arbekacin   Click here for help

GtoPdb Ligand ID: 7345

Synonyms: arbekacin sulfate | ME1100 | NPC-14
PDB Ligand
Compound class: Natural product or derivative
Comment: Arbekacin is a semisynthetic aminoglycoside antibiotic that has activity against both gram-positive and gram-negative bacteria [2]. Several aminoglycoside antibiotics have been reported to have the ability to promote mRNA translation even in the presence of premature termination codons (PTCs) in mutated genes. In the absence of pharmaceutical intervention, the ribosomal translation process produces truncated, often non-functional protein products. However, in the presence of such compounds the ribosomes 'readthrough' the PTCs, producing increased amounts of full-length, functional protein. This developing pharmaceutical intervention has been termed 'readthrough strategy'.
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 16
Hydrogen bond donors 11
Rotatable bonds 11
Topological polar surface area 297.27
Molecular weight 552.31
XLogP -5.86
No. Lipinski's rules broken 2
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES NCCC(C(=O)NC1CC(N)C(C(C1OC1OC(CO)C(C(C1O)N)O)O)OC1OC(CN)CCC1N)O
Isomeric SMILES NCC[C@@H](C(=O)N[C@@H]1C[C@H](N)[C@H]([C@@H]([C@H]1O[C@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)N)O)O)O[C@H]1O[C@H](CN)CC[C@H]1N)O
InChI InChI=1S/C22H44N6O10/c23-4-3-12(30)20(34)28-11-5-10(26)18(37-21-9(25)2-1-8(6-24)35-21)17(33)19(11)38-22-16(32)14(27)15(31)13(7-29)36-22/h8-19,21-22,29-33H,1-7,23-27H2,(H,28,34)/t8-,9+,10-,11+,12-,13+,14-,15+,16+,17-,18+,19-,21+,22+/m0/s1
InChI Key MKKYBZZTJQGVCD-XTCKQBCOSA-N
Classification Click here for help
Compound class Natural product or derivative
IUPAC Name Click here for help
(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-[(2R,3R,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy-2-[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-3-hydroxycyclohexyl]-2-hydroxybutanamide
International Nonproprietary Names Click here for help
INN number INN
5914 arbekacin
Synonyms Click here for help
arbekacin sulfate | ME1100 | NPC-14
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo 3
Other databases
CAS Registry No. 51025-85-5 (source: Scifinder)
ChEBI CHEBI:37922
ChEMBL Ligand CHEMBL426926
DrugBank Ligand DB06696
DrugCentral Ligand 235
GtoPdb PubChem SID 178103917
PubChem CID 68682
RCSB PDB Ligand 84G, 84G
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Wikipedia Arbekacin