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Record Information
Version4.0
Creation Date2012-09-06 15:16:52 UTC
Update Date2017-10-23 19:06:34 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
Thumb
Synonyms
ValueSource
ABKChEBI
ArbekacinaHMDB
ArbekacineHMDB
ArbekacinumHMDB
HabekacinHMDB
HaberacinHMDB
1-N-((S)-4-amino-2-Hydroxybutyryl)dibekacinMeSH
4-amino-2-HydroxybutylyldibekacinMeSH
Arbekacin sulfateMeSH
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
DescriptionThis compound belongs to the class of chemical entities known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic oxygen compounds
Sub ClassOrganooxygen compounds
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
Disposition

Biological Location:

  Subcellular:

  Biofluid and excreta:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Role

Industrial application:

  Pharmaceutical industry:

    Antimicrobial agent:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point178 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility41 g/LNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility41 g/LALOGPS
logP-2.9ALOGPS
logP-6.9ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)12.49ChemAxon
pKa (Strongest Basic)9.99ChemAxon
Physiological Charge5ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area297.27 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity129.08 m³·mol⁻¹ChemAxon
Polarizability56.65 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fai-9703350000-a39b12324064de97bb1bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-001i-9420023000-38418b391927687256eeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0f79-1139880000-5b853876efe4948c05adView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03fr-1389410000-37eb30c2012f87f6ec21View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-5293100000-00683c50ab260cc1f652View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ue9-3706490000-de4c5cf0381688661182View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-006x-4229230000-c96a218da739c2e31c33View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0udi-2439000000-56cd7ac5e0dfb04fbf04View in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
Pathways
NameSMPDB/PathwhizKEGG
Arbekacin Action PathwayPw000690Pw000690 greyscalePw000690 simpleNot Available
Displaying 1 entry
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB06696 details
UrineExpected but not Quantified Not AvailableNot AvailableTaking drug identified by DrugBank entry DB06696 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB06696
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB 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
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 ]