Gentamicin (CED0000782)

Record Information

Version

1.0

Creation Date

2016-05-25 03:28:24 UTC

Update Date

2026-08-21 20:23:39 UTC

Accession Number

CHEM021376

Identification

Common Name

Gentamicin

Class

Small Molecule

Description

Gentamicin is an organic compound with the formula C21H43N5O7 and an average molecular weight of 477.60 g/mol. Gentamicin belongs to the carbohydrates and carbohydrate conjugates, a subclass of organooxygen compounds within the organic compounds. It functions as a biological antimicrobial agent (PMC8622877). The compound acts upon two recorded protein targets: NH(3)-dependent NAD(+) synthetase (nadE) and the small ribosomal subunit protein uS12 (rpsL), for which it serves as a binder or inhibitor. This substance is found in seven recorded sources, including food preservation, magnets in electrical and electronic equipment, drinking water, and various healthcare, pharmaceutical, and veterinary products such as antiinfectives, aminoglycoside antibacterials, ophthalmological and otological preparations, and antibiotics. Exposure routes for the compound include oral, topical, intravenous, intramuscular, parenteral, ophthalmic, and auricular administration. Regarding its health effects, gentamicin is used as a treatment for plague (PMC7125859), listeriosis (PMC10967383), and osteomyelitis (PMC6615988). Additionally, the compound is associated with obesity (PMC11582170).

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
g Myticin	MeSH
g-Myticin	MeSH
GMyticin	MeSH
Garamycin	MeSH
Gentacycol	MeSH
Gentamicin sulfate	MeSH
Gentamicins	MeSH
Gentamycin	MeSH
Gentamycins	MeSH
Gentavet	MeSH
Genticin	MeSH
Sulfate, gentamicin	MeSH

Chemical Formula

C₂₁H₄₃N₅O₇

Average Molecular Mass

477.595 g/mol

Monoisotopic Mass

477.316 g/mol

CAS Registry Number

1403-66-3

IUPAC Name

2-{[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 Name

gentamicin

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 Key

CEAZRRDELHUEMR-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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminocyclitol 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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Applications

Not Available

Biological Roles

antimicrobial agent

Chemical Roles

Not Available

Organoleptic Effects

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	12.6 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-3.1	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	10.18	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	199.73 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	118.02 m³·mol⁻¹	ChemAxon
Polarizability	51.92 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum	splash10-052f-9110200000-10f63ec1d6d3b1a0b86f	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	splash10-000x-9610204000-09efa9e4adbb219c8742	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum	Not Available	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0i29-1319700000-e55d2931137c5abc8493	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-03di-0904000000-de986ac47725d8f3a72a	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0592-9602000000-c7fd77457525743faeba	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-014i-2911100000-93e47b752e7992b12263	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-014i-2958400000-7303bf3ebe16dd1c1d60	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0udi-2692000000-a8234ed8e0131019f62b	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-004i-0100900000-17ed47f7ad2a1624396e	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-05r3-0903300000-374167ef77fcfe6e2ea6	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-07wc-8911100000-2cdb7c32f191990ff2cd	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-004i-0600900000-eb22f68b27a08e0aa46c	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-004i-0933800000-2c6fb5d17dced93f420f	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0arc-6495200000-d771b6bc4379cd6e84da	Not Available	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, D₂O, predicted)	Not Available	Not Available	View Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, predicted)	Not Available	Not Available	View Spectrum

Toxicity Profile

Mechanism of Toxicity

Not Available

Carcinogenicity (IARC Classification)

Not Available

Minimum Risk Level

Not Available

Symptoms

Not Available

Treatment

Not Available

Toxicity Values

Toxicity Value	Unit	Value Range	Organism	Dose Descriptor	Route of Exposure	Predicted or Experimental	Reference
6821.0	Log mg/kg	[3800:12000]	Rat	LD50	oral	predicted	Not Available

Health Effects

Health Effect	Relationship	Direction	Reference
obesity	associated_with	Not Available	PMC11582170
osteomyelitis	is_treatment_for	Not Available	PMC6615988
listeriosis	is_treatment_for	Not Available	PMC10967383
plague	is_treatment_for	Not Available	PMC7125859
meningitis	is_treatment_for	Not Available	PMC12519648
Tularemia	is_treatment_for	Not Available	PMC13024352 , PMC13024352 , PMC9026340

