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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:50 UTC
Update Date2022-03-07 02:51:47 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. In humans, gentamicin is involved in the gentamicin action pathway. Gentamicin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Gentamicin.
Structure
Thumb
Synonyms
ValueSource
g MyticinMeSH
g-MyticinMeSH
GMyticinMeSH
GaramycinMeSH
GentacycolMeSH
Gentamicin sulfateMeSH
GentamicinsMeSH
GentamycinMeSH
GentamycinsMeSH
GentavetMeSH
GenticinMeSH
Sulfate, gentamicinMeSH
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
Physiological effectNot Available
Disposition
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point105 °C (decomposition)Not Available
Boiling PointNot AvailableNot Available
Water Solubility12.6 g/LNot Available
LogP-3.1Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
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 IDC00018016
Chemspider ID3348
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGentamicin
METLIN IDNot Available
PubChem Compound3467
PDB IDNot Available
ChEBI IDNot Available
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 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 ]