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
External chemical identifiers:
CID:1102; ChEMBL:CHEMBL19612; 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 0
Log P RDKit 0
Topological polar surface area (Å2) RDKit
Number of hydrogen bond acceptors RDKit
Number of hydrogen bond donors RDKit
Number of carbon atoms RDKit
Number of heavy atoms RDKit
Number of heteroatoms RDKit
Number of nitrogen atoms RDKit
Number of sulfur atoms RDKit
Number of chiral carbon atoms RDKit
Stereochemical complexity RDKit 0
Number of sp hybridized carbon atoms RDKit
Number of sp2 hybridized carbon atoms RDKit
Number of sp3 hybridized carbon atoms RDKit
Shape complexity RDKit
Number of rotatable bonds RDKit
Number of aliphatic carbocycles RDKit
Number of aliphatic heterocycles RDKit
Number of aliphatic rings RDKit
Number of aromatic carbocycles RDKit
Number of aromatic heterocycles RDKit
Number of aromatic rings RDKit
Total number of rings RDKit
Number of saturated carbocycles RDKit
Number of saturated heterocycles RDKit
Number of saturated rings RDKit
Number of Smallest Set of Smallest Rings (SSSR) RDKit
Spermidine
Drug-likeness properties
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 0.4295
Spermidine
ADMET 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 -7.9
Number of PAINS structural alerts SwissADME 0.0
Number of Brenk structural alerts SwissADME 0.0
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
Predicted human target proteins
Protein identifierHGNC symbolCombined score from STITCH database
ENSP00000210060DHPS968
ENSP00000219070MMP2800
ENSP00000224784ACTA2740
ENSP00000234111ODC1999
ENSP00000250937DOHH962
ENSP00000269298SAT2954
ENSP00000275493EGFR800
ENSP00000278060PAOX991
ENSP00000286574WIF1800
ENSP00000290378ACTC1815
ENSP00000292079FXYD2700
ENSP00000295822EIF5A2909
ENSP00000307252SMOX956
ENSP00000311857PTPN2800
ENSP00000312326AOC3986
ENSP00000336702EIF5A985
ENSP00000354193AOC1876
ENSP00000355645ACTA1740
ENSP00000355930SLC22A1900
ENSP00000357880AMD1999
ENSP00000359663CD40LG800
ENSP00000366156SRM992
ENSP00000368572SAT1998
ENSP00000383042KDM1A716
ENSP00000385746SMS989
ENSP00000434516TXNRD1819
The human target proteins were predicted using STITCH, a database of Chemical-Protein interaction networks.