Exposure Sources

Source ID	Source	Sector	Reference
10	Insecticides	Agriculture & land management	Not Available
115	Drinking water	Drinking water & water supply	Not Available
306	Antibiotics	Healthcare, pharmaceuticals & veterinary products	Not Available
344	Aminoglycoside antibacterials	Healthcare, pharmaceuticals & veterinary products	Not Available
395	Antiinfectives	Healthcare, pharmaceuticals & veterinary products	Not Available
407	Ophthalmological and otological preparations	Healthcare, pharmaceuticals & veterinary products	Not Available
527	Magnets	Electrical & Electronic Equipment	Not Available
545	Food Preservation	Food, food processing & cookware	Not Available
596	Acaricides	Agriculture & land management	Not Available
603	Nematocides	Agriculture & land management	Not Available
605	Pest Repellants	Agriculture & land management	Not Available
607	Rodenticides(1)	Agriculture & land management	Not Available
608	Rodenticides	Agriculture & land management	Not Available
611	Anti Perspirants Or Body Deoderants	Personal care & cosmetics	Not Available
615	Eye Makeup Products	Personal care & cosmetics	Not Available
618	Lip Makeup Products	Personal care & cosmetics	Not Available
662	Yarns Or Threads	Textiles, leather & furnishings	Not Available

Pathways

3 pathways

Gentamicin Action Pathway

Gentamicin Action Pathway (New)

Gentamicin Drug Metabolism Action Pathway

Targets

Structure	Protein	UniProt ID	Organism	Relationship	Details
Click to view 3D structure	Aminoglycoside acetyltransferase	Q70E71	Enterococcus durans	Predicted (SEA)	69.9865
Click to view 3D structure	DNA topoisomerase 2-alpha	P11388	Humans	Predicted (SEA)	3176.56
Click to view 3D structure	Sodium/potassium-transporting ATPase subunit alpha-1	P50997	Canis lupus familiaris	Predicted (SEA)	30.3612
Click to view 3D structure	CD44 antigen	P16070	Humans	Predicted (SEA)	43.1285
Click to view 3D structure	CD44 antigen	P15379	Mus musculus	Predicted (SEA)	43.1285
Click to view 3D structure	Voltage-gated inwardly rectifying potassium channel KCNH2	Q12809	Humans	Predicted (SEA)	7756.82
Click to view 3D structure	Signal transducer and activator of transcription 3	P40763	Humans	Predicted (SEA)	7330.59
Click to view 3D structure	Solute carrier organic anion transporter family member 1B2	Q9QZX8	Rattus norvegicus	Predicted (SEA)	38.224
Click to view 3D structure	E-selectin	P98105	Rattus norvegicus	Predicted (SEA)	22.8877
Click to view 3D structure	Alpha-glucosidase MAL12	P53341	Saccharomyces cerevisiae S288c	Predicted (SEA)	166.052
Click to view 3D structure	Alpha-amylase	Q7M328	Sus scrofa domesticus	Predicted (SEA)	42.1943
Click to view 3D structure	Streptokinase A	P10520	Streptococcus pyogenes serotype M1	Predicted (SEA)	7677.72
Click to view 3D structure	Protein Tat	P04326	Human immunodeficiency virus type 1 group M subtype B (isolate PCV12)(HIV-1)	Predicted (SEA)	40.248
Click to view 3D structure	DIS3-like exonuclease 2	Q8IYB7	Humans	Predicted (SEA)	51.2248
Click to view 3D structure	Gamma-aminobutyric acid receptor subunit alpha-4	P28471	Rattus norvegicus	Predicted (SEA)	71.4656
Click to view 3D structure	Asialoglycoprotein receptor 1	P07306	Humans	Predicted (SEA)	172.903
Click to view 3D structure	Cytochrome P450 3A4	P08684	Humans	Predicted (SEA)	7771.69
Click to view 3D structure	Vitamin D3 receptor A	Q9PTN2	Danio rerio	Predicted (SEA)	36.2777
Click to view 3D structure	Gap junction beta-2 protein	P29033	Humans	Predicted (SEA)	1.40129
Click to view 3D structure	Gap junction alpha-1 protein	P17302	Humans	Predicted (SEA)	1.40129
Click to view 3D structure	Human immunodeficiency virus type 1 REV	Q77Y21	Human immunodeficiency virus 1	Predicted (SEA)	0.778492
Click to view 3D structure	Beta-ketoacyl-[acyl-carrier-protein] synthase III	P0A6R0	Escherichia coli (strain K12)	Predicted (SEA)	2.41333
Click to view 3D structure	Heparanase	Q9Y251	Humans	Predicted (SEA)	51.8476
Click to view 3D structure	3-oxoacyl-[acyl-carrier-protein] synthase 3	C3TDZ2	Escherichia coli	Predicted (SEA)	3.19182
Click to view 3D structure	Endopolygalactyuronase	P79074	Chondrostereum purpureum	Predicted (SEA)	7.31783