P. aeruginosa Metabolome Database: spermidine (PAMDB110685)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB110685

Identification

Name:

spermidine

Description:

An ammonium ion that is the trication of spermidine, formed by protonation at all three nitrogens.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

N-(3-aminopropyl)butane-1,4-diamine

Chemical Formula:

C₇H₂₂N₃

Average Molecular Weight:

148.27

Monoisotopic Molecular Weight:

148.1813727218

InChI Key:

ATHGHQPFGPMSJY-UHFFFAOYSA-Q

InChI:

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

CAS number:

124-20-9

IUPAC Name:

(4-azaniumylbutyl)(3-azaniumylpropyl)azanium

Traditional IUPAC Name:

spermidine

SMILES:

C([N+])CC[N+]CCCC[N+]

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of chemical entities known as dialkylamines. These are organic compounds containing a dialkylamine group, characterized by two alkyl groups bonded to the amino nitrogen.

Kingdom

Chemical entities

Super Class

Organic compounds

Class

Organic nitrogen compounds

Sub Class

Organonitrogen compounds

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
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
Water Solubility	32.7 mg/mL	ALOGPS
logP	-0.62	ALOGPS
logP	-1.1	ChemAxon
logS	-0.65	ALOGPS
pKa (Strongest Basic)	10.9	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:

Not Available

Reactions:

spermidine + Water + Acceptor → propane-1,3-diamine + 4-aminobutanal + Donor-H2
acetyl-CoA + spermidine → N1-acetylspermidine + Hydrogen ion + coenzyme A

Pathways:

Methionine Metabolism pae00270

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-00di-5910000000-48794a2dc9d682aab28f	View in 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	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)	splash10-00rf-1900000000-c88ed717e55f237cf01c	View in 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	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (4 TMS)	splash10-0uki-5920000000-4aac8aba8d9635a96f1c	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-00rf-1900000000-f4b7d8b055a8d5025036	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-00di-1900000000-1be27daaf9f6d9e03752	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS	Not Available
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-00dj-9800000000-02b200749ad6548a5872	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-00di-9000000000-c294fdb7876cfc47c089	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00di-9000000000-d3055c2a8763c8034bd2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-052b-0900000000-f08a2a9ba7333f5b725c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-00b9-7900000000-062e21e4525351cbd0d4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-014i-0900000000-31b90f68c9fde4e03f60	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0002-0920000000-28adf399f8ddd0affc22	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0udj-0930000000-3ac88b6d5c40c65f1314	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-0006-9000000000-953c054969edecf62533	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-00b9-7900000000-8b03c45141b38c718dac	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positive	splash10-004i-0900000000-1e157eec324aa34dd64e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-0002-0900000000-f2ca6698501cf6a406df	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-00di-9300000000-2f23967aa87f8e5f5bc1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-00di-9000000000-91aef1c8b5a2507a16e9	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-00di-9000000000-18cdaecf173b5d79902a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-00di-9000000000-f0b03de09cb13146e794	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-1900000000-300fe40eb32167464ab8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0729-9800000000-1a8be3c6776f3924c8b7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0abc-9000000000-6401e12d220b44018fdf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-1900000000-79940496e89b73bb1682	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-3900000000-eb4eaf0bb3e88f274a1d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00du-9000000000-fe762fb3fcd81e27f9c7	View in MoNA
1D NMR	1H NMR Spectrum	Not Available
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available

References

References:

Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. [19212411 ]
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. [11419735 ]
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. [7350997 ]
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. [1176793 ]
El Baze P, Milano G, Verrando P, Renee N, Ortonne JP: Polyamine levels in normal human skin. A comparative study of pure epidermis, pure dermis, and suction blister fluid. Arch Dermatol Res. 1983;275(4):218-21. [6625645 ]
Mirzoian PA, Promyslov MSh: [Contents of putrescine, spermidine and spermine in tissue of the human brain glial tumors] Ukr Biokhim Zh. 1979 Sep-Oct;51(5):474-6. [516181 ]
Chaisiri P, Harper ME, Blamey RW, Peeling WB, Griffiths K: Plasma spermidine concentrations in patients with tumours of the breast or prostate or testis. Clin Chim Acta. 1980 Jul 1;104(3):367-75. [6156039 ]
Martinet N, Beninati S, Nigra TP, Folk JE: N1N8-bis(gamma-glutamyl)spermidine cross-linking in epidermal-cell envelopes. Comparison of cross-link levels in normal and psoriatic cell envelopes. Biochem J. 1990 Oct 15;271(2):305-8. [2241917 ]

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)

Links

External Links:

Resource	Link
CAS	124-20-9
ChEBI	57834
ChemSpider	5360248
HMDB	HMDB01257
IAF1260	34593
KEGG	C00315
MetaboLights	MTBLC57834
PubChem	6992097

spermidine (PAMDB110685)

Structure for spermidine (PAMDB110685)