IMPPAT Phytochemical information: 
Gramine

Gramine
Summary

SMILES: CN(Cc1c[nH]c2c1cccc2)C
InChI: InChI=1S/C11H14N2/c1-13(2)8-9-7-12-11-6-4-3-5-10(9)11/h3-7,12H,8H2,1-2H3
InChIKey: OCDGBSUVYYVKQZ-UHFFFAOYSA-N
DeepSMILES: CNCcc[nH]cc5cccc6))))))))))C
Scaffold Graph/Node/Bond level: c1ccc2[nH]ccc2c1
Scaffold Graph/Node level: C1CCC2NCCC2C1
Scaffold Graph level: C1CCC2CCCC2C1
Functional groups: CN(C)C; c[nH]c
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Organoheterocyclic compounds
ClassyFire Class: Indoles and derivatives
ClassyFire Subclass: Indoles
NP Classifier Biosynthetic pathway: Alkaloids
NP Classifier Superclass: Tryptophan alkaloids
NP Classifier Class: Simple indole alkaloids
Synonymous chemical names:
Gramine, gramine, donaxine
External chemical identifiers:
CID:CID_6890; ChEMBL:CHEMBL254348; ChEBI:CHEBI:28948; ZINC:ZINC000000073686; FDASRS:FGQ8A78L14; SureChEMBL:SCHEMBL63578; MolPort-001-759-339
Chemical structure download


Gramine
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 174.25
Log P RDKit 2.23
Topological polar surface area (Å2) RDKit 19.03
Number of hydrogen bond acceptors RDKit 1
Number of hydrogen bond donors RDKit 1
Number of carbon atoms RDKit 11
Number of heavy atoms RDKit 13
Number of heteroatoms RDKit 2
Number of nitrogen atoms RDKit 2
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 8
Number of sp3 hybridized carbon atoms RDKit 3
Shape complexity RDKit 0.27
Number of rotatable bonds RDKit 2
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 0
Number of aliphatic rings RDKit 0
Number of aromatic carbocycles RDKit 1
Number of aromatic heterocycles RDKit 1
Number of aromatic rings RDKit 2
Total number of rings RDKit 2
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 2


Gramine
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 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 0.739343


Gramine
ADME properties
Property nameToolProperty value
Bioavailability score SwissADME 0.55
Solubility class [ESOL] SwissADME Soluble
Solubility class [Silicos-IT] SwissADME Soluble
Blood Brain Barrier permeation SwissADME Yes
Gastrointestinal absorption SwissADME High
Log Kp (Skin permeation, cm/s) SwissADME -6.10
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 0
CYP1A2 inhibitor SwissADME Yes
CYP2C19 inhibitor SwissADME No
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME No
CYP3A4 inhibitor SwissADME No
P-glycoprotein substrate SwissADME No


Gramine
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_001700ENSG00000153956CACNA2D1781ChEMBL
TAR_EXP_000411ENSG00000165092ALDH1A1216NPASS
TAR_EXP_001697ENSG00000102001CACNA1F778ChEMBL
TAR_EXP_001695ENSG00000157388CACNA1D776ChEMBL
TAR_EXP_001694ENSG00000151067CACNA1C775ChEMBL
TAR_EXP_001693ENSG00000148408CACNA1B774ChEMBL
TAR_EXP_001698ENSG00000081248CACNA1S779ChEMBL
TAR_EXP_001696ENSG00000198216CACNA1E777ChEMBL
TAR_EXP_001706ENSG00000182389CACNB4785ChEMBL
TAR_EXP_001702ENSG00000165995CACNB2783ChEMBL
TAR_EXP_001703ENSG00000167535CACNB3784ChEMBL
TAR_EXP_001708ENSG00000108878CACNG1786ChEMBL, NPASS
TAR_EXP_001846ENSG00000100346CACNA1I8911ChEMBL
TAR_EXP_001847ENSG00000196557CACNA1H8912ChEMBL
TAR_EXP_001848ENSG00000006283CACNA1G8913ChEMBL
TAR_EXP_001888ENSG00000007402CACNA2D29254ChEMBL
TAR_EXP_001899ENSG00000284953CACNA2D493589ChEMBL
TAR_EXP_001701ENSG00000067191CACNB1782ChEMBL
TAR_EXP_001692ENSG00000141837CACNA1A773ChEMBL
TAR_EXP_001210ENSG00000157445CACNA2D355799ChEMBL
TAR_EXP_001351ENSG00000130433CACNG659285ChEMBL
TAR_EXP_000280ENSG00000160868CYP3A41576ChEMBL, NPASS
TAR_EXP_000586ENSG00000075461CACNG427092ChEMBL
TAR_EXP_000674ENSG00000123636BAZ2B29994NPASS
TAR_EXP_000276ENSG00000272532CYP2D61565ChEMBL, NPASS
TAR_EXP_000271ENSG00000165841CYP2C191557NPASS
TAR_EXP_000047ENSG00000166862CACNG210369ChEMBL
TAR_EXP_001631ENSG00000165409TSHR7253ChEMBL, NPASS
TAR_EXP_000676ENSG00000072506HSD17B103028ChEMBL, NPASS
TAR_EXP_000819ENSG00000235268KDM4E390245NPASS
TAR_EXP_000046ENSG00000006116CACNG310368ChEMBL
TAR_EXP_000880ENSG00000118058KMT2A4297NPASS
TAR_EXP_000966ENSG00000116044NFE2L24780NPASS
TAR_EXP_001206ENSG00000042088TDP155775ChEMBL, NPASS
TAR_EXP_000585ENSG00000075429CACNG527091ChEMBL
TAR_EXP_001349ENSG00000142408CACNG859283ChEMBL
TAR_EXP_001350ENSG00000105605CACNG759284ChEMBL