Showing Compound Card for Spermidine (CDB004901)

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Record Information
Version1.0
Created at2020-04-17 18:48:35 UTC
Updated at2022-12-13 23:36:25 UTC
CannabisDB IDCDB004901
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NameSpermidine
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 humans, spermidine participates in a number of enzymatic reactions. In particular, 5'-methylthioadenosine and spermidine can be biosynthesized from S-adenosylmethioninamine and putrescine; which is mediated by the enzyme spermidine synthase. In addition, S-adenosylmethioninamine and spermidine can be converted into 5'-methylthioadenosine and spermine through the action of the enzyme spermine synthase. In humans, spermidine is involved in spermidine and spermine biosynthesis. Outside of the human body, Spermidine is found, on average, in the highest concentration within milk (cow) and oats. Spermidine has also been detected, but not quantified in, several different foods, such as american cranberries, sour cherries, arctic blackberries, chinese broccoli, and arabica coffee. This could make spermidine a potential biomarker for the consumption of these foods. Spermidine is a potentially toxic compound. A triamine that is the 1,5,10-triaza derivative of decane. Spermidine is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
1,5,10-TriazadecaneChEBI
4-AzaoctamethylenediamineChEBI
4-Azaoctane-1,8-diamineChEBI
N-(3-Aminopropyl)-1,4-butane-diamineChEBI
SpermidinChEBI
1,8-Diamino-4-azaoctaneHMDB
AminopropylbutandiamineHMDB
N-(3-Aminopropyl)-1,4-butanediamineHMDB
N-(3-Aminopropyl)-1,4-diamino-butaneHMDB
N-(3-Aminopropyl)-1,4-diaminobutaneHMDB
N-(3-Aminopropyl)-4-aminobutylamineHMDB
N-(4-Aminobutyl)-1,3-diaminopropaneHMDB
N-(gamma-Aminopropyl)tetramethylenediamineHMDB
SPDHMDB
Chemical FormulaC7H19N3
Average Molecular Weight145.25
Monoisotopic Molecular Weight145.1579
IUPAC Name(4-aminobutyl)(3-aminopropyl)amine
Traditional Namespermidine
CAS Registry Number124-20-9
SMILES
NCCCCNCCCN
InChI Identifier
InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
InChI KeyATHGHQPFGPMSJY-UHFFFAOYSA-N
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
Ontology
Physiological effect

Health effect:

Disposition

Route of exposure:

Source:

Biological location:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point< 25 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility145 g/L at 20 °CWikipedia
logP0.0Wikipedia
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
MS/MS
NMR
Pathways
Pathways
Protein Targets
Enzymes
Transporters
Protein NameGene NameLocusUniprot IDDetails
Solute carrier family 22 member 4SLC22A45q31.1Q9H015 details
Solute carrier family 22 member 1SLC22A16q26O15245 details
Metal Bindings
Protein NameGene NameLocusUniprot IDDetails
Propionyl-CoA carboxylase alpha chain, mitochondrialPCCA13q32P05165 details
Gamma-butyrobetaine dioxygenaseBBOX111p14.2O75936 details
Betaine--homocysteine S-methyltransferase 1BHMT5q14.1Q93088 details
Agmatinase, mitochondrialAGMAT1p36.21Q9BSE5 details
Trimethyllysine dioxygenase, mitochondrialTMLHEXq28Q9NVH6 details
S-methylmethionine--homocysteine S-methyltransferase BHMT2BHMT25q13Q9H2M3 details
ReceptorsNot Available
Transcriptional FactorsNot Available
Concentrations Data
Cannabis CultivarStatusValueReferenceDetails
Alien DawgDetected and Quantified0.00153 mg/g dry wt
    • David S. Wishart,...
 details
GabriolaDetected and Quantified0.00115 mg/g dry wt
    • David S. Wishart,...
 details
Island HoneyDetected and Quantified0.00810 mg/g dry wt
    • David S. Wishart,...
 details
QuadraDetected and Quantified0.00458 mg/g dry wt
    • David S. Wishart,...
 details
Sensi StarDetected and Quantified0.00136 mg/g dry wt
    • David S. Wishart,...
 details
Tangerine DreamDetected and Quantified0.00208 mg/g dry wt
    • David S. Wishart,...
 details
HMDB IDHMDB0001257
DrugBank IDDB03566
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012039
KNApSAcK IDC00001431
Chemspider ID1071
KEGG Compound IDC00315
BioCyc IDSPERMIDINE
BiGG ID34593
Wikipedia LinkSpermidine
METLIN ID254
PubChem Compound1102
PDB IDNot Available
ChEBI ID16610
References
General ReferencesNot Available

Only showing the first 10 proteins. There are 33 proteins in total.

