IMPPAT Phytochemical information: 
Serpentine (alkaloid)

Serpentine (alkaloid)
Summary

SMILES: COC(=O)C1=CO[C@H]([C@@H]2[C@@H]1Cc1n(C2)ccc2-c1nc1c2cccc1)C
InChI: InChI=1S/C21H20N2O3/c1-12-16-10-23-8-7-14-13-5-3-4-6-18(13)22-20(14)19(23)9-15(16)17(11-26-12)21(24)25-2/h3-8,11-12,15-16H,9-10H2,1-2H3/t12-,15-,16+/m0/s1
InChIKey: WYTGDNHDOZPMIW-VBNZEHGJSA-N
DeepSMILES: COC=O)C=CO[C@H][C@@H][C@@H]6CcnC6)ccc-c6ncc5cccc6))))))))))))))))C
Scaffold Graph/Node/Bond level: C1=CC2Cc3c4nc5ccccc5c-4ccn3CC2CO1
Scaffold Graph/Node level: C1CCC2C(C1)NC1C2CCN2CC3COCCC3CC12
Scaffold Graph level: C1CCC2CC3C(CCC4C5CCCCC5CC34)CC2C1
Functional groups: COC(=O)C(=COC)C; cn(c)C; cnc
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Organoheterocyclic compounds
ClassyFire Class: Indoles and derivatives
ClassyFire Subclass: Pyridoindoles
NP Classifier Biosynthetic pathway: Alkaloids
NP Classifier Superclass: Tryptophan alkaloids
NP Classifier Class: Corynanthe type
Synonymous chemical names:
serpentine
External chemical identifiers:
CID:CID_73073; ChEBI:CHEBI:9119; ZINC:ZINC000005752357; FDASRS:B503RKE34F; SureChEMBL:SCHEMBL21962
Chemical structure download


Serpentine (alkaloid)
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 348.4
Log P RDKit 3.41
Topological polar surface area (Å2) RDKit 53.35
Number of hydrogen bond acceptors RDKit 5
Number of hydrogen bond donors RDKit 0
Number of carbon atoms RDKit 21
Number of heavy atoms RDKit 26
Number of heteroatoms RDKit 5
Number of nitrogen atoms RDKit 2
Number of sulfur atoms RDKit 0
Number of chiral carbon atoms RDKit 3
Stereochemical complexity RDKit 0.14
Number of sp hybridized carbon atoms RDKit 0
Number of sp2 hybridized carbon atoms RDKit 14
Number of sp3 hybridized carbon atoms RDKit 7
Shape complexity RDKit 0.33
Number of rotatable bonds RDKit 2
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 4
Number of aliphatic rings RDKit 4
Number of aromatic carbocycles RDKit 1
Number of aromatic heterocycles RDKit 0
Number of aromatic rings RDKit 1
Total number of rings RDKit 5
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 5


Serpentine (alkaloid)
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 0
Ghose filter RDKit Passed
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 0.632606


Serpentine (alkaloid)
ADME properties
Property nameToolProperty value
Bioavailability score SwissADME 0.85
Solubility class [ESOL] SwissADME Soluble
Solubility class [Silicos-IT] SwissADME Moderately soluble
Blood Brain Barrier permeation SwissADME Yes
Gastrointestinal absorption SwissADME High
Log Kp (Skin permeation, cm/s) SwissADME -6.59
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 0
CYP1A2 inhibitor SwissADME No
CYP2C19 inhibitor SwissADME Yes
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME Yes
CYP3A4 inhibitor SwissADME Yes
P-glycoprotein substrate SwissADME No


Serpentine (alkaloid)
Human target proteins
Protein identifierHGNC symbolCombined score from STITCH database
ENSP00000353820CYP2D6700
The human target proteins were predicted using STITCH, a database of Chemical-Protein interaction networks.