AFCDB: Spermidine (FDB012039)

Record Information

Version

1.0

Creation date

2010-04-08 22:09:57 UTC

Update date

2019-11-26 03:06:02 UTC

Primary ID

FDB012039

Secondary Accession Numbers

Not Available

Chemical Information

FooDB 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. 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 cottonseeds, orange bell peppers, mango, tea, and swedes. This could make spermidine a potential biomarker for the consumption of these foods. Spermidine is a potentially toxic compound.

CAS Number

124-20-9

Structure

MOL SDF PDB SMILES InChI

Synonyms

Synonym	Source
Not Available	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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Chemical Formula

C7H19N3

IUPAC name

(4-aminobutyl)(3-aminopropyl)amine

InChI Identifier

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

InChI Key

ATHGHQPFGPMSJY-UHFFFAOYSA-N

Isomeric SMILES

NCCCCNCCCN

Average Molecular Weight

145.2459

Monoisotopic Molecular Weight

145.157897623

Classification

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

No ontology term

Physico-Chemical Properties - Experimental

Property	Value	Reference
Physical state	Liquid
Physical Description	Not Available
Mass Composition	C 57.89%; H 13.18%; N 28.93%	DFC
Melting Point	Not Available
Boiling Point	Bp14 128-130°	DFC
Experimental Water Solubility	Not Available
Experimental logP	Not Available
Experimental pKa	Not Available
Isoelectric point	Not Available
Charge	Not Available
Optical Rotation	Not Available
Spectroscopic UV Data	Not Available
Density	Not Available
Refractive Index	Not Available

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
GC-MS	Sperminidine, 5 TMS, GC-MS Spectrum	splash10-00di-5910000000-48794a2dc9d682aab28f	Spectrum
GC-MS	Sperminidine, 5 TMS, GC-MS Spectrum	splash10-066u-1910000000-9fe6c1c8e8f166270be1	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-00rf-1900000000-c88ed717e55f237cf01c	Spectrum
GC-MS	Sperminidine, 5 TMS, GC-MS Spectrum	splash10-00di-6900000000-56396208515d9020bfeb	Spectrum
GC-MS	Sperminidine, 4 TMS, GC-MS Spectrum	splash10-0uki-5920000000-4aac8aba8d9635a96f1c	Spectrum
GC-MS	Sperminidine, 5 TMS, GC-MS Spectrum	splash10-00rf-1900000000-f4b7d8b055a8d5025036	Spectrum
GC-MS	Sperminidine, 5 TMS, GC-MS Spectrum	splash10-00di-1900000000-1be27daaf9f6d9e03752	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-05tf-0910000000-280a5c2a493fedd0e524	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-00di-5910000000-48794a2dc9d682aab28f	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-066u-1910000000-9fe6c1c8e8f166270be1	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-00rf-1900000000-c88ed717e55f237cf01c	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-00di-6900000000-56396208515d9020bfeb	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-0uki-5920000000-4aac8aba8d9635a96f1c	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-00rf-1900000000-f4b7d8b055a8d5025036	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-00di-1900000000-1be27daaf9f6d9e03752	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-00rf-1900000000-866eda2dc91354bf795b	Spectrum
GC-MS	Sperminidine, non-derivatized, GC-MS Spectrum	splash10-0uki-3920000000-2165a698c4bf674e814b	Spectrum
Predicted GC-MS	Sperminidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-001r-9200000000-e6ccea992bf8aff10122	Spectrum
Predicted GC-MS	Sperminidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-00dj-9800000000-02b200749ad6548a5872	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-9000000000-c294fdb7876cfc47c089	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00di-9000000000-d3055c2a8763c8034bd2	2012-07-24	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-052b-0900000000-f08a2a9ba7333f5b725c	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-00b9-7900000000-062e21e4525351cbd0d4	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-0900000000-31b90f68c9fde4e03f60	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0002-0920000000-28adf399f8ddd0affc22	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0udj-0930000000-3ac88b6d5c40c65f1314	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-9000000000-953c054969edecf62533	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-00b9-7900000000-8b03c45141b38c718dac	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-004i-0900000000-1e157eec324aa34dd64e	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-0002-0900000000-f2ca6698501cf6a406df	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-00di-9300000000-2f23967aa87f8e5f5bc1	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-00di-9000000000-91aef1c8b5a2507a16e9	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00di-9000000000-18cdaecf173b5d79902a	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-00di-9000000000-f0b03de09cb13146e794	2012-08-31	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-0092-5900000000-4bd537f0811cc264f2cb	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-00di-9200000000-75eacba217a63f3b8847	2017-09-14	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , positive	splash10-00di-9000000000-8a77bd9436d55b064332	2017-09-14	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-1900000000-300fe40eb32167464ab8	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0729-9800000000-1a8be3c6776f3924c8b7	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0abc-9000000000-6401e12d220b44018fdf	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-1900000000-79940496e89b73bb1682	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-3900000000-eb4eaf0bb3e88f274a1d	2015-05-27	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00du-9000000000-fe762fb3fcd81e27f9c7	2015-05-27	View Spectrum

NMR

Type	Description	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	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)	Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Spectrum

External Links

ChemSpider ID

ChEMBL ID

KEGG Compound ID

Pubchem Compound ID

Pubchem Substance ID

Not Available

ChEBI ID

16610

Phenol-Explorer ID

Not Available

DrugBank ID

DB03566

HMDB ID

HMDB01257

CRC / DFC (Dictionary of Food Compounds) ID

HCS12-B:HCS12-B

EAFUS ID

Not Available

Dr. Duke ID

BIGG ID

KNApSAcK ID

HET ID

Food Biomarker Ontology

Not Available

VMH ID

Not Available

Flavornet ID

Not Available

GoodScent ID

Not Available

SuperScent ID

Not Available

Wikipedia ID

Spermidine

Phenol-Explorer Metabolite ID

Not Available

Duplicate IDS

Not Available

Old DFC IDS

Not Available

Associated Foods

Food	Content Range	Average	Reference
Food			Reference

Biological Effects and Interactions

Health Effects / Bioactivities

Descriptor	ID	Definition	Reference
antioxidant	22586	A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. In European countries, E-numbers for permitted antioxidant food additives are from E 300 to E 324.	DUKE

Enzymes

Name	Gene Name	UniProt ID
Glycine amidinotransferase, mitochondrial	GATM	P50440
Histidine decarboxylase	HDC	P19113
Spermidine synthase	SRM	P19623
Diamine acetyltransferase 1	SAT1	P21673
Spermine synthase	SMS	P52788
S-methyl-5'-thioadenosine phosphorylase	MTAP	Q13126
Ornithine decarboxylase	ODC1	P11926
Ornithine decarboxylase antizyme 1	OAZ1	P54368
3-ketoacyl-CoA thiolase, mitochondrial	ACAA2	P42765
Propionyl-CoA carboxylase alpha chain, mitochondrial	PCCA	P05165

Pathways

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

Metabolism

Not Available

Biosynthesis

Not Available

Organoleptic Properties

Flavours

Not Available

Files

MSDS

show

References

Synthesis Reference

Not Available

General Reference

Not Available

Content Reference

— Shinbo, Y., et al. 'KNApSAcK: a comprehensive species-metabolite relationship database.' Plant Metabolomics. Springer Berlin Heidelberg, 2006. 165-181.
— Duke, James. 'Dr. Duke's Phytochemical and Ethnobotanical Databases. United States Department of Agriculture.' Agricultural Research Service, Accessed April 27 (2004).

Spermidine (FDB012039)

Structure for FDB012039 (Spermidine)