Livestock Metabolome Database: Showing metabocard for Spermidine (LMDB00311)

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-07-13 19:47:02 UTC

Update Date

2021-04-30 20:57:45 UTC

Lmdb

LMDB00311

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Spermidine

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 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.

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 Weight

145.2459

Monoisotopic Molecular Weight

145.157897623

IUPAC Name

(4-aminobutyl)(3-aminopropyl)amine

Traditional Name

spermidine

CAS Registry Number

124-20-9

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 )

Ontology

Status

Detected and Quantified

Origin

Not Available

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	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

Biological Properties

Cellular Locations

Not Available

Biofluid Locations and Tissue Locations

Milk
Plasma
Serum

Concentrations

Biofluid	Status	Value	Condition	Species	Reference	Details
Milk	Detected but not Quantified	Not Applicable	Not Available	Bovine	23438684	details
Plasma	Detected but not Quantified	Not Applicable	Not Available	Ovine	22242129	details
Plasma	Detected but not Quantified	Not Applicable	Not Available	Porcine	20231903	details
Serum	Detected and Quantified	0.142 +/- 0.2864 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.0435 +/- 0.0142 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.1 uM	Not Available	Porcine	Barbara U. Metzle...	details
Serum	Detected and Quantified	0.15 uM	Not Available	Porcine	Barbara U. Metzle...	details
Serum	Detected and Quantified	0.16 uM	Not Available	Porcine	Barbara U. Metzle...	details
Serum	Detected and Quantified	0.18 uM	Not Available	Porcine	Barbara U. Metzle...	details
Serum	Detected and Quantified	0.0687 +/- 0.0446 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.2088 +/- 0.3727 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.0517 +/- 0.013 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.0689 +/- 0.0595 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.1 +/- 0.05 uM	Not Available	Ovine	Candidate serum m...	details
Serum	Detected and Quantified	0.0842 +/- 0.0665 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.0524 +/- 0.0196 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.0578 +/- 0.0234 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.049 +/- 0.0119 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.0892 +/- 0.0774 uM	Normal	Ovine	Goldansaz et al.,...	details
Serum	Detected and Quantified	0.1073 +/- 0.2027 uM	Normal	Ovine	Goldansaz et al.,...	details