IMPPAT Phytochemical information: 
Agmatine

Agmatine
Summary

SMILES: NCCCCN=C(N)N
InChI: InChI=1S/C5H14N4/c6-3-1-2-4-9-5(7)8/h1-4,6H2,(H4,7,8,9)
InChIKey: QYPPJABKJHAVHS-UHFFFAOYSA-N
DeepSMILES: NCCCCN=CN)N
Functional groups: CN; CN=C(N)N
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Organic nitrogen compounds
ClassyFire Class: Organonitrogen compounds
ClassyFire Subclass: Guanidines
NP Classifier Biosynthetic pathway: Alkaloids
NP Classifier Superclass: Ornithine alkaloids
NP Classifier Class: Polyamines
Synonymous chemical names:
agmatine
External chemical identifiers:
CID:CID_199; ChEMBL:CHEMBL58343; ChEBI:CHEBI:17431; ZINC:ZINC000001532560; FDASRS:70J407ZL5Q; SureChEMBL:SCHEMBL19647; MolPort-001-792-881
Chemical structure download


Agmatine
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 130.2
Log P RDKit -1
Topological polar surface area (Å2) RDKit 90.42
Number of hydrogen bond acceptors RDKit 2
Number of hydrogen bond donors RDKit 3
Number of carbon atoms RDKit 5
Number of heavy atoms RDKit 9
Number of heteroatoms RDKit 4
Number of nitrogen atoms RDKit 4
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 1
Number of sp3 hybridized carbon atoms RDKit 4
Shape complexity RDKit 0.8
Number of rotatable bonds RDKit 4
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


Agmatine
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 3
Ghose filter RDKit Failed
Veber filter RDKit Good
Pfizer 3/75 filter RDKit Good
GSK 4/400 filter RDKit Good
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.25879


Agmatine
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 -8.19
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 2
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