Spermidine

Identification

Name
Spermidine
Accession Number
DB03566  (EXPT02942)
Type
Small Molecule
Groups
Experimental
Description

Spermidine is a polyamine formed from putrescine. It is found in almost all tissues in association with nucleic acids. It is found as a cation at all pH values, and is thought to help stabilize some membranes and nucleic acid structures. It is a precursor of spermine.

Structure
Thumb
Synonyms
  • 1,5,10-Triazadecane
  • 1,8-Diamino-4-azaoctane
  • 4-Azaoctane-1,8-diamine
  • N-(3-Aminopropyl)-1,4-butane-diamine
  • N-(3-Aminopropyl)-1,4-butanediamine
  • N-(3-Aminopropyl)-1,4-diaminobutane
  • N-(3-aminopropyl)butane-1,4-diamine
  • Spermidin
External IDs
Not Available
Product Ingredients
Not Available
Approved Prescription Products
Not Available
Approved Generic Prescription Products
Not Available
Approved Over the Counter Products
Not Available
Unapproved/Other Products
Not Available
International/Other Brands
Not Available
Brand mixtures
Not Available
Categories
UNII
U87FK77H25
CAS number
124-20-9
Weight
Average: 145.2459
Monoisotopic: 145.157897623
Chemical Formula
C7H19N3
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
SMILES
NCCCCNCCCN

Pharmacology

Indication
Not Available
Structured Indications
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UThioredoxin reductase 1, cytoplasmicNot AvailableHuman
UGentamicin 3'-acetyltransferaseNot AvailablePseudomonas aeruginosa
USpermidine/putrescine-binding periplasmic proteinNot AvailableEscherichia coli (strain K12)
UBeta-1 adrenergic receptorNot AvailableHuman
UBeta-2 adrenergic receptorNot AvailableHuman
Absorption
Not Available
Volume of distribution
Not Available
Protein binding
Not Available
Metabolism
Not Available
Route of elimination
Not Available
Half life
Not Available
Clearance
Not Available
Toxicity
Not Available
Affected organisms
Not Available
Pathways
PathwayCategory
Cystathionine Beta-Synthase DeficiencyDisease
Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation typeDisease
Methylenetetrahydrofolate Reductase Deficiency (MTHFRD)Disease
Spermidine and Spermine BiosynthesisMetabolic
S-Adenosylhomocysteine (SAH) Hydrolase DeficiencyDisease
Glycine N-methyltransferase DeficiencyDisease
Methionine MetabolismMetabolic
Methionine Adenosyltransferase DeficiencyDisease
HypermethioninemiaDisease
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

Synthesis Reference

Raymond J. Bergeron, Jr., "Methods and intermediates for the preparation of spermidine, homospermidine and norspermidine." U.S. Patent US4505861, issued July, 1981.

US4505861
General References
Not Available
External Links
Human Metabolome Database
HMDB01257
KEGG Compound
C00315
PubChem Compound
1102
PubChem Substance
46506086
ChemSpider
1071
BindingDB
50009353
ChEBI
16610
ChEMBL
CHEMBL19612
IUPHAR
2390
Guide to Pharmacology
GtP Drug Page
HET
SPD
Wikipedia
Spermidine
ATC Codes
Not Available
AHFS Codes
Not Available
PDB Entries
FDA label
Not Available
MSDS
Not Available

Clinical Trials

Clinical Trials
Not Available

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
PropertyValueSource
melting point (°C)< 25 °CPhysProp
boiling point (°C)129 °C at 1.40E+01 mm HgPhysProp
Predicted Properties
PropertyValueSource
Water Solubility32.7 mg/mLALOGPS
logP-0.62ALOGPS
logP-1.1ChemAxon
logS-0.65ALOGPS
pKa (Strongest Basic)10.9ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area64.07 Å2ChemAxon
Rotatable Bond Count7ChemAxon
Refractivity44.97 m3·mol-1ChemAxon
Polarizability18.8 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption+0.9215
Blood Brain Barrier+0.6345
Caco-2 permeable+0.7072
P-glycoprotein substrateNon-substrate0.5094
P-glycoprotein inhibitor INon-inhibitor0.9178
P-glycoprotein inhibitor IINon-inhibitor0.6414
Renal organic cation transporterNon-inhibitor0.6066
CYP450 2C9 substrateNon-substrate0.8863
CYP450 2D6 substrateNon-substrate0.5607
CYP450 3A4 substrateNon-substrate0.8262
CYP450 1A2 substrateInhibitor0.877
CYP450 2C9 inhibitorNon-inhibitor0.9072
CYP450 2D6 inhibitorNon-inhibitor0.9502
CYP450 2C19 inhibitorNon-inhibitor0.9026
CYP450 3A4 inhibitorNon-inhibitor0.9703
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9386
Ames testNon AMES toxic0.8957
CarcinogenicityNon-carcinogens0.6436
BiodegradationReady biodegradable0.5525
Rat acute toxicity2.4561 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.7691
hERG inhibition (predictor II)Non-inhibitor0.7739
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397 )

