Spermidine (ECMDB01257) (M2MDB000312)
| Record Information | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Version | 2.0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Creation Date | 2012-05-31 13:48:27 -0600 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Update Date | 2015-09-13 12:56:10 -0600 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Secondary Accession Numbers |
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| 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 |  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Synonyms: |
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| Chemical Formula: | C7H19N3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Weight: | Average: 145.2459 Monoisotopic: 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Kingdom | Organic compounds | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Super Class | Organic nitrogen compounds | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Class | Organonitrogen compounds | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sub Class | Amines | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Direct Parent | Dialkylamines | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Alternative Parents | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Substituents |
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| Molecular Framework | Aliphatic acyclic compounds | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| External Descriptors |
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| Physical Properties | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| State: | Liquid | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Charge: | 3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Melting point: | < 25 °C | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Experimental Properties: |
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| Predicted Properties |
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| Biological Properties | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cellular Locations: | Cytoplasm | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reactions: | Adenosine triphosphate + Water + Spermidine > ADP + Hydrogen ion + Phosphate + Spermidine Adenosine triphosphate + Water + Spermidine > ADP + Hydrogen ion + Phosphate + Spermidine S-Adenosylmethioninamine + Putrescine + Ethylenediamine <> 5'-Methylthioadenosine + Hydrogen ion + Spermidine Acetyl-CoA + Spermidine > N1-Acetylspermidine + Coenzyme A + Hydrogen ion Acetyl-CoA + Spermidine > Coenzyme A + Hydrogen ion + N8-Acetylspermidine Adenosine triphosphate + Glutathione + Spermidine <> ADP + Glutathionylspermidine + Hydrogen ion + Phosphate Glutathionylspermidine + Water <> Glutathione + Spermidine Adenosine triphosphate + Glutathione + Spermidine <> ADP + Phosphate + Glutathionylspermidine S-Adenosylmethioninamine + Putrescine <> 5'-Methylthioadenosine + Spermidine S-Adenosylmethioninamine + Spermidine <> 5'-Methylthioadenosine + Spermine Adenosine triphosphate + Spermidine + Water > ADP + Phosphate + Spermidine + Hydrogen ion Adenosine triphosphate + Spermidine + Water > ADP + Phosphate + Spermidine + Hydrogen ion Glutathionylspermidine + Water > Glutathione + Spermidine Spermidine + Glutathione + Adenosine triphosphate > Hydrogen ion + Glutathionylspermidine + ADP + Phosphate Acetyl-CoA + Spermidine <> N1-Acetylspermidine + Hydrogen ion + Coenzyme A Putrescine + S-Adenosylmethioninamine > Hydrogen ion + Spermidine + 5'-Methylthioadenosine Glutathione + Spermidine + Adenosine triphosphate > Glutathionylspermidine + ADP + Inorganic phosphate S-Adenosylmethioninamine + Putrescine > 5'-Methylthioadenosine + Spermidine Putrescine + S-Adenosylmethioninamine > Spermidine + Hydrogen ion + 5'-S-methyl-5'-thioadenosine Decarboxy-SAM + Putrescine > 5'-Methylthioadenosine + Spermidine + Hydrogen ion S-Adenosylmethioninamine + Putrescine + Ethylenediamine <>5 5'-Methylthioadenosine + Hydrogen ion + Spermidine S-Adenosylmethioninamine + Putrescine + Ethylenediamine <>5 5'-Methylthioadenosine + Hydrogen ion + Spermidine | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| SMPDB Pathways: |
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| KEGG Pathways: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| EcoCyc Pathways: |
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| Concentrations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Find out more about how we convert literature concentrations. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Spectra | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Spectra: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| References | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| References: |
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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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Material Safety Data Sheet (MSDS) | Download (PDF) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Links | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| External Links: |
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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
