da
Molarity of 1 μg/μl solution 77.68 μM Number of G-quadruplexes 3
G-Score 63 Function Target recognition
Sequence ACCATCTGTGTAAGGGGTAAGGGGTGGGGGTGGGTACGTCT
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 624
Target type Molecule
Target unique ID 30323
Activity 272 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
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_11 DNA AGAGGGGGGGGTCGGGGTGGGTCGC 58.54%
Apta_17 DNA AGGGGGGGGGGTGGGGGTGGGTCCC 58.54%
Apta_46 DNA CGGGTGGGAGTTGTGGGGGGGGGTGGGAGGGTT 58.54%
Apta_63 DNA GACCCGTGGTAGGGTAGGATGGGGTGGTC 58.54%
Apta_266 DNA TGGATGGTAGCTCGGTCGGGGTGGGTGGGTTGGCAAGTCT 58.54%
Apta_364 DNA TATGGTATGCTGTGTGGTATGGGGTGGCGTGCTCT 58.54%
Apta_851 DNA CCATGTTTTGTAGGTGTAATAGGTCATGTTAGGGTTTCTG 58.54%
Apta_488 DNA CGACCAGGGTGGGAGGGGGACGGGCTGGCGGCGCGCGGTAATG 58.14%
Apta_282 DNA ATCCATGGGGCGGAGATGAGGGGGAGGAGGGCGGGTACCCGGTTGAT 57.45%
Apta_22 DNA TGTGGGGGTGGACTGGGTGGGTACC 56.10%
Apta_47 DNA GACCTAGCAGTGGACATGTGGCAGGGTGAAGTGGCATCGTC 56.10%
Apta_62 DNA AGTCCGTGGTAGGGCAGGTTGGGGTGACT 56.10%
Apta_65 DNA CTACCGTGGTAGGGAAGGTTGGAGTGTAG 56.10%
Apta_69 DNA AGCGAGTAGGTTGGTGTGGTTGGGGCTCGCT 56.10%
Apta_75 DNA CACTGGTAGGTTGGTGTGGTTGGGGCCAGTG 56.10%
Apta_218 RNA AGCCGCGAGGGGAGGGAUAGGGUAGGGCGCGGCU 56.10%
Apta_245 DNA ACAGGGGTGTGGGGACAGGGGTGTGGGG 56.10%
Apta_744 DNA GTGGCCAGTCACTCAATTGGGTGTAGGGGTGGGGATTGTGGGTTG 55.56%
Apta_748 DNA AGCTTGAGGGTGGGCGGGTGGACGCGGTAGTGGTATATAGGTCGG 55.56%
Apta_79 DNA ATCTCGAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACTCGT 54.55%

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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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