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Identification
NameSpermidine
Accession NumberDB03566  (EXPT02942)
TypeSmall Molecule
GroupsExperimental
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 Identifiers Not Available
Prescription ProductsNot Available
Generic Prescription ProductsNot Available
Over the Counter ProductsNot Available
International BrandsNot Available
Brand mixturesNot Available
SaltsNot Available
CategoriesNot Available
CAS number124-20-9
WeightAverage: 145.2459
Monoisotopic: 145.157897623
Chemical FormulaC7H19N3
InChI KeyInChIKey=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
Taxonomy
DescriptionThis 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.
KingdomOrganic compounds
Super ClassOrganonitrogen compounds
ClassAmines
Sub ClassSecondary amines
Direct ParentDialkylamines
Alternative Parents
Substituents
  • Secondary aliphatic amine
  • Hydrocarbon derivative
  • Primary amine
  • Primary aliphatic amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Pharmacology
IndicationNot Available
PharmacodynamicsNot Available
Mechanism of actionNot Available
AbsorptionNot Available
Volume of distributionNot Available
Protein bindingNot Available
MetabolismNot Available
Route of eliminationNot Available
Half lifeNot Available
ClearanceNot Available
ToxicityNot Available
Affected organismsNot Available
PathwaysNot Available
SNP Mediated EffectsNot Available
SNP Mediated Adverse Drug ReactionsNot Available
ADMET
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 )
Pharmacoeconomics
ManufacturersNot Available
PackagersNot Available
Dosage formsNot Available
PricesNot Available
PatentsNot Available
Properties
StateSolid
Experimental Properties
PropertyValueSource
melting point< 25 °CPhysProp
boiling point129 °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 FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Mass Spec (NIST)Not Available
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-mz73100000-48794a2dc9d682aab28fView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-6z43100000-9fe6c1c8e8f166270be1View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-4z10000000-c88ed717e55f237cf01cView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)splash10-nz10000000-56396208515d9020bfebView in MoNA
GC-MSGC-MS Spectrum - GC-MS (4 TMS)splash10-jza0000000-4aac8aba8d9635a96f1cView in MoNA
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-5z10000000-f4b7d8b055a8d5025036View in MoNA
GC-MSGC-MS Spectrum - GC-MS (5 TMS)splash10-5z10000000-1be27daaf9f6d9e03752View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-zy00000000-02b200749ad6548a5872View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-z100000000-c294fdb7876cfc47c089View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-z000000000-d3055c2a8763c8034bd2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0z13000000-f08a2a9ba7333f5b725cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-sz00000000-062e21e4525351cbd0d4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0z00000000-31b90f68c9fde4e03f60View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0zb0000000-28adf399f8ddd0affc22View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0zd1000000-3ac88b6d5c40c65f1314View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-z200000000-953c054969edecf62533View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-rz00000000-8b03c45141b38c718dacView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Positivesplash10-0z00000000-1e157eec324aa34dd64eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-3z00000000-f2ca6698501cf6a406dfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-ze00000000-2f23967aa87f8e5f5bc1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-z200000000-91aef1c8b5a2507a16e9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-z000000000-18cdaecf173b5d79902aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-z000000000-f0b03de09cb13146e794View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-6z00000000-300fe40eb32167464ab8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-zx00000000-1a8be3c6776f3924c8b7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-z300000000-6401e12d220b44018fdfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-3z00000000-79940496e89b73bb1682View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-fz00000000-eb4eaf0bb3e88f274a1dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-z300000000-fe762fb3fcd81e27f9c7View in MoNA
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot 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 ReferencesNot Available
External Links
ATC CodesNot Available
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSNot Available
Interactions
Drug InteractionsNot Available
Food InteractionsNot Available

Targets

1. Thioredoxin reductase 1, cytoplasmic

Kind: Protein

Organism: Human

Pharmacological action: unknown

Components

Name UniProt ID Details
Thioredoxin reductase 1, cytoplasmic Q16881 Details

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
  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
  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

2. Gentamicin 3'-acetyltransferase

Kind: Protein

Organism: Pseudomonas aeruginosa

Pharmacological action: unknown

Components

Name UniProt ID Details
Gentamicin 3-N-acetyltransferase P23181 Details

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
  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

3. Spermidine/putrescine-binding periplasmic protein

Kind: Protein

Organism: Escherichia coli (strain K12)

Pharmacological action: unknown

Components

Name UniProt ID Details
Spermidine/putrescine-binding periplasmic protein P0AFK9 Details

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
  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

Transporters

1. Solute carrier family 22 member 4

Kind: Protein

Organism: Human

Pharmacological action: unknown

Actions: inhibitor

Components

Name UniProt ID Details
Solute carrier family 22 member 4 Q9H015 Details

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

2. Solute carrier family 22 member 1

Kind: Protein

Organism: Human

Pharmacological action: unknown

Actions: substrate

Components

Name UniProt ID Details
Solute carrier family 22 member 1 O15245 Details

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

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Drug created on June 13, 2005 07:24 / Updated on September 16, 2013 17:21