ContaminantDB: Neomycin

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References Targets (3)XML

Record Information

Version

1.0

Creation Date

2009-07-21 20:28:07 UTC

Update Date

2026-03-31 18:20:43 UTC

Accession Number

CHEM002314

Identification

Common Name

Neomycin

Class

Small Molecule

Description

A component of neomycin that is produced by Streptomyces fradiae. On hydrolysis it yields neamine and neobiosamine B. (From Merck Index, 11th ed). Neomycin is a bactericidal aminoglycoside antibiotic that binds to the 30S ribosome of susceptible organisms. Binding interferes with mRNA binding and acceptor tRNA sites and results in the production of non-functional or toxic peptides.

Contaminant Sources

HMDB Contaminants - Urine
STOFF IDENT Compounds
T3DB toxins

Contaminant Type

Amine
Aminoglycoside
Anti-Bacterial Agent
Antibiotic
Drug
Metabolite
Organic Compound
Synthetic Compound

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Fradiomycin b	ChEBI
Framicetina	ChEBI
Framycetine	ChEBI
Framycetinum	ChEBI
Neomycin b	ChEBI
Framycetin	Kegg
FRM	Kegg
Caswell no. 595	HMDB
Neomycin b sulfate	HMDB
Neomycin sulfate	HMDB
Neomycin sulphate	HMDB
USAF CB-19	HMDB
Fradiomycin sulfate	HMDB
Neomycin palmitate	HMDB
Palmitate, neomycin	HMDB
Sulfate, neomycin	HMDB
Sulfate, fradiomycin	HMDB
Antibiotic 10676	HMDB
Sulfate, framycetin	HMDB
Soframycin	HMDB
Sulfate, neomycin b	HMDB
Framycetin sulfate	HMDB

Chemical Formula

C₂₃H₄₆N₆O₁₃

Average Molecular Mass

614.644 g/mol

Monoisotopic Mass

614.312 g/mol

CAS Registry Number

1404-04-2

IUPAC Name

(2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(2R,3S,4R,5S)-5-{[(1R,2R,3S,5R,6S)-3,5-diamino-2-{[(2R,3R,4R,5S,6R)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-6-hydroxycyclohexyl]oxy}-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}oxane-3,4-diol

Traditional Name

neomycin

SMILES

NC[C@@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O[C@@H]3[C@@H](O)[C@H](N)C[C@H](N)[C@H]3O[C@H]3O[C@H](CN)[C@@H](O)[C@H](O)[C@H]3N)[C@@H]2O)[C@H](N)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C23H46N6O13/c24-2-7-13(32)15(34)10(28)21(37-7)40-18-6(27)1-5(26)12(31)20(18)42-23-17(36)19(9(4-30)39-23)41-22-11(29)16(35)14(33)8(3-25)38-22/h5-23,30-36H,1-4,24-29H2/t5-,6+,7-,8+,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1

InChI Key

PGBHMTALBVVCIT-VCIWKGPPSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C5-positions.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

4,5-disubstituted 2-deoxystreptamines

Alternative Parents

Substituents

4,5-disubstituted 2-deoxystreptamine
Disaccharide
Glycosyl compound
O-glycosyl compound
Aminocyclitol or derivatives
Cyclohexanol
Cyclohexylamine
Cyclitol or derivatives
Oxane
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
1,2-aminoalcohol
Acetal
Organoheterocyclic compound
Oxacycle
Primary alcohol
Hydrocarbon derivative
Organopnictogen compound
Primary aliphatic amine
Organonitrogen compound
Organic nitrogen compound
Amine
Alcohol
Primary amine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

aminoglycoside (CHEBI:7508 )
2-Deoxystreptamines (C01737 )

Biological Properties

Status

Detected and Not Quantified

Origin

Exogenous

Cellular Locations

Cytoplasm
Membrane

Biofluid Locations

Not Available

Tissue Locations

Not Available

Pathways

Name	SMPDB Link	KEGG Link
Neomycin Pathway	Not Available	Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Physical Properties

State

Solid

Appearance

White powder.

