ContaminantDB: Spermidine

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References Targets (19)XML

Record Information

Version

1.0

Creation Date

2014-08-29 05:48:44 UTC

Update Date

2026-05-14 17:50:39 UTC

Accession Number

CHEM003127

Identification

Common Name

Spermidine

Class

Small Molecule

Description

Spermidine is a uremic toxin. Uremic toxins can be subdivided into three major groups based upon their chemical and physical characteristics: 1) small, water-soluble, non-protein-bound compounds, such as urea; 2) small, lipid-soluble and/or protein-bound compounds, such as the phenols and 3) larger so-called middle-molecules, such as beta2-microglobulin. Chronic exposure of uremic toxins can lead to a number of conditions including renal damage, chronic kidney disease and cardiovascular disease. 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.

Contaminant Sources

FooDB Chemicals
HMDB Contaminants - Feces
HMDB Contaminants - Urine
T3DB toxins

Contaminant Type

Amine
Food Toxin
Metabolite
Natural Compound
Organic Compound
Uremic Toxin

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
1,5,10-Triazadecane	ChEBI
4-Azaoctamethylenediamine	ChEBI
4-Azaoctane-1,8-diamine	ChEBI
N-(3-Aminopropyl)-1,4-butane-diamine	ChEBI
Spermidin	ChEBI
1,8-Diamino-4-azaoctane	HMDB
Aminopropylbutandiamine	HMDB
N-(3-Aminopropyl)-1,4-butanediamine	HMDB
N-(3-Aminopropyl)-1,4-diamino-butane	HMDB
N-(3-Aminopropyl)-1,4-diaminobutane	HMDB
N-(3-Aminopropyl)-4-aminobutylamine	HMDB
N-(4-Aminobutyl)-1,3-diaminopropane	HMDB
N-(gamma-Aminopropyl)tetramethylenediamine	HMDB
SPD	HMDB

Chemical Formula

C₇H₁₉N₃

Average Molecular Mass

145.246 g/mol

Monoisotopic Mass

145.158 g/mol

CAS Registry Number

124-20-9

IUPAC Name

(4-aminobutyl)(3-aminopropyl)amine

Traditional Name

spermidine

SMILES

NCCCCNCCCN

InChI Identifier

InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2

InChI Key

ATHGHQPFGPMSJY-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.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

Dialkylamines

Alternative Parents

Substituents

Secondary aliphatic amine
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary aliphatic amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

triamine (CHEBI:16610 )
polyazaalkane (CHEBI:16610 )

Biological Properties

Status

Detected and Not Quantified

Origin

Endogenous

Cellular Locations

Cytoplasm
Extracellular

Biofluid Locations

Not Available

Tissue Locations

Brain
Erythrocyte
Fibroblasts
Intestine
Liver
Neuron
Platelet
Prostate
Skin
Testes

Pathways

Name	SMPDB Link	KEGG Link
Methionine Metabolism	SMP00033	map00270
Spermidine and Spermine Biosynthesis	SMP00445	Not Available

Applications

Not Available

Biological Roles

fundamental metabolite

Chemical Roles

Not Available

Physical Properties

State

Liquid

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	< 25°C
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	32.7 g/L	ALOGPS
logP	-0.62	ALOGPS
logP	-1.1	ChemAxon
logS	-0.65	ALOGPS
pKa (Strongest Basic)	10.68	ChemAxon
Physiological Charge	3	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	64.07 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	44.97 m³·mol⁻¹	ChemAxon
Polarizability	18.8 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-00di-5910000000-48794a2dc9d682aab28f	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-066u-1910000000-9fe6c1c8e8f166270be1	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)	splash10-00rf-1900000000-c88ed717e55f237cf01c	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-00di-6900000000-56396208515d9020bfeb	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-0uki-5920000000-4aac8aba8d9635a96f1c	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-00rf-1900000000-f4b7d8b055a8d5025036	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-00di-1900000000-1be27daaf9f6d9e03752	Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-05tf-0910000000-280a5c2a493fedd0e524	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-5910000000-48794a2dc9d682aab28f	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-066u-1910000000-9fe6c1c8e8f166270be1	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00rf-1900000000-c88ed717e55f237cf01c	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-6900000000-56396208515d9020bfeb	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0uki-5920000000-4aac8aba8d9635a96f1c	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00rf-1900000000-f4b7d8b055a8d5025036	Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-1900000000-1be27daaf9f6d9e03752	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00rf-1900000000-866eda2dc91354bf795b	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uki-3920000000-2165a698c4bf674e814b	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001r-9200000000-e6ccea992bf8aff10122	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-00dj-9800000000-02b200749ad6548a5872	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-9000000000-c294fdb7876cfc47c089	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00di-9000000000-d3055c2a8763c8034bd2	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-052b-0900000000-f08a2a9ba7333f5b725c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-00b9-7900000000-062e21e4525351cbd0d4	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-0900000000-31b90f68c9fde4e03f60	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0002-0920000000-28adf399f8ddd0affc22	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0udj-0930000000-3ac88b6d5c40c65f1314	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-9000000000-953c054969edecf62533	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-00b9-7900000000-8b03c45141b38c718dac	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-004i-0900000000-1e157eec324aa34dd64e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-0002-0900000000-f2ca6698501cf6a406df	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-00di-9300000000-2f23967aa87f8e5f5bc1	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-00di-9000000000-91aef1c8b5a2507a16e9	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00di-9000000000-18cdaecf173b5d79902a	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-00di-9000000000-f0b03de09cb13146e794	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0092-5900000000-4bd537f0811cc264f2cb	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-00di-9200000000-75eacba217a63f3b8847	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-00di-9000000000-8a77bd9436d55b064332	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-1900000000-300fe40eb32167464ab8	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0729-9800000000-1a8be3c6776f3924c8b7	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0abc-9000000000-6401e12d220b44018fdf	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-1900000000-79940496e89b73bb1682	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-3900000000-eb4eaf0bb3e88f274a1d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00du-9000000000-fe762fb3fcd81e27f9c7	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Toxicity Profile

