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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:50 UTC
Update Date2020-02-26 21:40:37 UTC
HMDB IDHMDB0014936
Secondary Accession Numbers
  • HMDB14936
Metabolite Identification
Common NameGentamicin
DescriptionGentamicin, also known as g-myticin or garamycin, belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines. Gentamicin is a drug which is used for treatment of serious infections caused by susceptible strains of the following microorganisms: p. aeruginosa, proteus species (indole-positive and indole-negative), e. coli, klebsiella-enterobactor-serratia species, citrobacter species and staphylococcus species (coagulase-positive and coagulase-negative). Gentamicin is a very strong basic compound (based on its pKa). In humans, gentamicin is involved in gentamicin action pathway. This region interacts with the wobble base in the anticodon of tRNA. May cause irreversible ototoxicity. In the past the aminoglycosides have been used in conjunction with penicillin-related antibiotics in streptococcal infections for their synergistic effects, particularly in endocarditis. They are broad-spectrum antibiotics, but may cause ear and kidney damage. Vestibular toxicity may cause vertigo, nausea, vomiting, dizziness and loss of balance.
Structure
Data?1582753237
Synonyms
ValueSource
Gentamicin sulfateHMDB
GentamicinsHMDB
GentamycinsHMDB
GenticinHMDB
g-MyticinHMDB
GaramycinHMDB
GentamycinHMDB
Sulfate, gentamicinHMDB
g MyticinHMDB
GMyticinHMDB
GentacycolHMDB
GentavetHMDB
Chemical FormulaC21H43N5O7
Average Molecular Weight477.5954
Monoisotopic Molecular Weight477.316248755
IUPAC Name2-{[4,6-diamino-3-({3-amino-6-[1-(methylamino)ethyl]oxan-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol
Traditional Namegentamicin
CAS Registry Number1403-66-3
SMILES
CNC(C)C1CCC(N)C(OC2C(N)CC(N)C(OC3OCC(C)(O)C(NC)C3O)C2O)O1
InChI Identifier
InChI=1S/C21H43N5O7/c1-9(25-3)13-6-5-10(22)19(31-13)32-16-11(23)7-12(24)17(14(16)27)33-20-15(28)18(26-4)21(2,29)8-30-20/h9-20,25-29H,5-8,22-24H2,1-4H3
InChI KeyCEAZRRDELHUEMR-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentAminocyclitol glycosides
Alternative Parents
Substituents
  • Amino cyclitol glycoside
  • 2-deoxystreptamine aminoglycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Aminocyclitol or derivatives
  • Cyclohexanol
  • Cyclohexylamine
  • Cyclitol or derivatives
  • Monosaccharide
  • Oxane
  • Tertiary alcohol
  • Cyclic alcohol
  • Secondary alcohol
  • 1,2-aminoalcohol
  • Secondary amine
  • Acetal
  • Organoheterocyclic compound
  • Secondary aliphatic amine
  • Oxacycle
  • Alcohol
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Organopnictogen compound
  • Organic nitrogen compound
  • Amine
  • Primary amine
  • Organonitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location:

Process

Naturally occurring process:

Role

Biological role:

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point105 °C (decomposition)Not Available
Boiling PointNot AvailableNot Available
Water Solubility12.6 g/LNot Available
LogP-3.1Not Available
Predicted Properties
PropertyValueSource
Water Solubility12.6 g/LALOGPS
logP-1.6ALOGPS
logP-3.1ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)12.55ChemAxon
pKa (Strongest Basic)10.18ChemAxon
Physiological Charge5ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area199.73 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity118.02 m³·mol⁻¹ChemAxon
Polarizability51.92 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-052f-9110200000-10f63ec1d6d3b1a0b86fSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-000x-9610204000-09efa9e4adbb219c8742Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0i29-1319700000-e55d2931137c5abc8493Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-0904000000-de986ac47725d8f3a72aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0592-9602000000-c7fd77457525743faebaSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-2911100000-93e47b752e7992b12263Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014i-2958400000-7303bf3ebe16dd1c1d60Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0udi-2692000000-a8234ed8e0131019f62bSpectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00798 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00798 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00798
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID3348
KEGG Compound IDC00505
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGentamicin
METLIN IDNot Available
PubChem Compound3467
PDB IDNot Available
ChEBI ID17833
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