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Enzymes

Enzyme Details
1. Diamine acetyltransferase 1
General function:
Involved in N-acetyltransferase activity
Specific function:
Enzyme which catalyzes the acetylation of polyamines. Substrate specificity: norspermidine = spermidine >> spermine > N(1)-acetylspermine > putrescine. This highly regulated enzyme allows a fine attenuation of the intracellular concentration of polyamines. Also involved in the regulation of polyamine transport out of cells. Acts on 1,3-diaminopropane, 1,5-diaminopentane, putrescine, spermidine (forming N(1)- and N(8)-acetylspermidine), spermine, N(1)-acetylspermidine and N(8)-acetylspermidine.
Gene Name:
SAT1
Uniprot ID:
P21673
Molecular weight:
20023.8
Enzyme Details
2. 3-ketoacyl-CoA thiolase, mitochondrial
General function:
Involved in transferase activity, transferring acyl groups other than amino-acyl groups
Specific function:
Abolishes BNIP3-mediated apoptosis and mitochondrial damage.
Gene Name:
ACAA2
Uniprot ID:
P42765
Molecular weight:
41923.82
Enzyme Details
3. Peroxisomal N(1)-acetyl-spermine/spermidine oxidase
General function:
Amino acid transport and metabolism
Specific function:
Flavoenzyme which catalyzes the oxidation of N(1)-acetylspermine to spermidine and is thus involved in the polyamine back-conversion. Can also oxidize N(1)-acetylspermidine to putrescine. Substrate specificity: N(1)-acetylspermine = N(1)-acetylspermidine > N(1),N(12)-diacylspermine >> spermine. Does not oxidize spermidine. Plays an important role in the regulation of polyamine intracellular concentration and has the potential to act as a determinant of cellular sensitivity to the antitumor polyamine analogs.
Gene Name:
PAOX
Uniprot ID:
Q6QHF9
Molecular weight:
55512.64
Enzyme Details
4. Thioredoxin reductase 1, cytoplasmic
General function:
Involved in oxidoreductase activity
Specific function:
Isoform 1 may possess glutaredoxin activity as well as thioredoxin reductase activity and induces actin and tubulin polymerization, leading to formation of cell membrane protrusions. Isoform 4 enhances the transcriptional activity of estrogen receptors alpha and beta while isoform 5 enhances the transcriptional activity of the beta receptor only. Isoform 5 also mediates cell death induced by a combination of interferon-beta and retinoic acid.
Gene Name:
TXNRD1
Uniprot ID:
Q16881
Molecular weight:
70905.58
Enzyme Details
5. Choline dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity, acting on CH-OH group of donors
Specific function:
Not Available
Gene Name:
CHDH
Uniprot ID:
Q8NE62
Molecular weight:
65358.005
Enzyme Details
6. Dimethylglycine dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
DMGDH
Uniprot ID:
Q9UI17
Molecular weight:
96810.135
Enzyme Details
7. Spermine synthase
General function:
Involved in spermine synthase activity
Specific function:
Catalyzes the production of spermine from spermidine and decarboxylated S-adenosylmethionine (dcSAM).
Gene Name:
SMS
Uniprot ID:
P52788
Molecular weight:
35278.2
Enzyme Details
8. Spermidine synthase
General function:
Involved in catalytic activity
Specific function:
Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM). Has a strong preference for putrescine as substrate, and has very low activity towards 1,3-diaminopropane. Has extremely low activity towards spermidine.
Gene Name:
SRM
Uniprot ID:
P19623
Molecular weight:
33824.455
Enzyme Details
9. 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:
DHPS
Uniprot ID:
P49366
Molecular weight:
40970.28
Enzyme Details
10. Propionyl-CoA carboxylase alpha chain, mitochondrial
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
PCCA
Uniprot ID:
P05165
Molecular weight:
80058.295

Transporters

Enzyme Details
1. Solute carrier family 22 member 4
General function:
Involved in ion transmembrane transporter activity
Specific function:
Sodium-ion dependent, low affinity carnitine transporter. Probably transports one sodium ion with one molecule of carnitine. Also transports organic cations such as tetraethylammonium (TEA) without the involvement of sodium. Relative uptake activity ratio of carnitine to TEA is 1.78. A key substrate of this transporter seems to be ergothioneine (ET)
Gene Name:
SLC22A4
Uniprot ID:
Q9H015
Molecular weight:
62154.5
Enzyme Details
2. Solute carrier family 22 member 1
General function:
Involved in ion transmembrane transporter activity
Specific function:
Translocates a broad array of organic cations with various structures and molecular weights including the model compounds 1-methyl-4-phenylpyridinium (MPP), tetraethylammonium (TEA), N-1-methylnicotinamide (NMN), 4-(4-(dimethylamino)styryl)- N-methylpyridinium (ASP), the endogenous compounds choline, guanidine, histamine, epinephrine, adrenaline, noradrenaline and dopamine, and the drugs quinine, and metformin. The transport of organic cations is inhibited by a broad array of compounds like tetramethylammonium (TMA), cocaine, lidocaine, NMDA receptor antagonists, atropine, prazosin, cimetidine, TEA and NMN, guanidine, cimetidine, choline, procainamide, quinine, tetrabutylammonium, and tetrapentylammonium. Translocates organic cations in an electrogenic and pH-independent manner. Translocates organic cations across the plasma membrane in both directions. Transports the polyamines spermine and spermidine. Transports pramipexole across the basolateral membrane of the proximal tubular epithelial cells. The choline transport is activated by MMTS. Regulated by various intracellular signaling pathways including inhibition by protein kinase A activation, and endogenously activation by the calmodulin complex, the calmodulin- dependent kinase II and LCK tyrosine kinase
Gene Name:
SLC22A1
Uniprot ID:
O15245
Molecular weight:
61187.4

Only showing the first 10 proteins. There are 33 proteins in total.

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