Human Metabolome Database: Showing metabocard for Amikacin (HMDB0014622)

You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.

Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

4.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:49 UTC

Update Date

2020-02-26 21:40:00 UTC

HMDB ID

HMDB0014622

Secondary Accession Numbers

HMDB14622

Metabolite Identification

Common Name

Amikacin

Description

Amikacin is a semi-synthetic aminoglycoside antibiotic derived from kanamycin A. Similar to other aminoglycosides, amikacin disrupts bacterial protein synthesis by binding to the 30S ribosome of susceptible organisms. Binding interferes with mRNA binding and tRNA acceptor sites leading to the production of non-functional or toxic peptides. Other mechanisms not fully understood may confer the bactericidal effects of amikacin. Amikacin is also nephrotoxic and ototoxic.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
1-N-(L(-)-gamma-Amino-alpha-hydroxybutyryl)kanamycin a	ChEBI
Amicacin	ChEBI
Amiglyde-V	ChEBI
Amikacina	ChEBI
Amikacine	ChEBI
Amikacinum	ChEBI
Amikavet	ChEBI
Briclin	ChEBI
O-3-Amino-3-deoxy-alpha-D-glucopyranosyl-(1->4)-O-(6-amino-6-deoxy-alpha-D-glucopyranosyl-(1->6))-N(3)-(4-amino-L-2-hydroxybutyryl)-2-deoxy-L-streptamine	ChEBI
AMK	Kegg
1-N-(L(-)-g-Amino-a-hydroxybutyryl)kanamycin a	Generator
1-N-(L(-)-Γ-amino-α-hydroxybutyryl)kanamycin a	Generator
O-3-Amino-3-deoxy-a-D-glucopyranosyl-(1->4)-O-(6-amino-6-deoxy-a-D-glucopyranosyl-(1->6))-N(3)-(4-amino-L-2-hydroxybutyryl)-2-deoxy-L-streptamine	Generator
O-3-Amino-3-deoxy-α-D-glucopyranosyl-(1->4)-O-(6-amino-6-deoxy-α-D-glucopyranosyl-(1->6))-N(3)-(4-amino-L-2-hydroxybutyryl)-2-deoxy-L-streptamine	Generator
Amikacin base	HMDB
Amikacin dihydrate	HMDB
Amikacin sulfate	HMDB
ANTIBIOTIC BB-K8	HMDB
BB-K8	HMDB
A.M.K	HMDB
Amikacina normon	HMDB
Amikafur	HMDB
Amikason's	HMDB
Amikin	HMDB
Bristol myers squibb brand OF amikacin sulfate	HMDB
Bristol-myers squibb brand OF amikacin sulfate	HMDB
Collins brand OF amikacin sulfate	HMDB
Fustery brand OF amikacin sulfate	HMDB
Galen brand OF amikacin sulfate	HMDB
Gamikal	HMDB
Medical, amikacina	HMDB
Normon, amikacina	HMDB
Son's brand OF amikacin sulfate	HMDB
Sulfate, amikacin	HMDB
Amikacina medical	HMDB
Amikalem	HMDB
Amiklin	HMDB
Apothecon brand OF amikacin sulfate	HMDB
BB K 8	HMDB
BB-K 8	HMDB
BBK 8	HMDB
Norman brand OF amikacin sulfate	HMDB
Amikayect	HMDB
Amukin	HMDB
BBK8	HMDB
Biclin	HMDB
Biklin	HMDB
Cryopharma brand OF amikacin sulfate	HMDB
Grossmann brand OF amikacin sulfate	HMDB
Kanbine	HMDB
Lemery brand OF amikacin sulfate	HMDB
Mead johnson brand OF amikacin sulfate	HMDB
Yectamid	HMDB
BB K8	HMDB
Medical brand OF amikacin sulfate	HMDB
Oprad	HMDB
Pisa brand OF amikacin sulfate	HMDB
Rovi brand OF amikacin sulfate	HMDB

Chemical Formula

C₂₂H₄₃N₅O₁₃

Average Molecular Weight

585.6025

Monoisotopic Molecular Weight

585.285736487

IUPAC Name

(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-2-{[(2S,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide

Traditional Name

amikacin

CAS Registry Number

37517-28-5

SMILES

NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](N)[C@H]1O

InChI Identifier

InChI=1S/C22H43N5O13/c23-2-1-8(29)20(36)27-7-3-6(25)18(39-22-16(34)15(33)13(31)9(4-24)37-22)17(35)19(7)40-21-14(32)11(26)12(30)10(5-28)38-21/h6-19,21-22,28-35H,1-5,23-26H2,(H,27,36)/t6-,7+,8-,9+,10+,11-,12+,13+,14+,15-,16+,17-,18+,19-,21+,22+/m0/s1

InChI Key

LKCWBDHBTVXHDL-RMDFUYIESA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as 4,6-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C6-positions.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

4,6-disubstituted 2-deoxystreptamines

Alternative Parents

Substituents

4,6-disubstituted 2-deoxystreptamine
Gamma amino acid or derivatives
Glycosyl compound
O-glycosyl compound
Aminocyclitol or derivatives
Cyclohexanol
Cyclohexylamine
Fatty acyl
Monosaccharide
N-acyl-amine
Cyclitol or derivatives
Fatty amide
Oxane
1,3-aminoalcohol
Cyclic alcohol
Carboxamide group
Secondary alcohol
Secondary carboxylic acid amide
Amino acid or derivatives
1,2-aminoalcohol
Carboxylic acid derivative
Polyol
Organoheterocyclic compound
Oxacycle
Acetal
Organic nitrogen compound
Primary aliphatic amine
Organonitrogen compound
Carbonyl group
Primary alcohol
Primary amine
Hydrocarbon derivative
Amine
Alcohol
Organic oxide
Organopnictogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

alpha-D-glucoside (CHEBI:2637 )
aminoglycoside (CHEBI:2637 )
carboxamide (CHEBI:2637 )
amino cyclitol glycoside (CHEBI:2637 )

Ontology

Disposition

Biological location:

Biofluid and excreta:

Subcellular:

Cytoplasm

Process

Naturally occurring process:

Biological process:

Biochemical pathway:

Amikacin Action Pathway

Role

Industrial application:

Drug

Household products:

Antimicrobial agent:

Antibacterial

Pharmaceutical industry:

Pharmaceutical

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	203 - 204 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	49.7 g/L	Not Available
LogP	-7.4	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	49.7 g/L	ALOGPS
logP	-3.2	ALOGPS
logP	-8.6	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	12.1	ChemAxon
pKa (Strongest Basic)	9.79	ChemAxon
Physiological Charge	4	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	13	ChemAxon
Polar Surface Area	331.94 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	129.84 m³·mol⁻¹	ChemAxon
Polarizability	58.2 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	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0hh9-9803480000-4e62c20842f82ac0dc88	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-001i-9400112000-f033c515f4f33f591c6d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0arr-0012930000-e9e5c2d0a10606a482a9	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-08fr-1172910000-aa60237b3c5b04a8a3e9	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03k9-4589400000-6018610d9123baec32bf	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0089-3804890000-fcfb985392039be545de	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00dl-7323930000-388eeb644330ca9e4545	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0229-9787300000-fe9d1c5ff399b6290a43	Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Amikacin Action Pathway		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00479	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00479	21059682	details