General function:
Involved in calcium ion binding
Specific function:
Acts together with cubilin to mediate HDL endocytosis. May participate in regulation of parathyroid- hormone and para-thyroid-hormone-related protein release
Gene Name:
LRP2
Uniprot ID:
P98164
Molecular weight:
521952.8
References
  1. Watanabe A, Nagai J, Adachi Y, Katsube T, Kitahara Y, Murakami T, Takano M: Targeted prevention of renal accumulation and toxicity of gentamicin by aminoglycoside binding receptor antagonists. J Control Release. 2004 Mar 24;95(3):423-33. [PubMed:15023454 ]
  2. Takamoto K, Kawada M, Ikeda D, Yoshida M: Apolipoprotein E3 (apoE3) safeguards pig proximal tubular LLC-PK1 cells against reduction in SGLT1 activity induced by gentamicin C. Biochim Biophys Acta. 2005 Apr 15;1722(3):247-53. [PubMed:15777622 ]
  3. Nagai J, Saito M, Adachi Y, Yumoto R, Takano M: Inhibition of gentamicin binding to rat renal brush-border membrane by megalin ligands and basic peptides. J Control Release. 2006 May 1;112(1):43-50. Epub 2006 Feb 20. [PubMed:16488503 ]

Transporters

General function:
Involved in ion transmembrane transporter activity
Specific function:
Involved in the renal elimination of endogenous and exogenous organic anions. Functions as organic anion exchanger when the uptake of one molecule of organic anion is coupled with an efflux of one molecule of endogenous dicarboxylic acid (glutarate, ketoglutarate, etc). Mediates the sodium-independent uptake of 2,3-dimercapto-1-propanesulfonic acid (DMPS). Mediates the sodium-independent uptake of p- aminohippurate (PAH), ochratoxin (OTA), acyclovir (ACV), 3'-azido- 3-'deoxythymidine (AZT), cimetidine (CMD), 2,4-dichloro- phenoxyacetate (2,4-D), hippurate (HA), indoleacetate (IA), indoxyl sulfate (IS) and 3-carboxy-4-methyl-5-propyl-2- furanpropionate (CMPF), cidofovir, adefovir, 9-(2- phosphonylmethoxyethyl) guanine (PMEG), 9-(2- phosphonylmethoxyethyl) diaminopurine (PMEDAP) and edaravone sulfate. PAH uptake is inhibited by p- chloromercuribenzenesulphonate (PCMBS), diethyl pyrocarbonate (DEPC), sulindac, diclofenac, carprofen, glutarate and okadaic acid. PAH uptake is inhibited by benzothiazolylcysteine (BTC), S-chlorotrifluoroethylcysteine (CTFC), cysteine S-conjugates S-dichlorovinylcysteine (DCVC), furosemide, steviol, phorbol 12-myristate 13-acetate (PMA), calcium ionophore A23187, benzylpenicillin, furosemide, indomethacin, bumetamide, losartan, probenecid, phenol red, urate, and alpha-ketoglutarate
Gene Name:
SLC22A6
Uniprot ID:
Q4U2R8
Molecular weight:
61815.8
References
  1. Jariyawat S, Sekine T, Takeda M, Apiwattanakul N, Kanai Y, Sophasan S, Endou H: The interaction and transport of beta-lactam antibiotics with the cloned rat renal organic anion transporter 1. J Pharmacol Exp Ther. 1999 Aug;290(2):672-7. [PubMed:10411577 ]