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)GC-MSsplash10-00di-5910000000-48794a2dc9d682aab28f
GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)GC-MSsplash10-066u-1910000000-9fe6c1c8e8f166270be1
GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)GC-MSsplash10-00rf-1900000000-c88ed717e55f237cf01c
GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)GC-MSsplash10-00di-6900000000-56396208515d9020bfeb
GC-MS Spectrum - GC-MS (4 TMS)GC-MSsplash10-0uki-5920000000-4aac8aba8d9635a96f1c
GC-MS Spectrum - GC-MS (5 TMS)GC-MSsplash10-00rf-1900000000-f4b7d8b055a8d5025036
GC-MS Spectrum - GC-MS (5 TMS)GC-MSsplash10-00di-1900000000-1be27daaf9f6d9e03752
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSNot Available
GC-MS Spectrum - EI-BGC-MSsplash10-05tf-0910000000-280a5c2a493fedd0e524
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-00di-5910000000-48794a2dc9d682aab28f
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-066u-1910000000-9fe6c1c8e8f166270be1
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-00rf-1900000000-c88ed717e55f237cf01c
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-00di-6900000000-56396208515d9020bfeb
GC-MS Spectrum - GC-MSGC-MSsplash10-0uki-5920000000-4aac8aba8d9635a96f1c
GC-MS Spectrum - GC-MSGC-MSsplash10-00rf-1900000000-f4b7d8b055a8d5025036
GC-MS Spectrum - GC-MSGC-MSsplash10-00di-1900000000-1be27daaf9f6d9e03752
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-00rf-1900000000-866eda2dc91354bf795b
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-0uki-3920000000-2165a698c4bf674e814b
LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)LC-MS/MSsplash10-00dj-9800000000-02b200749ad6548a5872
LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)LC-MS/MSsplash10-00di-9000000000-c294fdb7876cfc47c089
LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)LC-MS/MSsplash10-00di-9000000000-d3055c2a8763c8034bd2
LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , PositiveLC-MS/MSsplash10-052b-0900000000-f08a2a9ba7333f5b725c
LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , PositiveLC-MS/MSsplash10-00b9-7900000000-062e21e4525351cbd0d4
LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , PositiveLC-MS/MSsplash10-014i-0900000000-31b90f68c9fde4e03f60
LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , PositiveLC-MS/MSsplash10-0002-0920000000-28adf399f8ddd0affc22
LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , PositiveLC-MS/MSsplash10-0udj-0930000000-3ac88b6d5c40c65f1314
LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , PositiveLC-MS/MSsplash10-0006-9000000000-953c054969edecf62533
LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , PositiveLC-MS/MSsplash10-00b9-7900000000-8b03c45141b38c718dac
LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , PositiveLC-MS/MSsplash10-004i-0900000000-1e157eec324aa34dd64e
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, PositiveLC-MS/MSsplash10-0002-0900000000-f2ca6698501cf6a406df
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, PositiveLC-MS/MSsplash10-00di-9300000000-2f23967aa87f8e5f5bc1
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, PositiveLC-MS/MSsplash10-00di-9000000000-91aef1c8b5a2507a16e9
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, PositiveLC-MS/MSsplash10-00di-9000000000-18cdaecf173b5d79902a
LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, PositiveLC-MS/MSsplash10-00di-9000000000-f0b03de09cb13146e794
LC-MS/MS Spectrum - LC-ESI-QTOF , positiveLC-MS/MSsplash10-0092-5900000000-4bd537f0811cc264f2cb
LC-MS/MS Spectrum - LC-ESI-QTOF , positiveLC-MS/MSsplash10-00di-9200000000-75eacba217a63f3b8847
LC-MS/MS Spectrum - LC-ESI-QTOF , positiveLC-MS/MSsplash10-00di-9000000000-8a77bd9436d55b064332
Predicted LC-MS/MS Spectrum - 10V, PositivePredicted LC-MS/MSsplash10-004j-1900000000-300fe40eb32167464ab8
Predicted LC-MS/MS Spectrum - 20V, PositivePredicted LC-MS/MSsplash10-0729-9800000000-1a8be3c6776f3924c8b7
Predicted LC-MS/MS Spectrum - 40V, PositivePredicted LC-MS/MSsplash10-0abc-9000000000-6401e12d220b44018fdf
Predicted LC-MS/MS Spectrum - 10V, NegativePredicted LC-MS/MSsplash10-0006-1900000000-79940496e89b73bb1682
Predicted LC-MS/MS Spectrum - 20V, NegativePredicted LC-MS/MSsplash10-0006-3900000000-eb4eaf0bb3e88f274a1d
Predicted LC-MS/MS Spectrum - 40V, NegativePredicted LC-MS/MSsplash10-00du-9000000000-fe762fb3fcd81e27f9c7
1H NMR Spectrum1D NMRNot applicable
[1H,1H] 2D NMR Spectrum2D NMRNot applicable
[1H,13C] 2D NMR Spectrum2D NMRNot applicable

