IMPPAT Phytochemical information: 
Spermidine
Spermidine
Summary

SMILES: NCCCNCCCCN
InChI: InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
InChIKey: ATHGHQPFGPMSJY-UHFFFAOYSA-N
DeepSMILES: NCCCNCCCCN
Functional groups: CN; CNC
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Organic nitrogen compounds
ClassyFire Class: Organonitrogen compounds
ClassyFire Subclass: Amines
NP Classifier Biosynthetic pathway: Alkaloids
NP Classifier Superclass: Ornithine alkaloids
NP Classifier Class: Polyamines
Synonymous chemical names:
spermidine, Spermidine
External chemical identifiers:
CID:CID_1102; ChEMBL:CHEMBL19612; ChEBI:CHEBI:16610; ZINC:ZINC000001532612; FDASRS:U87FK77H25; SureChEMBL:SCHEMBL15618; MolPort-001-761-230
Chemical structure download
2D:2D MOL2D MOL22D SDF
3D:3D MOL3D MOL23D SDF3D PDB3D PDBQT
Spermidine
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 145.25
Log P RDKit -0.34
Topological polar surface area (Å2) RDKit 64.07
Number of hydrogen bond acceptors RDKit 3
Number of hydrogen bond donors RDKit 3
Number of carbon atoms RDKit 7
Number of heavy atoms RDKit 10
Number of heteroatoms RDKit 3
Number of nitrogen atoms RDKit 3
Number of sulfur atoms RDKit 0
Number of chiral carbon atoms RDKit 0
Stereochemical complexity RDKit 0
Number of sp hybridized carbon atoms RDKit 0
Number of sp2 hybridized carbon atoms RDKit 0
Number of sp3 hybridized carbon atoms RDKit 7
Shape complexity RDKit 1
Number of rotatable bonds RDKit 7
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 0
Number of aliphatic rings RDKit 0
Number of aromatic carbocycles RDKit 0
Number of aromatic heterocycles RDKit 0
Number of aromatic rings RDKit 0
Total number of rings RDKit 0
Number of saturated carbocycles RDKit 0
Number of saturated heterocycles RDKit 0
Number of saturated rings RDKit 0
Number of Smallest Set of Smallest Rings (SSSR) RDKit 0
Spermidine
Drug-likeness
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 0
Lipinski’s rule of 5 filter RDKit Passed
Number of Ghose filter violations RDKit 1
Ghose filter RDKit Failed
Veber filter RDKit Good
Pfizer 3/75 filter RDKit Bad
GSK 4/400 filter RDKit Good
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.429544
Spermidine
ADME properties
Property nameToolProperty value
Bioavailability score SwissADME 0.55
Solubility class [ESOL] SwissADME Highly soluble
Solubility class [Silicos-IT] SwissADME Soluble
Blood Brain Barrier permeation SwissADME No
Gastrointestinal absorption SwissADME High
Log Kp (Skin permeation, cm/s) SwissADME -7.90
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 0
CYP1A2 inhibitor SwissADME No
CYP2C19 inhibitor SwissADME No
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME No
CYP3A4 inhibitor SwissADME No
P-glycoprotein substrate SwissADME No
Spermidine
Phytochemical - Human target proteins supported by experimental evidence associations
Human target proteins supported by experimental evidence
IMPPAT target identifierGene identifierHGNC symbolEntrez Gene identifierSource
TAR_EXP_000095ENSG00000224143EHMT210919ChEMBL, NPASS
TAR_EXP_000263ENSG00000140505CYP1A21544ChEMBL, NPASS
TAR_EXP_000122ENSG00000169239CA5B11238BindingDB, ChEMBL, NPASS
TAR_EXP_001128ENSG00000067225PKM5315ChEMBL
TAR_EXP_001683ENSG00000133742CA1759BindingDB, ChEMBL, NPASS
TAR_EXP_001631ENSG00000165409TSHR7253NPASS
TAR_EXP_001619ENSG00000131747TOP2A7153NPASS
TAR_EXP_001607ENSG00000090534THPO7066ChEMBL, NPASS
TAR_EXP_001541ENSG00000197208SLC22A46583ChEMBL
TAR_EXP_001684ENSG00000104267CA2760BindingDB, ChEMBL, NPASS
TAR_EXP_000706ENSG00000291796APEX1328NPASS
TAR_EXP_000572ENSG00000108773KAT2A2648NPASS
TAR_EXP_000505ENSG00000198793MTOR2475NPASS
TAR_EXP_000273ENSG00000138109CYP2C91559ChEMBL, NPASS
TAR_EXP_000351ENSG00000148832PAOX196743ChEMBL
TAR_EXP_000412ENSG00000124491F13A12162ChEMBL
TAR_EXP_001685ENSG00000164879CA3761BindingDB, ChEMBL, NPASS
TAR_EXP_001686ENSG00000167434CA4762BindingDB, ChEMBL, NPASS
TAR_EXP_000503ENSG00000161905ALOX15246NPASS
TAR_EXP_000492ENSG00000118298CA1423632BindingDB, ChEMBL, NPASS
TAR_EXP_001691ENSG00000074410CA12771BindingDB, ChEMBL, NPASS
TAR_EXP_001728ENSG00000176208ATAD579915NPASS
TAR_EXP_000504ENSG00000179593ALOX15B247NPASS
TAR_EXP_001688ENSG00000131686CA6765ChEMBL, NPASS
TAR_EXP_001687ENSG00000174990CA5A763BindingDB, ChEMBL, NPASS
TAR_EXP_001689ENSG00000168748CA7766BindingDB, ChEMBL, NPASS
TAR_EXP_001690ENSG00000107159CA9768BindingDB, ChEMBL, NPASS