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Identification |
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YMDB ID | YMDB00232 |
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Name | Spermidine |
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Species | Saccharomyces cerevisiae |
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Strain | Baker's yeast |
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Description | Spermidine, 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 mediated 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. |
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Structure | |
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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
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CAS number | 124-20-9 |
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Weight | Average: 145.2459 Monoisotopic: 145.157897623 |
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InChI Key | ATHGHQPFGPMSJY-UHFFFAOYSA-N |
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InChI | InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2 |
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IUPAC Name | (4-aminobutyl)(3-aminopropyl)amine |
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Traditional IUPAC Name | spermidine |
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Chemical Formula | C7H19N3 |
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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] |
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Chemical Taxonomy |
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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. |
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Kingdom | Organic compounds |
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Super Class | Organic nitrogen compounds |
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Class | Organonitrogen compounds |
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Sub Class | Amines |
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Direct Parent | Dialkylamines |
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Alternative Parents | |
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Substituents | - Secondary aliphatic amine
- Organopnictogen compound
- Hydrocarbon derivative
- Primary amine
- Primary aliphatic amine
- Aliphatic acyclic compound
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Molecular Framework | Aliphatic acyclic compounds |
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External Descriptors | |
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Physical Properties |
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State | Liquid |
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Charge | 0 |
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Melting point | < 25 °C |
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Experimental Properties | Property | Value | Reference |
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Water Solubility | Not Available | PhysProp | LogP | Not Available | PhysProp |
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Predicted Properties | |
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Biological Properties |
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Cellular Locations | |
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Organoleptic Properties | Not Available |
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SMPDB Pathways | |
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KEGG Pathways | |
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SMPDB Reactions | |
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KEGG Reactions | |
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Concentrations |
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Intracellular Concentrations | Intracellular Concentration | Substrate | Growth Conditions | Strain | Citation |
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1339 ± 67 µM | YEB media with 0.5 mM glucose | aerobic | Baker's yeast | Experimentally Determined Not Available | Conversion Details Here |
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Extracellular Concentrations | Not Available |
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Spectra |
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Spectra | Spectrum Type | Description | Splash Key | View |
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GC-MS | GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS) | splash10-00di-5910000000-48794a2dc9d682aab28f | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS) | splash10-066u-1910000000-9fe6c1c8e8f166270be1 | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized) | splash10-00rf-1900000000-c88ed717e55f237cf01c | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS) | splash10-00di-6900000000-56396208515d9020bfeb | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-MS (4 TMS) | splash10-0uki-5920000000-4aac8aba8d9635a96f1c | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-MS (5 TMS) | splash10-00rf-1900000000-f4b7d8b055a8d5025036 | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-MS (5 TMS) | splash10-00di-1900000000-1be27daaf9f6d9e03752 | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - EI-B (Non-derivatized) | splash10-05tf-0910000000-280a5c2a493fedd0e524 | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-EI-TOF (Non-derivatized) | splash10-00di-5910000000-48794a2dc9d682aab28f | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-EI-TOF (Non-derivatized) | splash10-066u-1910000000-9fe6c1c8e8f166270be1 | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-EI-TOF (Non-derivatized) | splash10-00rf-1900000000-c88ed717e55f237cf01c | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-EI-TOF (Non-derivatized) | splash10-00di-6900000000-56396208515d9020bfeb | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-MS (Non-derivatized) | splash10-0uki-5920000000-4aac8aba8d9635a96f1c | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-MS (Non-derivatized) | splash10-00rf-1900000000-f4b7d8b055a8d5025036 | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-MS (Non-derivatized) | splash10-00di-1900000000-1be27daaf9f6d9e03752 | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-EI-TOF (Non-derivatized) | splash10-00rf-1900000000-866eda2dc91354bf795b | JSpectraViewer | MoNA | GC-MS | GC-MS Spectrum - GC-EI-TOF (Non-derivatized) | splash10-0uki-3920000000-2165a698c4bf674e814b | JSpectraViewer | MoNA | Predicted GC-MS | Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive | splash10-001r-9200000000-e6ccea992bf8aff10122 | JSpectraViewer | LC-MS/MS | LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated) | splash10-00dj-9800000000-02b200749ad6548a5872 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated) | splash10-00di-9000000000-c294fdb7876cfc47c089 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated) | splash10-00di-9000000000-d3055c2a8763c8034bd2 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive | splash10-052b-0900000000-f08a2a9ba7333f5b725c | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive | splash10-00b9-7900000000-062e21e4525351cbd0d4 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive | splash10-014i-0900000000-31b90f68c9fde4e03f60 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive | splash10-0002-0920000000-28adf399f8ddd0affc22 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive | splash10-0udj-0930000000-3ac88b6d5c40c65f1314 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive | splash10-0006-9000000000-953c054969edecf62533 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive | splash10-00b9-7900000000-8b03c45141b38c718dac | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive | splash10-004i-0900000000-1e157eec324aa34dd64e | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive | splash10-0002-0900000000-f2ca6698501cf6a406df | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive | splash10-00di-9300000000-2f23967aa87f8e5f5bc1 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive | splash10-00di-9000000000-91aef1c8b5a2507a16e9 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive | splash10-00di-9000000000-18cdaecf173b5d79902a | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive | splash10-00di-9000000000-f0b03de09cb13146e794 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QTOF , positive | splash10-0092-5900000000-4bd537f0811cc264f2cb | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QTOF , positive | splash10-00di-9200000000-75eacba217a63f3b8847 | JSpectraViewer | MoNA | LC-MS/MS | LC-MS/MS Spectrum - LC-ESI-QTOF , positive | splash10-00di-9000000000-8a77bd9436d55b064332 | JSpectraViewer | MoNA | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 10V, Positive | splash10-004j-1900000000-300fe40eb32167464ab8 | JSpectraViewer | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 20V, Positive | splash10-0729-9800000000-1a8be3c6776f3924c8b7 | JSpectraViewer | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 40V, Positive | splash10-0abc-9000000000-6401e12d220b44018fdf | JSpectraViewer | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 10V, Negative | splash10-0006-1900000000-79940496e89b73bb1682 | JSpectraViewer | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 20V, Negative | splash10-0006-3900000000-eb4eaf0bb3e88f274a1d | JSpectraViewer | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 40V, Negative | splash10-00du-9000000000-fe762fb3fcd81e27f9c7 | JSpectraViewer | 1D NMR | 1H NMR Spectrum | Not Available | JSpectraViewer | 2D NMR | [1H,1H] 2D NMR Spectrum | Not Available | JSpectraViewer | 2D NMR | [1H,13C] 2D NMR Spectrum | Not Available | JSpectraViewer |
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References |
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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
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Synthesis Reference: | Bergeron, Raymond J., Jr. Preparation and formulation spermidine analogues for pharmaceutical use as tumor growth inhibitors. U.S. (2001), 31 pp. |
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