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	6.47e+01 g/L

Predicted Properties

Property	Value	Source
Water Solubility	64.7 g/L	ALOGPS
logP	-2.8	ALOGPS
logP	-8.4	ChemAxon
logS	-0.98	ALOGPS
pKa (Strongest Acidic)	12.29	ChemAxon
pKa (Strongest Basic)	9.97	ChemAxon
Physiological Charge	6	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	13	ChemAxon
Polar Surface Area	353.11 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	135.9 m³·mol⁻¹	ChemAxon
Polarizability	60.87 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	0	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	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-7141290000-1d118bea988327c31f82	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-001i-9341105000-267bc688fe9cf91d65e8	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_9) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_10) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_11) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_12) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_13) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-059t-0119482000-ffdc0e43566451df2770	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-08mr-0928720000-996bb8f7855d3e85b860	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-074j-4926000000-c31af30f83e2c83c73c8	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03ki-6015593000-b65aa1924d1108bbb4b5	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fep-8628790000-7f5b87306932c4896d5f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0fn9-3849010000-bab816a750f8a64740c6	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014l-0800339000-6b946842d215c555103f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01ox-0900211000-595172ae6408734c4e48	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01ox-9511450000-c93dbeb27c933d5b5c00	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0201219000-3f9668d26af13f0bfc8f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03di-4424298000-6320ecb92950f4012b9e	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0fkc-4796600000-b980bdc4fed06048f4a4	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum

Toxicity Profile

Route of Exposure

Eye contact; topical (eye drops). Poorly absorbed from the normal gastrointestinal tract. Although only approximately 3% of neomycin is absorbed through intact intestinal mucosa, significant amounts may be absorbed through ulcerated or denuded mucosa or if inflammation is present.

Mechanism of Toxicity

Aminoglycosides like neomycin "irreversibly" bind to specific 30S-subunit proteins and 16S rRNA. Specifically neomycin 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 interference with the initiation complex, 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.

Metabolism

Neomycin undergoes negligible biotransformation after parenteral administration. Route of Elimination: The small absorbed fraction is rapidly distributed in the tissues and is excreted by the kidney in keeping with the degree of kidney function. Half Life: 2 to 3 hours

Toxicity Values

LD50: 200 mg/kg (Rat) (1)

Lethal Dose

Not Available

Carcinogenicity (IARC Classification)

No indication of carcinogenicity to humans (not listed by IARC).

Uses/Sources

Topical uses include treatment for superficial eye infections caused by susceptible bacteria (used in combination with other antiinfectives), treatment of otitis externa caused by susceptible bacteria, treatment or prevention of bacterial infections in skin lesions, and use as a continuous short-term irrigant or rinse to prevent bacteriuria and gram negative rod bacteremia in abacteriuric patients with indwelling catheters. May be used orally to treat hepatic encephalopathy, as a perioperative prophylactic agent, and as an adjunct to fluid and electrolyte replacement in the treatment of diarrhea caused to enteropathogenic E. coli (EPEC).

Minimum Risk Level

Not Available

Health Effects

Antibiotic resistance

Symptoms

Vestibular toxicity may result in vertigo, nausea and vomiting, dizziness and loss of balance.

Treatment

Hemodialysis will remove neomycin sulfate from the blood. (3)

Concentrations

Not Available

External Links

DrugBank ID

DB00452

HMDB ID

HMDB0015129

FooDB ID

Not Available

Phenol Explorer ID

Not Available

KNApSAcK ID

C00015577

BiGG ID

Not Available

BioCyc ID

CPD-14142

METLIN ID

Not Available

PDB ID

Not Available

Wikipedia Link

Chemspider ID

ChEBI ID

PubChem Compound ID

Kegg Compound ID

YMDB ID

Not Available

ECMDB ID

Not Available

References

Synthesis Reference

Jaehoon Yu, Jongkook Lee, Miyun Kwon, Ae Pae, Hun Koh, “Heterodimeric conjugates of neomycin-oxazolidinone, their preparation and their use.” U.S. Patent US20050222055, issued October 06, 2005.

MSDS

Link

General References

1. https://www.ncbi.nlm.nih.gov/pubmed/?term=25129497

2. https://www.ncbi.nlm.nih.gov/pubmed/?term=25230155

3. https://www.ncbi.nlm.nih.gov/pubmed/?term=25450807

4. https://www.ncbi.nlm.nih.gov/pubmed/?term=25588492

5. https://www.ncbi.nlm.nih.gov/pubmed/?term=8548964

Neomycin (CHEM002314)

Structure for CHEM002314: Neomycin