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Accession NumberDB06696
TypeSmall Molecule
DescriptionAn semisynthetic aminoglycoside antibiotic. Often used for treatment of multi-resistant bacterial infection such as methicillin-resistant Staphylococcus aureus (MRSA). Amikacin is also nephrotoxic and ototoxic.
External Identifiers
  • 1665-RB
  • HABA-Dibekacin
  • HBK
Approved Prescription ProductsNot Available
Approved Generic Prescription ProductsNot Available
Approved Over the Counter ProductsNot Available
Unapproved/Other Products Not Available
International BrandsNot Available
Brand mixturesNot Available
Arbekacin Sulfate
ThumbNot applicableDBSALT001108
CAS number51025-85-5
WeightAverage: 552.619
Monoisotopic: 552.311891658
Chemical FormulaC22H44N6O10
NCC[[email protected]](O)C(=O)N[C@@H]1C[[email protected]](N)[C@@H](O[[email protected]]2O[[email protected]](CN)CC[[email protected]]2N)[[email protected]](O)[[email protected]]1O[[email protected]]1O[[email protected]](CO)[C@@H](O)[[email protected]](N)[[email protected]]1O
IndicationArbekacin is used for the short term treatment of multi-resistant bacterial infections, such as methicillin-resistant Staphylococcus aureus (MRSA).
Structured Indications Not Available
PharmacodynamicsAminoglycosides, such as Arbekacin, work by binding to the bacterial 30S ribosomal subunit, causing misreading of t-RNA which consequently, leaves the bacterium unable to synthesize proteins vital to its growth. Energy is needed for aminoglycoside uptake into the bacterial cell. Anaerobes have less energy available for this uptake, so aminoglycosides are less active against anaerobes. Aminoglycosides are useful primarily in infections involving aerobic, gram-negative bacteria, such as Pseudomonas, Acinetobacter, and Enterobacter.
Mechanism of actionAminoglycosides, such as Arbekacin, inhibit protein synthesis in susceptible bacteria by irreversibly binding to bacterial 30S and 16S ribosomal subunits. Specifically Arbekacin binds to four nucleotides of 16S rRNA and a single amino acid of protein S12. This interferes with decoding site in the vicinity of nucleotide 1400 in 16S rRNA of 30S subunit. This region interacts with the wobble base in the anticodon of tRNA. This leads to misreading of mRNA so incorrect amino acids are inserted into the polypeptide leading to nonfunctional or toxic peptides and the breakup of polysomes into nonfunctional monosomes.
TargetKindPharmacological actionActionsOrganismUniProt ID
30S ribosomal protein S12Proteinyes
Escherichia coli (strain K12)P0A7S3 details
Related Articles
AbsorptionAminoglycosides are not well absorbed from the gastrointestinal tract. Their absorption is markedly improved by parenteral administration.
Volume of distributionNot Available
Protein binding3-12%
MetabolismNot Available
Route of eliminationNot Available
Half life3 hours
ClearanceNot Available
ToxicityOtotoxicity and nephrotoxicity are the most serious adverse effects of aminoglycoside therapy and are more likely to occur in patients with a history of renal impairment or who are receiving other ototoxic and/or nephrotoxic drugs. Normal duration of IM or IV aminoglycoside therapy is 7-10 days. Although a longer duration may be necessary in some cases, toxicity is more likely to occur when aminoglycoside treatment is continued for longer than 10 days.
Affected organisms
  • Enteric bacteria and other eubacteria
  • Escherichia coli
  • Staphylococcus aureus
  • Acinetobacter
PathwayCategorySMPDB ID
Arbekacin Action PathwayDrug actionSMP00713
SNP Mediated EffectsNot Available
SNP Mediated Adverse Drug ReactionsNot Available
Drug InteractionsNot Available
Food InteractionsNot Available
Synthesis Reference

Shinichi Kondo, Seiji Shibahara, Takayuki Usui, Toshiaki Kudo, Shuichi Gomi, Atsushi Tamura, Yoko Ikeda, Daishiro Ikeda, Tomio Takeuchi, “Dibekacin derivatives and arbekacin derivatives active against resistant bacteria, and the production thereof.” U.S. Patent US5618795, issued October, 1989.

