Spermidine (YMDB00232)

You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Identification

YMDB ID

YMDB00232

Name

Spermidine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

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 yeast, spermidine participates in a number of enzymatic reactions. In particular, 5'-methylthioadenosine and spermidine can be biosynthesized from putrescine and S-adenosylmethioninamine; which is catalyzed by the enzyme spermidine synthase. In addition, spermidine and S-adenosylmethioninamine can be converted into 5'-methylthioadenosine and spermine; which is mediated by the enzyme spermine synthase. In yeast, spermidine is involved in the metabolic pathway called the beta-alanine metabolism pathway. Spermidine is a potentially toxic compound.

Structure

MOL SDF PDB SMILES InChI

Synonyms

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

CAS number

124-20-9

Weight

Average: 145.2459
Monoisotopic: 145.157897623

InChI Key

ATHGHQPFGPMSJY-UHFFFAOYSA-N

InChI

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

IUPAC Name

(4-aminobutyl)(3-aminopropyl)amine

Traditional IUPAC Name

spermidine

Chemical Formula

C₇H₁₉N₃

SMILES

[H]N([H])C([H])([H])C([H])([H])C([H])([H])N([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])N([H])[H]

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

Liquid

Charge

Melting point

< 25 °C

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

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	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

extracellular
cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Glutathione metabolism	PW002395
beta-Alanine metabolism	PW002381

KEGG Pathways

Arginine and proline metabolism	ec00330
Glutathione metabolism	ec00480
beta-Alanine metabolism	ec00410

SMPDB Reactions

Spermine + water + oxygen → Hydrogen peroxide + 3-Aminopropionaldehyde + Spermidine

Putrescine + S-Adenosylmethioninamine → hydron + 5'-Methylthioadenosine + Spermidine

Spermidine + S-Adenosylmethioninamine → hydron + 5'-Methylthioadenosine + Spermine

KEGG Reactions

Concentrations

Intracellular Concentrations

Intracellular Concentration	Substrate	Growth Conditions	Strain	Citation
1339 ± 67 µM	YEB media with 0.5 mM glucose	aerobic	Baker's yeast	Experimentally Determined Not Available
Conversion Details Here

Extracellular Concentrations

Not Available

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

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Pirkov, I., Norbeck, J., Gustafsson, L., Albers, E. (2008). "A complete inventory of all enzymes in the eukaryotic methionine salvage pathway." FEBS J 275:4111-4120.18625006
Uemura, T., Kashiwagi, K., Igarashi, K. (2007). "Polyamine uptake by DUR3 and SAM3 in Saccharomyces cerevisiae." J Biol Chem 282:7733-7741.17218313

Synthesis Reference:

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

External Links:

Resource	Link
CHEBI ID	16610
HMDB ID	HMDB01257
Pubchem Compound ID	1102
Kegg ID	C00315
ChemSpider ID	1071
FOODB ID	FDB012039
Wikipedia	Spermidine
BioCyc ID	SPERMIDINE

Enzymes

Protein Details

1. 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:: DYS1
Uniprot ID:: P38791
Molecular weight:: 42891.80078

Reactions

[eIF5A-precursor]-lysine + spermidine → [eIF5A-precursor]-deoxyhypusine + propane-1,3-diamine.

Protein Details

2. Polyamine oxidase FMS1

General function:: Amino acid transport and metabolism
Specific function:: Involved in the production of beta-alanine, a precursor of pantothenic acid. Multicopy suppressor of fenpropimorph resistance
Gene Name:: FMS1
Uniprot ID:: P50264
Molecular weight:: 57805.10156

Reactions

Spermine + O(2) + H(2)O → spermidine + 3-aminopropanal + H(2)O(2).
Spermidine + O(2) + H(2)O → putrescine + 3-aminopropanal + H(2)O(2).
N(1)-acetylspermine + O(2) + H(2)O → spermidine + 3-acetamidopropanal + H(2)O(2).
N(1)-acetylspermidine + O(2) + H(2)O → putrescine + 3-acetamidopropanal + H(2)O(2).
N(8)-acetylspermidine + O(2) + H(2)O → 4-acetamidobutanal + trimethylenediamine + H(2)O(2).

Protein Details

3. Spermine synthase

General function:: Involved in catalytic activity
Specific function:: S-adenosylmethioninamine + spermidine = 5'- methylthioadenosine + spermine
Gene Name:: SPE4
Uniprot ID:: Q12455
Molecular weight:: 34090.5

Reactions

S-adenosylmethioninamine + spermidine → 5'-methylthioadenosine + spermine.

Protein Details

4. Spermidine synthase

General function:: Involved in catalytic activity
Specific function:: S-adenosylmethioninamine + putrescine = 5'-S- methyl-5'-thioadenosine + spermidine
Gene Name:: SPE3
Uniprot ID:: Q12074
Molecular weight:: 33323.80078

Reactions

S-adenosylmethioninamine + putrescine → 5'-S-methyl-5'-thioadenosine + spermidine.

Transporters

Protein Details

1. General amino-acid permease GAP1

General function:: Involved in transport
Specific function:: Permease for various amino acids as well as for GABA. Can also transport L-cysteine and beta-alanine
Gene Name:: GAP1
Uniprot ID:: P19145
Molecular weight:: 65654.89844

Protein Details

2. Urea active transporter

General function:: Involved in transporter activity
Specific function:: Required for active transport of urea
Gene Name:: DUR3
Uniprot ID:: P33413
Molecular weight:: 80616.10156

Protein Details

3. Polyamine transporter TPO5

General function:: Involved in transport
Specific function:: Required for polyamine transport. Transports putrescine effectively and spermidine less effectively
Gene Name:: TPO5
Uniprot ID:: P36029
Molecular weight:: 69242.0

Protein Details

4. Polyamine transporter 1

General function:: Involved in transmembrane transport
Specific function:: Cell membrane polyamine/proton antiporter, involved in the detoxification of excess polyamines in the cytoplasm. Catalyzes polyamine uptake at alkaline pH and excretion at acidic pH. Recognizes spermidine, spermine and putrescine, the polyamine analogs methylglyoxal bis(guanylhydrazone) (MGBG) and paraquat, the antimalarial drug quinidine, and cycloheximide. Confers resistance to the non-steroidal anti-inflammatory drug indomethacin
Gene Name:: TPO1
Uniprot ID:: Q07824
Molecular weight:: 64271.60156

Protein Details

5. S-adenosylmethionine permease SAM3

General function:: Involved in transport
Specific function:: High-affinity S-adenosylmethionine permease, required for utilization of S-adenosylmethionine as a sulfur source
Gene Name:: SAM3
Uniprot ID:: Q08986
Molecular weight:: 64353.0

Protein Details

6. General amino acid permease AGP2

General function:: Involved in transport
Specific function:: General amino acid permease with broad substrate specificity. Can also transport carnitine
Gene Name:: AGP2
Uniprot ID:: P38090
Molecular weight:: 67261.29688

Structure for #<Compound:0xa8862114>

Enzymes

Reactions

Reactions

Reactions

Reactions

Transporters