Record Information
Version1.0
Creation date2010-04-08 22:09:57 UTC
Update date2018-05-29 00:55:26 UTC
Primary IDFDB012039
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameSpermidine
DescriptionSpermidine, also known as SPD, belongs to the class of organic compounds known as dialkylamines. These are organic compounds containing a dialkylamine group, characterized by two alkyl groups bonded to the amino nitrogen. Spermidine is a very strong basic compound (based on its pKa). Spermidine exists in all living species, ranging from bacteria to humans. Spermidine is found, on average, in the highest concentration in oats. Spermidine has also been detected, but not quantified in, several different foods, such as ceylon cinnamons, asparagus, white cabbages, climbing beans, and bamboo shoots. This could make spermidine a potential biomarker for the consumption of these foods. Spermidine is a potentially toxic compound.
CAS Number124-20-9
Structure
Thumb
Synonyms
SynonymSource
1,5,10-TriazadecaneChEBI
4-AzaoctamethylenediamineChEBI
4-Azaoctane-1,8-diamineChEBI
N-(3-Aminopropyl)-1,4-butane-diamineChEBI
SpermidinChEBI
1,8-Diamino-4-azaoctaneHMDB
AminopropylbutandiamineHMDB
N-(3-Aminopropyl)-1,4-butanediamineHMDB
N-(3-Aminopropyl)-1,4-diamino-butaneHMDB
N-(3-Aminopropyl)-1,4-diaminobutaneHMDB
N-(3-Aminopropyl)-4-aminobutylamineHMDB
N-(4-Aminobutyl)-1,3-diaminopropaneHMDB
N-(gamma-Aminopropyl)tetramethylenediamineHMDB
SPDHMDB
1,4-Butanediamine, N-(3-aminopropyl)-biospider
1,4-Butanediamine, N1-(3-aminopropyl)-biospider
1,4-Diaminobutane, N-(3-aminopropyl)-biospider
N-(3-Aminopropyl)-1,4-butanediamine, 9CIdb_source
N-(3-Aminopropyl)butane-1,4-diaminebiospider
Predicted Properties
PropertyValueSource
Water Solubility32.7 g/LALOGPS
logP-0.62ALOGPS
logP-1.1ChemAxon
logS-0.65ALOGPS
pKa (Strongest Basic)10.68ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area64.07 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity44.97 m³·mol⁻¹ChemAxon
Polarizability18.8 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Chemical FormulaC7H19N3
IUPAC name(4-aminobutyl)(3-aminopropyl)amine
InChI IdentifierInChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
InChI KeyATHGHQPFGPMSJY-UHFFFAOYSA-N
Isomeric SMILESNCCCCNCCCN
Average Molecular Weight145.2459
Monoisotopic Molecular Weight145.157897623
Classification
Description belongs to the class of organic compounds known as dialkylamines. These are organic compounds containing a dialkylamine group, characterized by two alkyl groups bonded to the amino nitrogen.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentDialkylamines
Alternative Parents
Substituents
  • Secondary aliphatic amine
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary aliphatic amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
OntologyNo ontology term
Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateLiquid
Physical DescriptionNot Available
Mass CompositionC 57.89%; H 13.18%; N 28.93%DFC
Melting PointNot Available
Boiling PointBp14 128-130°DFC
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-00di-5910000000-48794a2dc9d682aab28fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-066u-1910000000-9fe6c1c8e8f166270be1JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-00rf-1900000000-c88ed717e55f237cf01cJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-00di-6900000000-56396208515d9020bfebJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0uki-5920000000-4aac8aba8d9635a96f1cJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-00rf-1900000000-f4b7d8b055a8d5025036JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-00di-1900000000-1be27daaf9f6d9e03752JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-05tf-0910000000-280a5c2a493fedd0e524JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-5910000000-48794a2dc9d682aab28fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-066u-1910000000-9fe6c1c8e8f166270be1JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00rf-1900000000-c88ed717e55f237cf01cJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-6900000000-56396208515d9020bfebJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0uki-5920000000-4aac8aba8d9635a96f1cJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00rf-1900000000-f4b7d8b055a8d5025036JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