Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 208
Aptamer sequence: CCAAGGCTTTAGGTCTGAGATCTCCC
Target unique ID: P04585
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_204 PF1-26ntC Protein POL_HV1H2 ~ 500 nM 50 mM Tris-HCl, pH 8, 1mM DTT, 80 mM KCl, 6 mM MgCl2 for ten minutes 22554064
Structure information of aptamer
Aptamer Sequence: CCAAGGCTTTAGGTCTGAGATCTCCC
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_204 Description PF1-26ntC
Aptamer chemistry DNA Length 26 nt
GC content 53.8% Molecular weight 8,162.05 Da
Molarity of 1 μg/μl solution 122.52 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted therapy
Sequence CCAAGGCTTTAGGTCTGAGATCTCCC
Applications Inhibiting function against the WT HIV-1 RT
Target information
Type Detail Type Detail
Uniprot ID P04585 Protein name Gag-Pol polyprotein (Pr160Gag-Pol) [Cleaved into: Matrix protein p17 (MA); Capsid protein p24 (CA); Spacer peptide 1 (SP1) (p2); Nucleocapsid protein p7 (NC); Transframe peptide (TF); p6-pol (p6*); Protease (EC 3.4.23.16) (PR) (Retropepsin); Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2) (p66 RT); p51 RT; p15; Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]
Gene name(s) gag-pol Organism Gag-Pol polyprotein (Pr160Gag-Pol) [Cleaved into: Matrix protein p17 (MA); Capsid protein p24 (CA); Spacer peptide 1 (SP1) (p2); Nucleocapsid protein p7 (NC); Transframe peptide (TF); p6-pol (p6*); Protease (EC 3.4.23.16) (PR) (Retropepsin); Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2) (p66 RT); p51 RT; p15; Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]
Status reviewed in uniprot database Length 1435
Mass 162,042 Activity regulation The viral protease is inhibited by many synthetic protease inhibitors (PIs), such as amprenavir, atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and saquinavir
Involvement in disease N/A Catalytic activity Reaction=Specific for a P1 residue that is hydrophobic, and P1' variable
PDB ID(s)
1A30;1BV7;1BV9;1BVE;1BVG;1BWA;1BWB;1C0T;1C0U;1C1B;1C1C;1DMP;1DTQ;1DTT;1E6J;1EP4;1ESK;1EX4;1EXQ;1FB7;1FK9;1FKO;1FKP;1G6L;1HIV;1HVH;1HVR;1HWR;1HXB;1JKH;1JLA;1JLB;1JLC;1JLE;1JLF;1JLG;1JLQ;1KLM;1LV1;1LW0;1LW2;1LWC;1LWE;1LWF;1NCP;1O1W;1ODW;1ODY;1QBR;1QBS;1QBT;1QBU;1REV;1RT1;1RT2;1RT3;1RT4;1RT5;1RT6;1RT7;1RTD;1RTH;1RTI;1RTJ;1S1T;1S1U;1S1V;1S1W;1S1X;1T05;1TAM;1TKT;1TKX;1TKZ;1TL1;1TL3;1VRT;1VRU;2HND;2HNY;2HNZ;2KOD;2NPH;2OPP;2OPQ;2OPR;2OPS;2RF2;2RKI;2WHH;2WOM;2WON;2YNF;2YNG;2YNH;2YNI;3AO2;3C6T;3C6U;3DI6;3DLE;3DLG;3DM2;3DMJ;3DOK;3DOL;3DOX;3DRP;3DRR;3DRS;3DYA;3E01;3FFI;3I0R;3I0S;3KJV;3KK1;3KK2;3KK3;3KT2;3KT5;3LAK;3LAL;3LAM;3LAN;3LP0;3LP1;3LP2;3M8P;3M8Q;3MEC;3MED;3MEE;3MEG;3N3I;3NBP;3PHV;3QIN;3QIO;3QIP;3T19;3T1A;3TAM;4B3O;4B3P;4B3Q;4I7F;4KSE;4KV8;4NCG;4Q1W;4Q1X;4Q1Y;4Q5M;4QLH;4U1H;4U1I;4U1J;4U7Q;4U7V;5DGU;5DGW;5EU7;5HRN;5HRP;5HRR;5HRS;5IM7;5J2M;5J2N;5J2P;5J2Q;5K14;5KAO;5T82;5TC2;5VZ6;5XOS;5XOT;5YRS;6BJ2;6BJ3;6BSG;6BSH;6BSI;6BSJ;6DIF;6DIL;6DJ1;6DJ2;6DJ5;6DJ7;6DV0;6DV4;6E7J;6E9A;6EWA;6EX9;6GL1;6J1V;6J1W;6OR7;6OTZ;6P1I;6P1X;6P2G;6PYL;6SKK;6SKM;6SKN;6SLQ;6SLU;6SMU;6UIR;6UIS;6UIT;6UJX;6UJY;6UJZ;6UK0;6VPZ;6VQ2;6VQD;6VQE;6VQY;6VQZ;6WAZ;6WB1;6WPF;6WPH;6WPJ;
Function Mediates, with Gag polyprotein, the essential events in virion assembly, including binding the plasma membrane.
Activity data

