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Spermidine (YMDB00232)

Identification
YMDB IDYMDB00232
NameSpermidine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
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. Within yeast, spermidine participates in a number of enzymatic reactions. In particular, 5'-methylthioadenosine and spermidine can be biosynthesized from putrescine and S-adenosylmethioninamine; which is catalyzed by the enzyme spermidine synthase. In addition, spermidine and S-adenosylmethioninamine can be converted into 5'-methylthioadenosine and spermine; which is catalyzed by the enzyme spermine synthase. In yeast, spermidine is involved in the metabolic pathway called the beta-alanine metabolism pathway. Spermidine is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1,5,10-Triazadecane
  • 1,8-Diamino-4-azaoctane
  • 4-Azaoctamethylenediamine
  • 4-Azaoctane-1,8-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-(4-Aminobutyl)-1,3-diaminopropane
  • N-(gamma-aminopropyl)tetramethylenediamine
  • SPD
  • Spermidin
  • Spermidine
CAS number124-20-9
WeightAverage: 145.2459
Monoisotopic: 145.157897623
InChI KeyATHGHQPFGPMSJY-UHFFFAOYSA-N
InChIInChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
IUPAC Name(4-aminobutyl)(3-aminopropyl)amine
Traditional IUPAC Namespermidine
Chemical FormulaC7H19N3
SMILES[H]N([H])C([H])([H])C([H])([H])C([H])([H])N([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])N([H])[H]
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
Physical Properties
StateLiquid
Charge0
Melting point< 25 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Glutathione metabolismPW002395 ThumbThumb?image type=greyscaleThumb?image type=simple
beta-Alanine metabolismPW002381 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Arginine and proline metabolismec00330 Map00330
Glutathione metabolismec00480 Map00480
beta-Alanine metabolismec00410 Map00410
SMPDB Reactions
Spermine + water + oxygen → Hydrogen peroxide + 3-Aminopropionaldehyde + Spermidine
Putrescine + S-Adenosylmethioninamine → hydron + 5'-Methylthioadenosine + Spermidine
Spermidine + S-Adenosylmethioninamine → hydron + 5'-Methylthioadenosine + Spermine
KEGG Reactions
Spermidine + Ubiquinone-6 + water → 1,3-Diaminopropane + Ubiquinol-6 + 4-aminobutanal
Spermine + water + oxygen → Spermidine + 3-Aminopropionaldehyde + Hydrogen peroxide
Spermidine + Acetyl-CoA → hydron + Coenzyme A + N1-Acetylspermidine
Putrescine + S-Adenosylmethioninamine → Spermidine + hydron + 5'-Methylthioadenosine
Spermidine + S-Adenosylmethioninamine → Spermine + hydron + 5'-Methylthioadenosine
Concentrations
Intracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
1339 ± 67 µM YEB media with 0.5 mM glucoseaerobicBaker's yeastExperimentally Determined
Not Available
Conversion Details Here
Extracellular ConcentrationsNot 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
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Pirkov, I., Norbeck, J., Gustafsson, L., Albers, E. (2008). "A complete inventory of all enzymes in the eukaryotic methionine salvage pathway." FEBS J 275:4111-4120.18625006
  • Uemura, T., Kashiwagi, K., Igarashi, K. (2007). "Polyamine uptake by DUR3 and SAM3 in Saccharomyces cerevisiae." J Biol Chem 282:7733-7741.17218313
Synthesis Reference:Bergeron, Raymond J., Jr. Preparation and formulation spermidine analogues for pharmaceutical use as tumor growth inhibitors. U.S. (2001), 31 pp.
External Links:
ResourceLink
CHEBI ID16610
HMDB IDHMDB01257
Pubchem Compound ID1102
Kegg IDC00315
ChemSpider ID1071
FOODB IDFDB012039
WikipediaSpermidine
BioCyc IDSPERMIDINE

