Neomycin (T3D2951)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesGene RegulationTargets (3)XML
Targets (3)
Record Information
Version2.0
Creation Date2009-07-21 20:28:07 UTC
Update Date2014-12-24 20:25:54 UTC
Accession NumberT3D2951
Identification
Common NameNeomycin
ClassSmall Molecule
DescriptionA 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.
Compound Type
  • Amine
  • Aminoglycoside
  • Anti-Bacterial Agent
  • Antibiotic
  • Drug
  • Metabolite
  • Organic Compound
  • Synthetic Compound
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Synonym
Caswell No. 595
Myacyne
Mycifradin
Myciguent
Neo-Fradin
Neo-Rx
Neobiotic
Neomycin B Sulfate
Neomycin Sulfate
Neomycin Sulphate
Nivemycin
USAF CB-19
Chemical FormulaC23H46N6O13
Average Molecular Mass614.644 g/mol
Monoisotopic Mass614.312 g/mol
CAS Registry Number1404-04-2
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 Nameneomycin
SMILES[H][C@]1(CO)O[C@@]([H])(O[C@]2([H])[C@@]([H])(O)[C@]([H])(N)C[C@]([H])(N)[C@@]2([H])O[C@@]2([H])O[C@]([H])(CN)[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])N)[C@]([H])(O)[C@]1([H])O[C@@]1([H])O[C@@]([H])(CN)[C@@]([H])(O)[C@]([H])(O)[C@@]1([H])N
InChI IdentifierInChI=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 KeyInChIKey=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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct Parent4,5-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 FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Cytoplasm
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
Pathways
NameSMPDB LinkKEGG Link
Neomycin PathwayNot AvailableNot Available
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
Solubility6.47e+01 g/L
LogP-7.8
Predicted Properties
PropertyValueSource
Water Solubility64.7 g/LALOGPS
logP-2.8ALOGPS
logP-8.4ChemAxon
logS-0.98ALOGPS
pKa (Strongest Acidic)12.29ChemAxon
pKa (Strongest Basic)9.97ChemAxon
Physiological Charge6ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area353.11 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity135.9 m³·mol⁻¹ChemAxon
Polarizability60.87 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-7141290000-1d118bea988327c31f822017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-001i-9341105000-267bc688fe9cf91d65e82017-10-06View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_9) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_10) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_11) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_12) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_13) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot Available2021-10-16View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-059t-0119482000-ffdc0e43566451df27702016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-08mr-0928720000-996bb8f7855d3e85b8602016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-074j-4926000000-c31af30f83e2c83c73c82016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03ki-6015593000-b65aa1924d1108bbb4b52016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fep-8628790000-7f5b87306932c4896d5f2016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0fn9-3849010000-bab816a750f8a64740c62016-08-03View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014l-0800339000-6b946842d215c555103f2021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01ox-0900211000-595172ae6408734c4e482021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01ox-9511450000-c93dbeb27c933d5b5c002021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0201219000-3f9668d26af13f0bfc8f2021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03di-4424298000-6320ecb92950f4012b9e2021-10-11View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0fkc-4796600000-b980bdc4fed06048f4a42021-10-11View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
Toxicity Profile
Route of ExposureEye 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 ToxicityAminoglycosides 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.
MetabolismNeomycin 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 ValuesLD50: 200 mg/kg (Rat) (1)
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesTopical 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 LevelNot Available
Health EffectsAntibiotic resistance
SymptomsVestibular toxicity may result in vertigo, nausea and vomiting, dizziness and loss of balance.
TreatmentHemodialysis will remove neomycin sulfate from the blood. (3)
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDDB00994
HMDB IDHMDB15129
PubChem Compound ID8378
ChEMBL IDCHEMBL449118
ChemSpider ID8075
KEGG IDC00384
UniProt IDNot Available
OMIM ID
ChEBI ID7507
BioCyc IDNot Available
CTD IDNot Available
Stitch IDNeomycin
PDB IDNMY
ACToR IDNot Available
Wikipedia LinkNeomycin
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.

MSDSLink
General References
  1. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M: DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6. Epub 2007 Nov 29. [18048412 ]
  2. Drugs.com [Link]
  3. RxList: The Internet Drug Index (2009). [Link]
Gene Regulation
Up-Regulated GenesNot Available
Down-Regulated GenesNot Available

Targets

Target Details
1. 16S RNA
References
  1. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M: DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6. Epub 2007 Nov 29. [18048412 ]
Target Details
2. Extracellular calcium-sensing receptor
General Function:
Phosphatidylinositol phospholipase c activity
Specific Function:
Senses changes in the extracellular concentration of calcium ions. The activity of this receptor is mediated by a G-protein that activates a phosphatidylinositol-calcium second messenger system.
Gene Name:
CASR
Uniprot ID:
P41180
Molecular Weight:
120672.385 Da
References
  1. Molostvov G, James S, Fletcher S, Bennett J, Lehnert H, Bland R, Zehnder D: Extracellular calcium-sensing receptor is functionally expressed in human artery. Am J Physiol Renal Physiol. 2007 Sep;293(3):F946-55. Epub 2007 May 30. [17537980 ]
3. RNA
References
  1. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M: DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6. Epub 2007 Nov 29. [18048412 ]