Record Information
Version1.0
Creation Date2016-09-30 22:43:10 UTC
Update Date2020-06-04 20:47:30 UTC
BMDB IDBMDB0001257
Secondary Accession Numbers
  • BMDB01257
Metabolite Identification
Common 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 exists as a solid, possibly soluble (in water), and a very strong basic compound (based on its pKa) molecule. Spermidine exists in all living species, ranging from bacteria to humans. Spermidine is a potentially toxic compound.
Structure
Thumb
Synonyms
ValueSource
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
Chemical FormulaC7H19N3
Average Molecular Weight145.2459
Monoisotopic Molecular Weight145.157897623
IUPAC Name(4-aminobutyl)(3-aminopropyl)amine
Traditional Namespermidine
CAS Registry Number124-20-9
SMILES
NCCCCNCCCN
InChI Identifier
InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
InChI KeyATHGHQPFGPMSJY-UHFFFAOYSA-N
Chemical Taxonomy
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
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point< 25 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-00di-5910000000-48794a2dc9d682aab28fView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-066u-1910000000-9fe6c1c8e8f166270be1View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-00rf-1900000000-c88ed717e55f237cf01cView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-00di-6900000000-56396208515d9020bfebView in MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-0uki-5920000000-4aac8aba8d9635a96f1cView in MoNA
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-00rf-1900000000-f4b7d8b055a8d5025036View in MoNA
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-00di-1900000000-1be27daaf9f6d9e03752View in MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-05tf-0910000000-280a5c2a493fedd0e524View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-5910000000-48794a2dc9d682aab28fView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-066u-1910000000-9fe6c1c8e8f166270be1View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00rf-1900000000-c88ed717e55f237cf01cView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00di-6900000000-56396208515d9020bfebView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0uki-5920000000-4aac8aba8d9635a96f1cView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00rf-1900000000-f4b7d8b055a8d5025036View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-00di-1900000000-1be27daaf9f6d9e03752View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-00rf-1900000000-866eda2dc91354bf795bView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0uki-3920000000-2165a698c4bf674e814bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001r-9200000000-e6ccea992bf8aff10122View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00dj-9800000000-02b200749ad6548a5872View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00di-9000000000-c294fdb7876cfc47c089View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-00di-9000000000-d3055c2a8763c8034bd2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-052b-0900000000-f08a2a9ba7333f5b725cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-00b9-7900000000-062e21e4525351cbd0d4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-014i-0900000000-31b90f68c9fde4e03f60View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0002-0920000000-28adf399f8ddd0affc22View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0udj-0930000000-3ac88b6d5c40c65f1314View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0006-9000000000-953c054969edecf62533View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-00b9-7900000000-8b03c45141b38c718dacView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-004i-0900000000-1e157eec324aa34dd64eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-0002-0900000000-f2ca6698501cf6a406dfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-00di-9300000000-2f23967aa87f8e5f5bc1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-00di-9000000000-91aef1c8b5a2507a16e9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-00di-9000000000-18cdaecf173b5d79902aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-00di-9000000000-f0b03de09cb13146e794View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0092-5900000000-4bd537f0811cc264f2cbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00di-9200000000-75eacba217a63f3b8847View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00di-9000000000-8a77bd9436d55b064332View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004j-1900000000-300fe40eb32167464ab8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0729-9800000000-1a8be3c6776f3924c8b7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0abc-9000000000-6401e12d220b44018fdfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-1900000000-79940496e89b73bb1682View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-3900000000-eb4eaf0bb3e88f274a1dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00du-9000000000-fe762fb3fcd81e27f9c7View in MoNA
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
2D NMR[1H, 1H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)Not AvailableView in JSpectraViewer
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Brain
  • Epidermis
  • Erythrocyte
  • Fibroblasts
  • Intestine
  • Liver
  • Longissimus Thoracis Muscle
  • Mammary Gland
  • Milk
  • Neuron
  • Placenta
  • Platelet
  • Prostate Tissue
  • Ruminal Fluid
  • Semimembranosus Muscle
  • Testis
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.2 +/- 0.1 uMNot SpecifiedNot Specified
Normal
    • Aidin Foroutan, C...
details
BrainExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
EpidermisExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
ErythrocyteExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
FibroblastsExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
IntestineExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
LiverExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Longissimus Thoracis MuscleDetected and Quantified0.09 +/- 0.03 nmol/g of tissueNot SpecifiedNot Specified
Normal
    • Aidin Foroutan, C...
details
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
details
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
details
MilkDetected and Quantified13.2 uMNot SpecifiedNot Specified
Normal
details
MilkDetected and Quantified2.200 - 4.400 uMNot SpecifiedNot Specified
Normal
details
MilkDetected and Quantified0.88 +/- 0.02 uMNot SpecifiedNot Specified
Normal
details
MilkDetected and Quantified0.89 +/- 0.02 uMNot SpecifiedNot Specified
Normal
details
MilkDetected and Quantified0.84 +/- 0.02 uMNot SpecifiedNot Specified
Normal
details
MilkDetected and Quantified0.70 +/- 0.03 uMNot SpecifiedNot Specified
Normal
details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
details
NeuronExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
PlacentaExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
PlateletExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Prostate TissueExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
details
Ruminal FluidDetected and Quantified37 +/- 22 uMNot SpecifiedNot Specified
Normal
    • Aidin Foroutan, C...
