Spermidine

Identification

Generic Name
Spermidine
DrugBank Accession Number
DB03566
Background

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.

Type
Small Molecule
Groups
Experimental
Structure
Weight
Average: 145.2459
Monoisotopic: 145.157897623
Chemical Formula
C7H19N3
Synonyms
  • 1,5,10-triazadecane
  • 4-azaoctamethylenediamine
  • 4-azaoctane-1,8-diamine
  • N-(3-Aminopropyl)-1,4-butane-diamine
  • N-(3-aminopropyl)butane-1,4-diamine
  • Spermidin
  • Spermidine

Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UBeta-1 adrenergic receptorNot AvailableHumans
UBeta-2 adrenergic receptorNot AvailableHumans
UThioredoxin reductase 1, cytoplasmicNot AvailableHumans
UGentamicin 3'-acetyltransferaseNot AvailablePseudomonas aeruginosa
USpermidine/putrescine-binding periplasmic proteinNot AvailableEscherichia coli (strain K12)
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

Adverse Effects
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Toxicity

Not Available

Pathways
PathwayCategory
Cystathionine beta-Synthase DeficiencyDisease
Methionine MetabolismMetabolic
Methionine Adenosyltransferase DeficiencyDisease
Spermidine and Spermine BiosynthesisMetabolic
S-Adenosylhomocysteine (SAH) Hydrolase DeficiencyDisease
Glycine N-Methyltransferase DeficiencyDisease
Methylenetetrahydrofolate Reductase Deficiency (MTHFRD)Disease
HypermethioninemiaDisease
Homocystinuria-Megaloblastic Anemia Due to Defect in Cobalamin Metabolism, cblG Complementation TypeDisease
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
DrugInteraction
AcyclovirThe risk or severity of adverse effects can be increased when Acyclovir is combined with Spermidine.
AmantadineThe risk or severity of adverse effects can be increased when Amantadine is combined with Spermidine.
ChlorpheniramineThe risk or severity of adverse effects can be increased when Chlorpheniramine is combined with Spermidine.
CholineThe risk or severity of adverse effects can be increased when Choline is combined with Spermidine.
Choline salicylateThe risk or severity of adverse effects can be increased when Choline salicylate is combined with Spermidine.
Food Interactions
Not Available

Categories

Drug Categories
Chemical TaxonomyProvided by Classyfire
Description
This compound 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
Organopnictogen compounds / Monoalkylamines / Hydrocarbon derivatives
Substituents
Aliphatic acyclic compound / Hydrocarbon derivative / Organopnictogen compound / Primary aliphatic amine / Primary amine / Secondary aliphatic amine
Molecular Framework
Aliphatic acyclic compounds
External Descriptors
triamine, polyazaalkane (CHEBI:16610)
Affected organisms
Not Available

Chemical Identifiers

UNII
U87FK77H25
CAS number
124-20-9
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

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
Human Metabolome Database
HMDB0001257
KEGG Compound
C00315
PubChem Compound
1102
PubChem Substance
46506086
ChemSpider
1071
BindingDB
50009353
RxNav
1483262
ChEBI
16610
ChEMBL
CHEMBL19612
ZINC
ZINC000001532612
Guide to Pharmacology
GtP Drug Page
PDBe Ligand
SPD
Wikipedia
Spermidine
PDB Entries
1bo4 / 1i2x / 1pot / 1poy / 1typ / 293d / 2elg / 2hmp / 2o07 / 2p18
show 167 more

Clinical Trials

Clinical Trials
PhaseStatusPurposeConditionsCount
3RecruitingTreatmentHypertension1

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)10.68Chemaxon
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-MSsplash10-001r-9200000000-e6ccea992bf8aff10122
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
MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)LC-MS/MSsplash10-00dj-9800000000-02b200749ad6548a5872
MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)LC-MS/MSsplash10-00di-9000000000-c294fdb7876cfc47c089
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
LC-MS/MS Spectrum - LC-ESI-QTOF , positiveLC-MS/MSsplash10-00di-9000000000-53ef0689f6b4e47cb1a3
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-0002-0900000000-f2ca6698501cf6a406df
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-00di-9300000000-6716ccbd090bf8fe3521
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-00di-9000000000-a17975b66ed2c6f80f05
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-00di-9000000000-18cdaecf173b5d79902a
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-00di-9000000000-f0b03de09cb13146e794
LC-MS/MS Spectrum - LC-ESI-ITFT , positiveLC-MS/MSsplash10-00b9-7900000000-062e21e4525351cbd0d4
LC-MS/MS Spectrum - LC-ESI-ITFT , positiveLC-MS/MSsplash10-00b9-7900000000-8b03c45141b38c718dac
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-00ba-5900000000-9bca95c4bbaf70b891a8
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0006-0900000000-9e9861a8189cd8af2377
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-0229-9300000000-2d1e3b86800d4bfff587
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-0006-0900000000-c456c19c134f56b471ee
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-053r-9100000000-d5d24b17786116f50b6a
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-006x-9000000000-711b8e8d334c9f984c0c
1H NMR Spectrum1D NMRNot Applicable
Predicted 1H NMR Spectrum1D NMRNot Applicable
Predicted 13C NMR Spectrum1D NMRNot Applicable
[1H,1H] 2D NMR Spectrum2D NMRNot Applicable
[1H,13C] 2D NMR Spectrum2D NMRNot Applicable
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-137.830226
predicted
DarkChem Lite v0.1.0
[M-H]-137.598426
predicted
DarkChem Lite v0.1.0
[M-H]-133.21223
predicted
DeepCCS 1.0 (2019)
[M+H]+138.022426
predicted
DarkChem Lite v0.1.0
[M+H]+138.187326
predicted
DarkChem Lite v0.1.0
[M+H]+135.6681
predicted
DeepCCS 1.0 (2019)
[M+Na]+138.049826
predicted
DarkChem Lite v0.1.0
[M+Na]+137.805726
predicted
DarkChem Lite v0.1.0
[M+Na]+144.5403
predicted
DeepCCS 1.0 (2019)

Targets

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insights and accelerate drug research.
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Kind
Protein
Organism
Humans
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. [Article]
Kind
Protein
Organism
Humans
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. [Article]
Kind
Protein
Organism
Humans
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. [Article]
  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. [Article]
  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. [Article]
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. [Article]
  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. [Article]
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. [Article]
  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. [Article]

Transporters

Kind
Protein
Organism
Humans
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. [Article]
Kind
Protein
Organism
Humans
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. [Article]
  2. Li DC, Nichols CG, Sala-Rabanal M: Role of a Hydrophobic Pocket in Polyamine Interactions with the Polyspecific Organic Cation Transporter OCT3. J Biol Chem. 2015 Nov 13;290(46):27633-43. doi: 10.1074/jbc.M115.668913. Epub 2015 Sep 24. [Article]

Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52