General References
  1. Inoue M, Nonoyama M, Okamoto R, Ida T: Antimicrobial activity of arbekacin, a new aminoglycoside antibiotic, against methicillin-resistant Staphylococcus aureus. Drugs Exp Clin Res. 1994;20(6):233-9. [PubMed:7758395 ]
  2. Morikawa K, Nonaka M, Yoshikawa Y, Torii I: Synergistic effect of fosfomycin and arbekacin on a methicillin-resistant Staphylococcus aureus-induced biofilm in a rat model. Int J Antimicrob Agents. 2005 Jan;25(1):44-50. [PubMed:15620825 ]
  3. Doi Y, Yokoyama K, Yamane K, Wachino J, Shibata N, Yagi T, Shibayama K, Kato H, Arakawa Y: Plasmid-mediated 16S rRNA methylase in Serratia marcescens conferring high-level resistance to aminoglycosides. Antimicrob Agents Chemother. 2004 Feb;48(2):491-6. [PubMed:14742200 ]
  4. Antimicrobial agents and Chemotherapy [Link]
External Links
ATC CodesJ01GB12
AHFS Codes
  • 08:12.02
PDB EntriesNot Available
FDA labelNot Available
MSDSNot Available
Predicted ADMET features
Human Intestinal Absorption-0.9365
Blood Brain Barrier-0.9659
Caco-2 permeable-0.7588
P-glycoprotein substrateSubstrate0.5786
P-glycoprotein inhibitor INon-inhibitor0.7254
P-glycoprotein inhibitor IINon-inhibitor0.8424
Renal organic cation transporterNon-inhibitor0.8676
CYP450 2C9 substrateNon-substrate0.8204
CYP450 2D6 substrateNon-substrate0.8289
CYP450 3A4 substrateNon-substrate0.559
CYP450 1A2 substrateNon-inhibitor0.933
CYP450 2C9 inhibitorNon-inhibitor0.9392
CYP450 2D6 inhibitorNon-inhibitor0.909
CYP450 2C19 inhibitorNon-inhibitor0.9122
CYP450 3A4 inhibitorNon-inhibitor0.9564
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9002
Ames testNon AMES toxic0.7048
BiodegradationNot ready biodegradable0.6627
Rat acute toxicity1.8593 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9902
hERG inhibition (predictor II)Non-inhibitor0.5444
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397 )
ManufacturersNot Available
PackagersNot Available
Dosage formsNot Available
PricesNot Available
PatentsNot Available
Experimental Properties
melting point178Not Available
Predicted Properties
Water Solubility41.0 mg/mLALOGPS
pKa (Strongest Acidic)12.49ChemAxon
pKa (Strongest Basic)9.99ChemAxon
Physiological Charge5ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area297.27 Å2ChemAxon
Rotatable Bond Count10ChemAxon
Refractivity129.08 m3·mol-1ChemAxon
Polarizability56.65 Å3ChemAxon
Number of Rings3ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Mass Spec (NIST)Not Available
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
DescriptionThis compound belongs to the class of organic compounds known as amino sugars. These are sugars having one alcoholic hydroxy group replaced by an amino group; systematically known as x-amino-x-deoxymonosaccharides. These compounds do not include Glycosylamines.
KingdomOrganic compounds
Super ClassOrganooxygen compounds
ClassCarbohydrates and carbohydrate conjugates
Sub ClassAminosaccharides
Direct ParentAmino sugars
Alternative Parents
  • 4,6-disubstituted 2-deoxystreptamine
  • Aminoglycoside core
  • 2-deoxystreptamine aminoglycoside
  • Gamma amino acid or derivatives
  • Glucosamine
  • Amino sugar
  • O-glycosyl compound
  • Glycosyl compound
  • Cyclohexylamine
  • Cyclohexanol
  • Fatty acyl
  • Oxane
  • N-acyl-amine
  • Monosaccharide
  • Fatty amide
  • Cyclic alcohol
  • 1,3-aminoalcohol
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • 1,2-aminoalcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Carboxylic acid amide
  • Acetal
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors


Escherichia coli (strain K12)
Pharmacological action
General Function:
Trna binding
Specific Function:
With S4 and S5 plays an important role in translational accuracy.Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluste...
Gene Name:
Uniprot ID:
Molecular Weight:
13736.995 Da
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Funatsu G, Yaguchi M, Wittmann-Liebold B: Primary stucture of protein S12 from the small Escherichia coli ribosomal subunit. FEBS Lett. 1977 Jan 15;73(1):12-7. [PubMed:320034 ]
  4. Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V: Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 2000 Sep 21;407(6802):340-8. [PubMed:11014183 ]
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Drug created on May 05, 2010 10:31 / Updated on August 17, 2016 12:24