details
Semimembranosus MuscleDetected and Quantified0.11 +/- 0.04 nmol/g of tissueNot SpecifiedNot Specified
Normal
    • Aidin Foroutan, C...
details
TestisDetected and Quantified0.4 +/- 0.2 nmol/g of tissueNot SpecifiedNot Specified
Normal
    • Aidin Foroutan, C...
details
Abnormal Concentrations
Not Available
HMDB IDHMDB0001257
DrugBank IDDB03566
Phenol Explorer Compound IDNot Available
FooDB IDFDB012039
KNApSAcK IDC00001431
Chemspider ID1071
KEGG Compound IDC00315
BioCyc IDSPERMIDINE
BiGG ID34593
Wikipedia LinkSpermidine
METLIN ID254
PubChem Compound1102
PDB IDNot Available
ChEBI ID16610
References
Synthesis ReferenceBergeron, Raymond J., Jr. Preparation and formulation spermidine analogues for pharmaceutical use as tumor growth inhibitors. U.S. (2001), 31 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Motyl T, Ploszaj T, Wojtasik A, Kukulska W, Podgurniak M: Polyamines in cow's and sow's milk. Comp Biochem Physiol B Biochem Mol Biol. 1995 Jul;111(3):427-33. [PubMed:7613766 ]
  2. Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743. [PubMed:23438684 ]
  3. A. Foroutan et al. (2019). A. Foroutan et al. The Chemical Composition of Commercial Cow's Milk (in preparation). Journal of Agricultural and Food Chemistry.

Enzymes

General function:
Amino acid transport and metabolism
Specific function:
Catalyzes the production of spermine from spermidine and decarboxylated S-adenosylmethionine (dcSAM).
Gene Name:
SMS
Uniprot ID:
Q3SZA5
Molecular weight:
41224.0
Reactions
S-Adenosylmethioninamine + Spermidine → 5'-Methylthioadenosine + Sperminedetails
General function:
Posttranslational modification, protein turnover, chaperones
Specific function:
Catalyzes the NAD-dependent oxidative cleavage of spermidine and the subsequent transfer of the butylamine moiety of spermidine to the epsilon-amino group of a critical lysine residue of the eIF-5A precursor protein to form the intermediate deoxyhypusine residue. This is the first step of the post-translational modification of that lysine into an unusual amino acid residue named hypusine. Hypusination is unique to mature eIF-5A factor and is essential for its function.
Gene Name:
DHPS
Uniprot ID:
Q6EWQ6
Molecular weight:
41029.0
General function:
Involved in electron carrier activity
Specific function:
Flavoenzyme which catalyzes the oxidation of N(1)-acetylspermine to spermidine and is thus involved in the polyamine back-conversion. Can also oxidize N(1)-acetylspermidine to putrescine. Substrate specificity: N(1)-acetylspermine = N(1)-acetylspermidine > N(1),N(12)-diacylspermine >> spermine. Does not oxidize spermidine. Plays an important role in the regulation of polyamine intracellular concentration.
Gene Name:
PAOX
Uniprot ID:
Q865R1
Molecular weight:
56325.0
General function:
Carbohydrate transport and metabolism
Specific function:
Translocates a broad array of organic cations with various structures and molecular weights including the model compounds 1-methyl-4-phenylpyridinium (MPP), tetraethylammonium (TEA), N-1-methylnicotinamide (NMN), 4-(4-(dimethylamino)styryl)-N-methylpyridinium (ASP), the endogenous compounds choline, guanidine, histamine, epinephrine, adrenaline, noradrenaline and dopamine, and the drugs quinine, and metformin. The transport of organic cations is inhibited by a broad array of compounds like tetramethylammonium (TMA), cocaine, lidocaine, NMDA receptor antagonists, atropine, prazosin, cimetidine, TEA and NMN, guanidine, cimetidine, choline, procainamide, quinine, tetrabutylammonium, and tetrapentylammonium. Translocates organic cations in an electrogenic and pH-independent manner. Translocates organic cations across the plasma membrane in both directions. Transports the polyamines spermine and spermidine. Transports pramipexole across the basolateral membrane of the proximal tubular epithelial cells. The choline transport is activated by MMTS. Regulated by various intracellular signaling pathways including inhibition by protein kinase A activation, and endogenously activation by the calmodulin complex, the calmodulin-dependent kinase II and LCK tyrosine kinase (By similarity).
Gene Name:
SLC22A1
Uniprot ID:
A7MBE0
Molecular weight:
62502.0
General function:
Not Available
Specific function:
Not Available
Gene Name:
SRM
Uniprot ID:
E1BM12
Molecular weight:
33981.0
Reactions
S-Adenosylmethioninamine + Putrescine → 5'-Methylthioadenosine + Spermidinedetails