Milk Composition Database: Showing metabocard for Spermidine (BMDB0001257)

Identification Taxonomy Physical properties Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:43:10 UTC

Update Date

2020-06-04 20:47:30 UTC

MCDB ID

BMDB0001257

Secondary Accession Numbers

BMDB01257

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 exists as a solid, possibly soluble (in water), and a very strong basic compound (based on its pKa) molecule. Spermidine exists in all living species, ranging from bacteria to humans. Spermidine is a potentially toxic compound.

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 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	< 25 °C	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	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	Deposition Date	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	2014-06-16	View 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	2014-06-16	View 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	2014-06-16	View 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	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-0uki-5920000000-4aac8aba8d9635a96f1c	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-00rf-1900000000-f4b7d8b055a8d5025036	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-00di-1900000000-1be27daaf9f6d9e03752	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-05tf-0910000000-280a5c2a493fedd0e524	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-5910000000-48794a2dc9d682aab28f	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-066u-1910000000-9fe6c1c8e8f166270be1	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00rf-1900000000-c88ed717e55f237cf01c	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-6900000000-56396208515d9020bfeb	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0uki-5920000000-4aac8aba8d9635a96f1c	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00rf-1900000000-f4b7d8b055a8d5025036	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-00di-1900000000-1be27daaf9f6d9e03752	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00rf-1900000000-866eda2dc91354bf795b	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0uki-3920000000-2165a698c4bf674e814b	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001r-9200000000-e6ccea992bf8aff10122	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-00dj-9800000000-02b200749ad6548a5872	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-9000000000-c294fdb7876cfc47c089	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00di-9000000000-d3055c2a8763c8034bd2	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-052b-0900000000-f08a2a9ba7333f5b725c	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-00b9-7900000000-062e21e4525351cbd0d4	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-0900000000-31b90f68c9fde4e03f60	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0002-0920000000-28adf399f8ddd0affc22	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0udj-0930000000-3ac88b6d5c40c65f1314	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-9000000000-953c054969edecf62533	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-00b9-7900000000-8b03c45141b38c718dac	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-004i-0900000000-1e157eec324aa34dd64e	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-0002-0900000000-f2ca6698501cf6a406df	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-00di-9300000000-2f23967aa87f8e5f5bc1	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-00di-9000000000-91aef1c8b5a2507a16e9	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00di-9000000000-18cdaecf173b5d79902a	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-00di-9000000000-f0b03de09cb13146e794	2012-08-31	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0092-5900000000-4bd537f0811cc264f2cb	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-00di-9200000000-75eacba217a63f3b8847	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-00di-9000000000-8a77bd9436d55b064332	2017-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-1900000000-300fe40eb32167464ab8	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0729-9800000000-1a8be3c6776f3924c8b7	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0abc-9000000000-6401e12d220b44018fdf	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-1900000000-79940496e89b73bb1682	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-3900000000-eb4eaf0bb3e88f274a1d	2015-05-27	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00du-9000000000-fe762fb3fcd81e27f9c7	2015-05-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Not Available	2012-12-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-29	View Spectrum
2D NMR	[¹H, ¹H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)	Not Available	2012-12-04	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Not Available	2012-12-05	View Spectrum

Concentrations

Status	Value	Reference	Details
Detected and Quantified	13.2 uM	PMID: 7613766	details
Detected and Quantified	2.2 - 4.4 uM	PMID: 7613766	details
Detected but not Quantified	Not Applicable	PMID: 23438684	details
Detected and Quantified	0.88 +/- 0.02 uM	PMID: 30994344	details
Detected and Quantified	0.89 +/- 0.02 uM	PMID: 30994344	details
Detected and Quantified	0.84 +/- 0.02 uM	PMID: 30994344	details
Detected and Quantified	0.70 +/- 0.03 uM	PMID: 30994344	details

External Links

HMDB ID

HMDB0001257

DrugBank ID

DB03566

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

16610

References

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)

General References

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. [PubMed:7613766 ]
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. [PubMed:23438684 ]
A. Foroutan et al. (2019). A. Foroutan et al. The Chemical Composition of Commercial Cow's Milk (in preparation). Journal of Agricultural and Food Chemistry.

Showing metabocard for Spermidine (BMDB0001257)

Structure for BMDB0001257 (Spermidine)