Details of Metabolite

General Information of MET (ID: META00395)
Name Spermidine
Synonyms   Click to Show/Hide Synonyms of This Metabolite
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
Source Endogenous;Escherichia Coli Metabolite;Yeast Metabolite;Food;Drug;Toxins/Pollutant;TCM Ingredients;Microbial
Structure Type   Amines  (Click to Show/Hide the Complete Structure Type Hierarchy)
Organic nitrogen compounds
Organonitrogen compounds
Amines
PubChem CID
1102
HMDB ID
HMDB0001257
Formula
C7H19N3
Structure
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3D MOL 2D MOL
  Click to Show/Hide the Molecular/Functional Data (External Links/Property/Function) of This Metabolite
KEGG ID
C00315
DrugBank ID
DB03566
ChEBI ID
16610
FooDB ID
FDB012039
ChemSpider ID
1071
METLIN ID
254
Physicochemical Properties Molecular Weight 145.25 Topological Polar Surface Area 64.099
XlogP -1 Complexity 56.8
Heavy Atom Count 10 Rotatable Bond Count 7
Hydrogen Bond Donor Count 3 Hydrogen Bond Acceptor Count 3
Function
Spermidine is a polyamine formed from putrescine. It is found in almost all tissues in association with nucleic acids. It has been identified as a uremic toxin according to the European Uremic Toxin Working Group. Spermidine 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.
Regulatory Network
Full List of Protein(s) Regulating This Metabolite
      Hydrolases (EC 3)
            Leukotriene-C4 hydrolase (GGT1) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [1]
                      Introduced Variation Knockdown (siRNA) of GGT1
                      Induced Change Spermidine concentration: increase
                      Summary Introduced Variation         Induced Change 
                      Disease Status Renal cell carcinoma [ICD-11: 2C90]
                      Details It is reported that knockdown of GGT1 leads to the increase of spermidine levels compared with control group.
            Sulfatase sulf-1 (SULF1) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [2]
                      Introduced Variation Knockdown (shRNA) of SULF1
                      Induced Change Spermidine concentration: increase (FC = 1.33 / 1.38)
                      Summary Introduced Variation         Induced Change 
                      Disease Status Ovarian cancer [ICD-11: 2C73]
                      Details It is reported that knockdown of SULF1 leads to the increase of spermidine levels compared with control group.
      Oxidoreductases (EC 1)
            Alcohol dehydrogenase iron 1 (ADHFE1) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [3]
                      Introduced Variation Overexpression of ADHFE1
                      Induced Change Spermidine concentration: increase
                      Summary Introduced Variation         Induced Change 
                      Disease Status Breast cancer [ICD-11: 2C60]
                      Details It is reported that overexpression of ADHFE1 leads to the increase of spermidine levels compared with control group.
      Transferases (EC 2)
            Pyridoxal kinase (PDXK) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [4]
                      Introduced Variation Knockout (CRISPR/Cas9 sgRNA) of Pdxk
                      Induced Change Spermidine concentration: decrease
                      Summary Introduced Variation         Induced Change 
                      Disease Status Acute myeloid leukaemia [ICD-11: 2A60]
                      Details It is reported that knockout of Pdxk leads to the decrease of spermidine levels compared with control group.
      Translocases (EC 7)
            Polyamine-transporting ATPase 13A2 (ATP13A2) Click to Show/Hide the Full List of Regulating Pair(s):   1 Pair(s)
               Detailed Information Protein   Info click to show the details of this protein
               Regulating Pair Experim Info click to show the details of experiment for validating this pair [5]
                      Introduced Variation Knockout of ATP13A2
                      Induced Change Spermidine concentration: decrease
                      Summary Introduced Variation         Induced Change 
                      Disease Status Brain cancer [ICD-11: 2A00]
                      Details It is reported that knockout of ATP13A2 leads to the decrease of spermidine levels compared with control group.
References
1 Impairment of gamma-glutamyl transferase 1 activity in the metabolic pathogenesis of chromophobe renal cell carcinoma. Proc Natl Acad Sci U S A. 2018 Jul 3;115(27):E6274-E6282.
2 Erratum to: Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer. Cancer Metab. 2014 Nov 4;2:24.
3 ADHFE1 is a breast cancer oncogene and induces metabolic reprogramming. J Clin Invest. 2018 Jan 2;128(1):323-340.
4 Vitamin B6 Addiction in Acute Myeloid Leukemia. Cancer Cell. 2020 Jan 13;37(1):71-84.e7.
5 ATP13A2 deficiency disrupts lysosomal polyamine export. Nature. 2020 Feb;578(7795):419-424.

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