00di-1900000000-1be27daaf9f6d9e03752JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00rf-1900000000-866eda2dc91354bf795bJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0uki-3920000000-2165a698c4bf674e814bJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001r-9200000000-e6ccea992bf8aff10122JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00dj-9800000000-02b200749ad6548a5872JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00di-9000000000-c294fdb7876cfc47c089JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-00di-9000000000-d3055c2a8763c8034bd2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-052b-0900000000-f08a2a9ba7333f5b725cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-00b9-7900000000-062e21e4525351cbd0d4JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-014i-0900000000-31b90f68c9fde4e03f60JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0002-0920000000-28adf399f8ddd0affc22JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0udj-0930000000-3ac88b6d5c40c65f1314JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0006-9000000000-953c054969edecf62533JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-00b9-7900000000-8b03c45141b38c718dacJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-004i-0900000000-1e157eec324aa34dd64eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-0002-0900000000-f2ca6698501cf6a406dfJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-00di-9300000000-2f23967aa87f8e5f5bc1JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-00di-9000000000-91aef1c8b5a2507a16e9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-00di-9000000000-18cdaecf173b5d79902aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-00di-9000000000-f0b03de09cb13146e794JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0092-5900000000-4bd537f0811cc264f2cbJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00di-9200000000-75eacba217a63f3b8847JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00di-9000000000-8a77bd9436d55b064332JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004j-1900000000-300fe40eb32167464ab8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0729-9800000000-1a8be3c6776f3924c8b7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0abc-9000000000-6401e12d220b44018fdfJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-1900000000-79940496e89b73bb1682JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-3900000000-eb4eaf0bb3e88f274a1dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00du-9000000000-fe762fb3fcd81e27f9c7JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
ChemSpider ID1071
ChEMBL IDCHEMBL19612
KEGG Compound IDC00315
Pubchem Compound ID1102
Pubchem Substance IDNot Available
ChEBI ID16610
Phenol-Explorer IDNot Available
DrugBank IDDB03566
HMDB IDHMDB01257
CRC / DFC (Dictionary of Food Compounds) IDHCS12-B:HCS12-B
EAFUS IDNot Available
Dr. Duke IDSPERMIDINE
BIGG ID34593
KNApSAcK IDC00001431
HET IDSPD
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDSpermidine
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / Bioactivities
DescriptorIDDefinitionReference
antioxidant22586 A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. In European countries, E-numbers for permitted antioxidant food additives are from E 300 to E 324.DUKE
Enzymes
NameGene NameUniProt ID
Glycine amidinotransferase, mitochondrialGATMP50440
Histidine decarboxylaseHDCP19113
Spermidine synthaseSRMP19623
Diamine acetyltransferase 1SAT1P21673
Spermine synthaseSMSP52788
S-methyl-5'-thioadenosine phosphorylaseMTAPQ13126
Ornithine decarboxylaseODC1P11926
Ornithine decarboxylase antizyme 1OAZ1P54368
3-ketoacyl-CoA thiolase, mitochondrialACAA2P42765
Propionyl-CoA carboxylase alpha chain, mitochondrialPCCAP05165
Pathways
NameSMPDB LinkKEGG Link
Methionine MetabolismSMP00033 map00270
Spermidine and Spermine BiosynthesisSMP00445 Not Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSshow
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference— Shinbo, Y., et al. 'KNApSAcK: a comprehensive species-metabolite relationship database.' Plant Metabolomics. Springer Berlin Heidelberg, 2006. 165-181.
— Duke, James. 'Dr. Duke's Phytochemical and Ethnobotanical Databases. United States Department of Agriculture.' Agricultural Research Service, Accessed April 27 (2004).