No relevant experimental diagram

 Interaction ID 208
Target type Protein
Target unique ID P04585
Activity ~ 500 nM
Binding Conditions/Buffer

50 mM Tris-HCl, pH 8, 1mM DTT, 80 mM KCl, 6 mM MgCl2 for ten minutes
Assay

N/A
PubMed ID 22554064
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_185 DNA ACCAAGGCTTTAGGTCTGAGATCTCCCAAT
86.67%
Apta_203 DNA GGAAGGCTTTAGGTCTGAGATCTCGG
84.62%
Apta_205 DNA TTAAGGCTTTAGGTCTGAGATCTCTT
84.62%
Apta_196 DNA AGGAAGGCTTTAGGTCTGAGATCTC
80.77%
Apta_202 DNA AAGGCTTTAGGTCTGAGATCTCGGAAT 74.07%
Apta_184 DNA AGGAAGGCTTTAGGTCTGAGATCTCGGAAT 73.33%
Apta_187 DNA ACCAACCCTTTACCTCTGAGATCTCCCAAT 73.33%
Apta_193 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGAAT 70.97%
Apta_186 DNA AGGAACGCTTTAGGTCTGAGATCTCGGAAT 70.00%
Apta_192 DNA AGGAAGGCTTTAGCTCTGAGATCTCGGAAT 70.00%
Apta_215 DNA AGGAAGGCTTTAGGTCCGAGATCTCGGAAT 70.00%
Apta_194 DNA AGGAAGGCTTTAGGGTCTGAGATCTCGGGAAT 68.75%
Apta_195 DNA AGGAAGGCTTTAGGGGTCTGAGATCTCGGAAT 68.75%
Apta_190 DNA AGGAACCCTTTAGGTCTGAGATCTCGGAAT 66.67%
Apta_191 DNA AGGAAGGCTTTACCTCTGAGATCTCGGAAT 66.67%
Apta_197 DNA GGCTTTAGGTCTGAGATCTCGGAAT 65.38%
Apta_214 DNA AGGAAGGCTTTAGGTTTCCTAAAGCCTTCC 63.33%
Apta_198 DNA AGGAAGGCTTTAGGTCTGAG 61.54%
Apta_188 DNA AAAAAAACTTTAAATCTGAGATCTCAAAAT 60.00%
Apta_189 DNA AGGAACCCTTTACCTCTGAGATCTCGGAAT 60.00%

ABOUT

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

HELP CENTER

>Contact us
>LMMD Group
>School of Pharmacy

DEV TOOL
Page last updated at 2022-05-25 10:01:57 (Asia/Shanghai) | You are visitor No. 43982
Copyright © 2019-2020 Laboratory of Molecular Modeling and Design, School of Pharmacy, East China University of Science and Technology. All rights reserved.