- Uniprot ID:
- P09158
- Molecular weight:
- 32321
Reactions
| S-adenosylmethioninamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine. |
- General function:
- Involved in N-acetyltransferase activity
- Specific function:
- Regulates polyamine concentration by their degradation. Acts on spermidine, forming N(1)- and N(8)-acetylspermidine
- Gene Name:
- speG
- Uniprot ID:
- P0A951
- Molecular weight:
- 21887
Reactions
| Acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine. |
- General function:
- Amino acid transport and metabolism
- Specific function:
- Catalyzes the formation of an amide bond between glutathione and spermidine coupled with hydrolysis of ATP; also catalyzes the hydrolysis of glutathionylspermidine to glutathione and spermidine
- Gene Name:
- gsp
- Uniprot ID:
- P0AES0
- Molecular weight:
- 70531
Reactions
| Glutathione + spermidine + ATP = glutathionylspermidine + ADP + phosphate. |
| Glutathionylspermidine + H(2)O = glutathione + 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
- Uniprot ID:
- P69874
- Molecular weight:
- 43028
Reactions
| ATP + H(2)O + polyamine(Out) = ADP + phosphate + polyamine(In). |
- General function:
- Involved in transporter activity
- Specific function:
- Probably part of the binding-protein-dependent transport system ydcSTUV
- Gene Name:
- ydcS
- Uniprot ID:
- P76108
- Molecular weight:
- 42295
- General function:
- Involved in nucleotide binding
- Specific function:
- Probably part of a binding-protein-dependent transport system ydcSTUV. Probably responsible for energy coupling to the transport system
- Gene Name:
- ydcT
- Uniprot ID:
- P77795
- Molecular weight:
- 37040
- General function:
- Involved in transporter activity
- Specific function:
- Probably part of the binding-protein-dependent transport system ydcSTUV; probably responsible for the translocation of the substrate across the membrane
- Gene Name:
- ydcU
- Uniprot ID:
- P77156
- Molecular weight:
- 34360
- General function:
- Involved in transporter activity
- Specific function:
- Probably part of the binding-protein-dependent transport system ydcSTUV; probably responsible for the translocation of the substrate across the membrane
- Gene Name:
- ydcV
- Uniprot ID:
- P0AFR9
- Molecular weight:
- 28722
- 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
- Uniprot ID:
- P0AFK4
- Molecular weight:
- 31062
- 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
- Uniprot ID:
- P0AFK6
- Molecular weight:
- 29111
- 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
- Uniprot ID:
- P0AFK9
- Molecular weight:
- 38867
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
- Uniprot ID:
- P69874
- Molecular weight:
- 43028
Reactions
| ATP + H(2)O + polyamine(Out) = ADP + phosphate + polyamine(In). |
- General function:
- Involved in transporter activity
- Specific function:
- Probably part of the binding-protein-dependent transport system ydcSTUV
- Gene Name:
- ydcS
- Uniprot ID:
- P76108
- Molecular weight:
- 42295
- General function:
- Involved in nucleotide binding
- Specific function:
- Probably part of a binding-protein-dependent transport system ydcSTUV. Probably responsible for energy coupling to the transport system
- Gene Name:
- ydcT
- Uniprot ID:
- P77795
- Molecular weight:
- 37040
- General function:
- Involved in transporter activity
- Specific function:
- Probably part of the binding-protein-dependent transport system ydcSTUV; probably responsible for the translocation of the substrate across the membrane
- Gene Name:
- ydcU
- Uniprot ID:
- P77156
- Molecular weight:
- 34360
- General function:
- Involved in transporter activity
- Specific function:
- Probably part of the binding-protein-dependent transport system ydcSTUV; probably responsible for the translocation of the substrate across the membrane
- Gene Name:
- ydcV
- Uniprot ID:
- P0AFR9
- Molecular weight:
- 28722
- 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
- Uniprot ID:
- P0AFK4
- Molecular weight:
- 31062
- 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
- Uniprot ID:
- P0AFK6
- Molecular weight:
- 29111
- 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
- Uniprot ID:
- P69210
- Molecular weight:
- 11720
- 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
- Uniprot ID:
- P69212
- Molecular weight:
- 13115
- General function:
- Involved in transporter activity
- Specific function:
- Non-specific porin
- Gene Name:
- ompN
- Uniprot ID:
- P77747
- Molecular weight:
- 41220
- General function:
- Involved in transporter activity
- Specific function:
- Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
- Gene Name:
- phoE
- Uniprot ID:
- P02932
- Molecular weight:
- 38922
- General function:
- Involved in transporter activity
- Specific function:
- OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
- Gene Name:
- ompF
- Uniprot ID:
- P02931
- Molecular weight:
- 39333
- General function:
- Involved in transporter activity
- Specific function:
- Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
- Gene Name:
- ompC
- Uniprot ID:
- P06996
- Molecular weight:
- 40368
- 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
- Uniprot ID:
- P0AFK9
- Molecular weight:
- 38867