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
Organopnictogen compounds / Monoalkylamines / Hydrocarbon derivatives
Substituents
Secondary aliphatic amine / Organopnictogen compound / Hydrocarbon derivative / Primary amine / Primary aliphatic amine / Aliphatic acyclic compound
Molecular Framework
Aliphatic acyclic compounds
External Descriptors
triamine, polyazaalkane (CHEBI:16610 )

Targets

Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Thioredoxin-disulfide reductase activity
Specific Function
Isoform 1 may possess glutaredoxin activity as well as thioredoxin reductase activity and induces actin and tubulin polymerization, leading to formation of cell membrane protrusions. Isoform 4 enha...
Gene Name
TXNRD1
Uniprot ID
Q16881
Uniprot Name
Thioredoxin reductase 1, cytoplasmic
Molecular Weight
70905.58 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]
Kind
Protein
Organism
Pseudomonas aeruginosa
Pharmacological action
Unknown
General Function
Aminoglycoside 3-n-acetyltransferase activity
Specific Function
Responsible for gentamicin resistance and has a limited substrate range.
Gene Name
aacC1
Uniprot ID
P23181
Uniprot Name
Gentamicin 3-N-acetyltransferase
Molecular Weight
19441.81 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Polyamine-transporting atpase activity
Specific Function
Required for the activity of the bacterial periplasmic transport system of putrescine and spermidine. Polyamine binding protein.
Gene Name
potD
Uniprot ID
P0AFK9
Uniprot Name
Spermidine/putrescine-binding periplasmic protein
Molecular Weight
38866.745 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Receptor signaling protein activity
Specific Function
Beta-adrenergic receptors mediate the catecholamine-induced activation of adenylate cyclase through the action of G proteins. This receptor binds epinephrine and norepinephrine with approximately e...
Gene Name
ADRB1
Uniprot ID
P08588
Uniprot Name
Beta-1 adrenergic receptor
Molecular Weight
51322.1 Da
References
  1. Meana C, Bordallo J, Bordallo C, Suarez L, Cantabrana B, Sanchez M: Functional effects of polyamines via activation of human beta1- and beta2-adrenoceptors stably expressed in CHO cells. Pharmacol Rep. 2010 Jul-Aug;62(4):696-706. [PubMed:20885010 ]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
General Function
Protein homodimerization activity
Specific Function
Beta-adrenergic receptors mediate the catecholamine-induced activation of adenylate cyclase through the action of G proteins. The beta-2-adrenergic receptor binds epinephrine with an approximately ...
Gene Name
ADRB2
Uniprot ID
P07550
Uniprot Name
Beta-2 adrenergic receptor
Molecular Weight
46458.32 Da
References
  1. Meana C, Bordallo J, Bordallo C, Suarez L, Cantabrana B, Sanchez M: Functional effects of polyamines via activation of human beta1- and beta2-adrenoceptors stably expressed in CHO cells. Pharmacol Rep. 2010 Jul-Aug;62(4):696-706. [PubMed:20885010 ]

Transporters

Kind
Protein
Organism
Human
Pharmacological action
Unknown
Actions
Inhibitor
General Function
Symporter activity
Specific Function
Sodium-ion dependent, low affinity carnitine transporter. Probably transports one sodium ion with one molecule of carnitine. Also transports organic cations such as tetraethylammonium (TEA) without...
Gene Name
SLC22A4
Uniprot ID
Q9H015
Uniprot Name
Solute carrier family 22 member 4
Molecular Weight
62154.48 Da
References
  1. Yabuuchi H, Tamai I, Nezu J, Sakamoto K, Oku A, Shimane M, Sai Y, Tsuji A: Novel membrane transporter OCTN1 mediates multispecific, bidirectional, and pH-dependent transport of organic cations. J Pharmacol Exp Ther. 1999 May;289(2):768-73. [PubMed:10215651 ]
Kind
Protein
Organism
Human
Pharmacological action
Unknown
Actions
Substrate
General Function
Secondary active organic cation transmembrane transporter activity
Specific Function
Translocates a broad array of organic cations with various structures and molecular weights including the model compounds 1-methyl-4-phenylpyridinium (MPP), tetraethylammonium (TEA), N-1-methylnico...
Gene Name
SLC22A1
Uniprot ID
O15245
Uniprot Name
Solute carrier family 22 member 1
Molecular Weight
61153.345 Da
References
  1. Busch AE, Quester S, Ulzheimer JC, Waldegger S, Gorboulev V, Arndt P, Lang F, Koepsell H: Electrogenic properties and substrate specificity of the polyspecific rat cation transporter rOCT1. J Biol Chem. 1996 Dec 20;271(51):32599-604. [PubMed:8955087 ]
Drug created on June 13, 2005 07:24 / Updated on September 01, 2017 11:06