Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000312
Identification
Name: Spermidine
Description:Spermidine is a polyamine formed from putrescine. It is found in almost all tissues in association with nucleic acids. It is found as a cation at all pH values, and is thought to help stabilize some membranes and nucleic acid structures. It is a precursor of spermine.
Structure
Thumb
Synonyms:
  • 1,5,10-Triazadecane
  • 1,8-Diamino-4-azaoctane
  • 4-Azaoctamethylenediamine
  • 4-Azaoctane-1,8-diamine
  • N-(3-aminopropyl)butane-1,4-diamine
  • Aminopropylbutandiamine
  • N-(3-Aminopropyl)-1,4-butane-diamine
  • N-(3-Aminopropyl)-1,4-butanediamine
  • N-(3-Aminopropyl)-1,4-diamino-butane
  • N-(3-Aminopropyl)-1,4-diaminobutane
  • N-(3-Aminopropyl)-4-aminobutylamine
  • N-(3-Aminopropyl)butane-1,4-diamine
  • N-(4-Aminobutyl)-1,3-diaminopropane
  • N-(g-Aminopropyl)tetramethylenediamine
  • N-(gamma-Aminopropyl)tetramethylenediamine
  • N-(γ-Aminopropyl)tetramethylenediamine
  • SPD
  • Spermidin
  • Spermidine
Chemical Formula: C7H19N3
Average Molecular Weight: 145.2459
Monoisotopic Molecular Weight: 145.157897623
InChI Key: ATHGHQPFGPMSJY-UHFFFAOYSA-N
InChI:InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
CAS number: 124-20-9
IUPAC Name:(4-aminobutyl)(3-aminopropyl)amine
Traditional IUPAC Name: spermidine
SMILES:NCCCCNCCCN
Chemical Taxonomy
Taxonomy DescriptionThis compound 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.
Kingdom Organic compounds
Super ClassOrganonitrogen compounds
Class Amines
Sub ClassSecondary amines
Direct Parent Dialkylamines
Alternative Parents
Substituents
  • Secondary aliphatic amine
  • Hydrocarbon derivative
  • Primary amine
  • Primary aliphatic amine
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Liquid
Charge:3
Melting point: < 25 °C
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility32.7 mg/mLALOGPS
logP-0.62ALOGPS
logP-1.1ChemAxon
logS-0.65ALOGPS
pKa (Strongest Basic)10.9ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area64.07 Å2ChemAxon
Rotatable Bond Count7ChemAxon
Refractivity44.97 m3·mol-1ChemAxon
Polarizability18.8 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pathways:
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)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 - GC-MSNot Available
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
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 SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Chaisiri P, Harper ME, Blamey RW, Peeling WB, Griffiths K: Plasma spermidine concentrations in patients with tumours of the breast or prostate or testis. Clin Chim Acta. 1980 Jul 1;104(3):367-75. Pubmed: 6156039
  • El Baze P, Milano G, Verrando P, Renee N, Ortonne JP: Polyamine levels in normal human skin. A comparative study of pure epidermis, pure dermis, and suction blister fluid. Arch Dermatol Res. 1983;275(4):218-21. Pubmed: 6625645
  • Hamana, K. (1996). "Distribution of diaminopropane and acetylspermidine in Enterobacteriaceae." Can J Microbiol 42:107-114. Pubmed: 8742354
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Martinet N, Beninati S, Nigra TP, Folk JE: N1N8-bis(gamma-glutamyl)spermidine cross-linking in epidermal-cell envelopes. Comparison of cross-link levels in normal and psoriatic cell envelopes. Biochem J. 1990 Oct 15;271(2):305-8. Pubmed: 2241917
  • Mirzoian PA, Promyslov MSh: [Contents of putrescine, spermidine and spermine in tissue of the human brain glial tumors] Ukr Biokhim Zh. 1979 Sep-Oct;51(5):474-6. Pubmed: 516181
  • Proctor MS, Fletcher HV Jr, Shukla JB, Rennert OM: Elevated spermidine and spermine levels in the blood of psoriasis patients. J Invest Dermatol. 1975 Oct;65(4):409-11. Pubmed: 1176793
  • Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
  • Uehara N, Shirakawa S, Uchino H, Saeki Y: Elevated contents of spermidine and spermine in the erythrocytes of cancer patients. Cancer. 1980 Jan 1;45(1):108-11. Pubmed: 7350997
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Venza M, Visalli M, Cicciu D, Teti D: Determination of polyamines in human saliva by high-performance liquid chromatography with fluorescence detection. J Chromatogr B Biomed Sci Appl. 2001 Jun 5;757(1):111-7. Pubmed: 11419735
  • Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. Pubmed: 18402659
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Bergeron, 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) Download (PDF)
External Links:
ResourceLink
CHEBI ID1643
HMDB IDHMDB01257
Pubchem Compound ID1102
Kegg IDC00315
ChemSpider ID1071
WikipediaSpermidine
BioCyc IDSPERMIDINE
EcoCyc IDSPERMIDINE
Ligand ExpoSPD

Enzymes

General function:
Involved in catalytic activity
Specific function:
Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM), which serves as an aminopropyl donor
Gene Name:
speE
Locus Tag:
PA1687
Molecular weight:
32.2 kDa
Reactions
S-adenosylmethioninamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine.
General function:
Involved in nucleotide binding
Specific function:
Part of the ABC transporter complex PotABCD involved in spermidine/putrescine import. Responsible for energy coupling to the transport system
Gene Name:
potA
Locus Tag:
PA3607
Molecular weight:
40 kDa
Reactions
ATP + H(2)O + polyamine(Out) = ADP + phosphate + polyamine(In).
General function:
Involved in transporter activity
Specific function:
Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine
Gene Name:
potB
Locus Tag:
PA3608
Molecular weight:
32.7 kDa
General function:
Involved in transporter activity
Specific function:
Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine
Gene Name:
potC
Locus Tag:
PA3609
Molecular weight:
27.7 kDa
General function:
Involved in transporter activity
Specific function:
Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine. Polyamine binding protein
Gene Name:
potD
Locus Tag:
PA3610
Molecular weight:
39.3 kDa

Transporters

General function:
Involved in nucleotide binding
Specific function:
Part of the ABC transporter complex PotABCD involved in spermidine/putrescine import. Responsible for energy coupling to the transport system
Gene Name:
potA
Locus Tag:
PA3607
Molecular weight:
40 kDa
Reactions
ATP + H(2)O + polyamine(Out) = ADP + phosphate + polyamine(In).
General function:
Involved in transporter activity
Specific function:
Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine
Gene Name:
potB
Locus Tag:
PA3608
Molecular weight:
32.7 kDa
General function:
Involved in transporter activity
Specific function:
Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine
Gene Name:
potC
Locus Tag:
PA3609
Molecular weight:
27.7 kDa
General function:
Involved in spermidine transmembrane transporter activity
Specific function:
Catalyzes the excretion of spermidine. Can also confer resistance to deoxycholate and SDS
Gene Name:
mdtI
Locus Tag:
PA1540
Molecular weight:
11.8 kDa
General function:
Involved in spermidine transmembrane transporter activity
Specific function:
Catalyzes the excretion of spermidine. Can also confer resistance to deoxycholate and SDS
Gene Name:
mdtJ
Locus Tag:
PA1541
Molecular weight:
12.7 kDa
General function:
Involved in transporter activity
Specific function:
Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine. Polyamine binding protein
Gene Name:
potD
Locus Tag:
PA3610
Molecular weight:
39.3 kDa