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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:52 UTC
Update Date2022-03-07 02:52:03 UTC
HMDB IDHMDB0015642
Secondary Accession Numbers
  • HMDB15642
Metabolite Identification
Common NameArbekacin
DescriptionArbekacin is only found in individuals that have used or taken this drug. It is an 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.Aminoglycosides, 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.
Structure
Data?1582753319
Synonyms
ValueSource
ABKChEBI
ArbekacinaHMDB
ArbekacineHMDB
ArbekacinumHMDB
HabekacinHMDB
HaberacinHMDB
1-N-((S)-4-Amino-2-hydroxybutyryl)dibekacinHMDB
4-Amino-2-hydroxybutylyldibekacinHMDB
Arbekacin sulfateHMDB
Chemical FormulaC22H44N6O10
Average Molecular Weight552.619
Monoisotopic Molecular Weight552.311891658
IUPAC Name(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-2-{[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2R,3R,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide
Traditional Namearbekacin
CAS Registry Number51025-85-5
SMILES
NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)CC[C@H]2N)[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](N)[C@H]1O
InChI Identifier
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 KeyMKKYBZZTJQGVCD-XTCKQBCOSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct Parent4,6-disubstituted 2-deoxystreptamines
Alternative Parents
Substituents
  • 4,6-disubstituted 2-deoxystreptamine
  • Glycosyl compound
  • O-glycosyl compound
  • Aminocyclitol or derivatives
  • Cyclohexanol
  • Cyclohexylamine
  • Cyclitol or derivatives
  • Monosaccharide
  • Oxane
  • Cyclic alcohol
  • 1,3-aminoalcohol
  • Secondary alcohol
  • 1,2-aminoalcohol
  • Acetal
  • Carboximidic acid
  • Carboximidic acid derivative
  • Propargyl-type 1,3-dipolar organic compound
  • Oxacycle
  • Organic 1,3-dipolar compound
  • Organoheterocyclic compound
  • Primary amine
  • Primary alcohol
  • Organonitrogen compound
  • Alcohol
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Amine
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point178 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility41 g/LNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB06696 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB06696 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB06696
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID61936
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkArbekacin
METLIN IDNot Available
PubChem Compound68682
PDB IDNot Available
ChEBI ID37922
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
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. Akins RL, Rybak MJ: In vitro activities of daptomycin, arbekacin, vancomycin, and gentamicin alone and/or in combination against glycopeptide intermediate-resistant Staphylococcus aureus in an infection model. Antimicrob Agents Chemother. 2000 Jul;44(7):1925-9. [PubMed:10858356 ]
  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. 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 ]