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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
SynonymLanguageCode
1,5,10-TriazadecaneNot AvailableNot Available
1,8-Diamino-4-azaoctaneNot AvailableNot Available
4-Azaoctane-1,8-diamineNot AvailableNot Available
N-(3-Aminopropyl)-1,4-butane-diamineNot AvailableNot Available
N-(3-Aminopropyl)-1,4-butanediamineNot AvailableNot Available
N-(3-Aminopropyl)-1,4-diaminobutaneNot AvailableNot Available
N-(3-aminopropyl)butane-1,4-diamineNot AvailableNot Available
SpermidinNot AvailableNot Available
SaltsNot Available
Brand namesNot Available
Brand mixturesNot Available
CategoriesNot Available
CAS number124-20-9
WeightAverage: 145.2459
Monoisotopic: 145.157897623
Chemical FormulaC7H19N3
InChI KeyATHGHQPFGPMSJY-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
Mass SpecNot Available
Taxonomy
KingdomOrganic Compounds
SuperclassOrganonitrogen Compounds
ClassAmines
SubclassPolyamines
Direct parentPolyamines
Alternative parentsDialkylamines; Monoalkylamines
Substituentsprimary aliphatic amine; primary amine
Classification descriptionThis compound belongs to the polyamines. These are compounds containing more than one amine group.
Pharmacology
IndicationNot Available
PharmacodynamicsNot Available
Mechanism of actionNot Available
AbsorptionNot Available
Volume of distributionNot Available
Protein bindingNot Available
Metabolism
Route of eliminationNot Available
Half lifeNot Available
ClearanceNot Available
ToxicityNot Available
Affected organismsNot Available
Pathways
PathwayCategorySMPDB ID
Spermidine and Spermine BiosynthesisMetabolicSMP00445
HypermethioninemiaDiseaseSMP00341
Glycine N-methyltransferase DeficiencyDiseaseSMP00222
Cystathionine Beta-Synthase DeficiencyDiseaseSMP00177
Methionine Adenosyltransferase DeficiencyDiseaseSMP00221
Methylenetetrahydrofolate Reductase Deficiency (MTHFRD)DiseaseSMP00340
Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation typeDiseaseSMP00570
Methionine MetabolismMetabolicSMP00033
S-Adenosylhomocysteine (SAH) Hydrolase DeficiencyDiseaseSMP00214
SNP Mediated EffectsNot Available
SNP Mediated Adverse Drug ReactionsNot Available
ADMET
Predicted ADMET features
Property Value Probability
Human Intestinal Absorption + 0.9215
Blood Brain Barrier + 0.6345
Caco-2 permeable + 0.7072
P-glycoprotein substrate Non-substrate 0.5094
P-glycoprotein inhibitor I Non-inhibitor 0.9178
P-glycoprotein inhibitor II Non-inhibitor 0.6414
Renal organic cation transporter Non-inhibitor 0.6066
CYP450 2C9 substrate Non-substrate 0.8863
CYP450 2D6 substrate Non-substrate 0.5607
CYP450 3A4 substrate Non-substrate 0.8262
CYP450 1A2 substrate Inhibitor 0.877
CYP450 2C9 substrate Non-inhibitor 0.9072
CYP450 2D6 substrate Non-inhibitor 0.9502
CYP450 2C19 substrate Non-inhibitor 0.9026
CYP450 3A4 substrate Non-inhibitor 0.9703
CYP450 inhibitory promiscuity Low CYP Inhibitory Promiscuity 0.9386
Ames test Non AMES toxic 0.8957
Carcinogenicity Non-carcinogens 0.6436
Biodegradation Ready biodegradable 0.5525
Rat acute toxicity 2.4561 LD50, mol/kg Not applicable
hERG inhibition (predictor I) Weak inhibitor 0.7691
hERG inhibition (predictor II) Non-inhibitor 0.7739
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 Solubility32.7ALOGPS
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
Spectra
SpectraGC-MSMS/MSLC-MS1D NMR2D NMR
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 ReferenceNot Available
External Links
ResourceLink
KEGG CompoundC00315
PubChem Compound1102
PubChem Substance46506086
ChEBI16610
ChEMBL
IUPHAR2390
Guide to Pharmacology2390
HETSPD
WikipediaSpermidine
ATC CodesNot Available
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSNot Available
Interactions
Drug InteractionsNot Available
Food InteractionsNot Available

Targets

1. 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

2. 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

3. Gentamicin 3'-acetyltransferase

Kind: protein

Organism: Pseudomonas aeruginosa

Pharmacological action: unknown

Components

Name UniProt ID Details
Gentamicin 3'-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

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