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 properties
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 0
Lipinski’s rule of 5 RDKit Passed
Number of Ghose rule violations RDKit 1
Ghose rule RDKit Failed
Veber rule RDKit Good
Egan rule RDKit Good
GSK 4/400 rule RDKit Good
Pfizer 3/75 rule RDKit Bad
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.43
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
Human target proteins
Protein identifierHGNC symbolCombined score from STITCH database
ENSP00000366156SRM992
ENSP00000368572SAT1998
ENSP00000269298SAT2954
ENSP00000210060DHPS968
ENSP00000234111ODC1999
ENSP00000224784ACTA2740
ENSP00000219070MMP2800
ENSP00000359663CD40LG800
ENSP00000250937DOHH962
ENSP00000275493EGFR800
ENSP00000355645ACTA1740
ENSP00000286574WIF1800
ENSP00000290378ACTC1815
ENSP00000295822EIF5A2909
ENSP00000307252SMOX956
ENSP00000311857PTPN2800
ENSP00000312326AOC3986
ENSP00000336702EIF5A985
ENSP00000354193AOC1876
ENSP00000355930SLC22A1900
ENSP00000357880AMD1999
ENSP00000278060PAOX991
ENSP00000383042KDM1A716
ENSP00000292079FXYD2700
ENSP00000434516TXNRD1819
ENSP00000385746SMS989
The human target proteins were predicted using STITCH, a database of Chemical-Protein interaction networks.