Enzymes

Protein Details
1. Deoxyhypusine synthase
General function:
Involved in peptidyl-lysine modification to hypusine
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 specific lysine residue of the eIF-5A precursor protein to form the intermediate deoxyhypusine residue
Gene Name:
DYS1
Uniprot ID:
P38791
Molecular weight:
42891.80078
Reactions
[eIF5A-precursor]-lysine + spermidine → [eIF5A-precursor]-deoxyhypusine + propane-1,3-diamine.
Protein Details
2. Polyamine oxidase FMS1
General function:
Amino acid transport and metabolism
Specific function:
Involved in the production of beta-alanine, a precursor of pantothenic acid. Multicopy suppressor of fenpropimorph resistance
Gene Name:
FMS1
Uniprot ID:
P50264
Molecular weight:
57805.10156
Reactions
Spermine + O(2) + H(2)O → spermidine + 3-aminopropanal + H(2)O(2).
Spermidine + O(2) + H(2)O → putrescine + 3-aminopropanal + H(2)O(2).
N(1)-acetylspermine + O(2) + H(2)O → spermidine + 3-acetamidopropanal + H(2)O(2).
N(1)-acetylspermidine + O(2) + H(2)O → putrescine + 3-acetamidopropanal + H(2)O(2).
N(8)-acetylspermidine + O(2) + H(2)O → 4-acetamidobutanal + trimethylenediamine + H(2)O(2).
Protein Details
3. Spermine synthase
General function:
Involved in catalytic activity
Specific function:
S-adenosylmethioninamine + spermidine = 5'- methylthioadenosine + spermine
Gene Name:
SPE4
Uniprot ID:
Q12455
Molecular weight:
34090.5
Reactions
S-adenosylmethioninamine + spermidine → 5'-methylthioadenosine + spermine.
Protein Details
4. Spermidine synthase
General function:
Involved in catalytic activity
Specific function:
S-adenosylmethioninamine + putrescine = 5'-S- methyl-5'-thioadenosine + spermidine
Gene Name:
SPE3
Uniprot ID:
Q12074
Molecular weight:
33323.80078
Reactions
S-adenosylmethioninamine + putrescine → 5'-S-methyl-5'-thioadenosine + spermidine.

Transporters

Protein Details
1. General amino-acid permease GAP1
General function:
Involved in transport
Specific function:
Permease for various amino acids as well as for GABA. Can also transport L-cysteine and beta-alanine
Gene Name:
GAP1
Uniprot ID:
P19145
Molecular weight:
65654.89844
Protein Details
2. Urea active transporter
General function:
Involved in transporter activity
Specific function:
Required for active transport of urea
Gene Name:
DUR3
Uniprot ID:
P33413
Molecular weight:
80616.10156
Protein Details
3. Polyamine transporter TPO5
General function:
Involved in transport
Specific function:
Required for polyamine transport. Transports putrescine effectively and spermidine less effectively
Gene Name:
TPO5
Uniprot ID:
P36029
Molecular weight:
69242.0
Protein Details
4. Polyamine transporter 1
General function:
Involved in transmembrane transport
Specific function:
Cell membrane polyamine/proton antiporter, involved in the detoxification of excess polyamines in the cytoplasm. Catalyzes polyamine uptake at alkaline pH and excretion at acidic pH. Recognizes spermidine, spermine and putrescine, the polyamine analogs methylglyoxal bis(guanylhydrazone) (MGBG) and paraquat, the antimalarial drug quinidine, and cycloheximide. Confers resistance to the non-steroidal anti-inflammatory drug indomethacin
Gene Name:
TPO1
Uniprot ID:
Q07824
Molecular weight:
64271.60156
Protein Details
5. S-adenosylmethionine permease SAM3
General function:
Involved in transport
Specific function:
High-affinity S-adenosylmethionine permease, required for utilization of S-adenosylmethionine as a sulfur source
Gene Name:
SAM3
Uniprot ID:
Q08986
Molecular weight:
64353.0
Protein Details
6. General amino acid permease AGP2
General function:
Involved in transport
Specific function:
General amino acid permease with broad substrate specificity. Can also transport carnitine
Gene Name:
AGP2
Uniprot ID:
P38090
Molecular weight:
67261.29688