Route of Exposure

Endogenous, Ingestion, Dermal (contact)

Mechanism of Toxicity

Uremic toxins such as spermidine are actively transported into the kidneys via organic ion transporters (especially OAT3). Increased levels of uremic toxins can stimulate the production of reactive oxygen species. This seems to be mediated by the direct binding or inhibition by uremic toxins of the enzyme NADPH oxidase (especially NOX4 which is abundant in the kidneys and heart) (3). Reactive oxygen species can induce several different DNA methyltransferases (DNMTs) which are involved in the silencing of a protein known as KLOTHO. KLOTHO has been identified as having important roles in anti-aging, mineral metabolism, and vitamin D metabolism. A number of studies have indicated that KLOTHO mRNA and protein levels are reduced during acute or chronic kidney diseases in response to high local levels of reactive oxygen species (4).

Metabolism

Uremic toxins tend to accumulate in the blood either through dietary excess or through poor filtration by the kidneys. Most uremic toxins are metabolic waste products and are normally excreted in the urine or feces.

Toxicity Values

Not Available

Lethal Dose

Not Available

Carcinogenicity (IARC Classification)

No indication of carcinogenicity to humans (not listed by IARC).

Uses/Sources

Naturally produced by the body (endogenous).

Minimum Risk Level

Not Available

Health Effects

Chronic exposure to uremic toxins can lead to a number of conditions including renal damage, chronic kidney disease and cardiovascular disease.

Symptoms

As a uremic toxin, this compound can cause uremic syndrome. Uremic syndrome may affect any part of the body and can cause nausea, vomiting, loss of appetite, and weight loss. It can also cause changes in mental status, such as confusion, reduced awareness, agitation, psychosis, seizures, and coma. Abnormal bleeding, such as bleeding spontaneously or profusely from a very minor injury can also occur. Heart problems, such as an irregular heartbeat, inflammation in the sac that surrounds the heart (pericarditis), and increased pressure on the heart can be seen in patients with uremic syndrome. Shortness of breath from fluid buildup in the space between the lungs and the chest wall (pleural effusion) can also be present.

Treatment

Kidney dialysis is usually needed to relieve the symptoms of uremic syndrome until normal kidney function can be restored.

Concentrations

Not Available

External Links

DrugBank ID

DB03566

HMDB ID

HMDB0001257

FooDB ID

FDB012039

Phenol Explorer ID

Not Available

KNApSAcK ID

BiGG ID

BioCyc ID

METLIN ID

PDB ID

Not Available

Wikipedia Link

Chemspider ID

ChEBI ID

PubChem Compound ID

Kegg Compound ID

YMDB ID

ECMDB ID

References

Synthesis Reference

Raymond J. Bergeron, Jr., “Methods and intermediates for the preparation of spermidine, homospermidine and norspermidine.” U.S. Patent US4505861, issued July, 1981.

MSDS

Link

General References

1. Bergeron, Raymond J., Jr. Preparation and formulation spermidine analogues for pharmaceutical use as tumor growth inhibitors. U.S. (2001), 31 pp.

2. Motyl T, Ploszaj T, Wojtasik A, Kukulska W, Podgurniak M: Polyamines in cow's and sow's milk. Comp Biochem Physiol B Biochem Mol Biol. 1995 Jul;111(3):427-33.

3. Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743.

4. A. Foroutan et al. The Chemical Composition of Commercial Cow's Milk (in preparation)

5. Bergeron, Raymond J., Jr. Preparation and formulation spermidine analogues for pharmaceutical use as tumor growth inhibitors. U.S. (2001), 31 pp.

6. Venza M, Visalli M, Cicciu D, Teti D: Determination of polyamines in human saliva by high-performance liquid chromatography with fluorescence detection. J Chromatogr B Biomed Sci Appl. 2001 Jun 5;757(1):111-7.

7. Uehara N, Shirakawa S, Uchino H, Saeki Y: Elevated contents of spermidine and spermine in the erythrocytes of cancer patients. Cancer. 1980 Jan 1;45(1):108-11.

8. Proctor MS, Fletcher HV Jr, Shukla JB, Rennert OM: Elevated spermidine and spermine levels in the blood of psoriasis patients. J Invest Dermatol. 1975 Oct;65(4):409-11.

9. Mirzoian PA, Promyslov MSh: [Contents of putrescine, spermidine and spermine in tissue of the human brain glial tumors]. Ukr Biokhim Zh (1978). 1979 Sep-Oct;51(5):474-6.