IMPPAT Phytochemical information: 
Bergamottin

Bergamottin
Summary

SMILES: C/C(=C\COc1c2ccoc2cc2c1ccc(=O)o2)/CCC=C(C)C
InChI: InChI=1S/C21H22O4/c1-14(2)5-4-6-15(3)9-11-24-21-16-7-8-20(22)25-19(16)13-18-17(21)10-12-23-18/h5,7-10,12-13H,4,6,11H2,1-3H3/b15-9+
InChIKey: DBMJZOMNXBSRED-OQLLNIDSSA-N
DeepSMILES: C/C=C\COccccoc5ccc9ccc=O)o6))))))))))))))))/CCC=CC)C
Scaffold Graph/Node/Bond level: O=c1ccc2cc3ccoc3cc2o1
Scaffold Graph/Node level: OC1CCC2CC3CCOC3CC2O1
Scaffold Graph level: CC1CCC2CC3CCCC3CC2C1
Functional groups: C/C=C(\C)C; cOC; coc; c=O; CC=C(C)C
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Lipids and lipid-like molecules
ClassyFire Class: Prenol lipids
ClassyFire Subclass: Terpene lactones
NP Classifier Biosynthetic pathway: Shikimates and Phenylpropanoids
NP Classifier Superclass: Coumarins
NP Classifier Class: Furocoumarins|Simple coumarins
Synonymous chemical names:
alpha bergamottin, bergamottin(5-geranyloxy psoralen), Bergamottin, bergamotine, bergamottin, bergamotin
External chemical identifiers:
CID:CID_5471349; ChEMBL:CHEMBL1078442; ChEBI:CHEBI:70476; ZINC:ZINC000001658570; FDASRS:JMU611YFRB; SureChEMBL:SCHEMBL569529; MolPort-000-881-227
Chemical structure download


Bergamottin
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 338.4
Log P RDKit 5.61
Topological polar surface area (Å2) RDKit 52.58
Number of hydrogen bond acceptors RDKit 4
Number of hydrogen bond donors RDKit 0
Number of carbon atoms RDKit 21
Number of heavy atoms RDKit 25
Number of heteroatoms RDKit 4
Number of nitrogen atoms RDKit 0
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 15
Number of sp3 hybridized carbon atoms RDKit 6
Shape complexity RDKit 0.29
Number of rotatable bonds RDKit 6
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 2
Number of aromatic rings RDKit 3
Total number of rings RDKit 3
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 3


Bergamottin
Drug-likeness
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 1
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 Bad
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.432794


Bergamottin
ADME properties
Property nameToolProperty value
Bioavailability score SwissADME 0.55
Solubility class [ESOL] SwissADME Moderately soluble
Solubility class [Silicos-IT] SwissADME Poorly soluble
Blood Brain Barrier permeation SwissADME Yes
Gastrointestinal absorption SwissADME High
Log Kp (Skin permeation, cm/s) SwissADME -4.61
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 2
CYP1A2 inhibitor SwissADME Yes
CYP2C19 inhibitor SwissADME Yes
CYP2C9 inhibitor SwissADME Yes
CYP2D6 inhibitor SwissADME No
CYP3A4 inhibitor SwissADME Yes
P-glycoprotein substrate SwissADME No


Bergamottin
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_001923ENSG00000066135KDM4A9682NPASS
TAR_EXP_001206ENSG00000042088TDP155775NPASS
TAR_EXP_000264ENSG00000138061CYP1B11545BindingDB, NPASS
TAR_EXP_000270ENSG00000197408CYP2B61555ChEMBL, NPASS
TAR_EXP_001125ENSG00000127445PIN15300NPASS
TAR_EXP_001106ENSG00000085563ABCB15243ChEMBL, NPASS
TAR_EXP_000271ENSG00000165841CYP2C191557ChEMBL, NPASS
TAR_EXP_000273ENSG00000138109CYP2C91559ChEMBL, NPASS
TAR_EXP_000276ENSG00000272532CYP2D61565ChEMBL, NPASS
TAR_EXP_000277ENSG00000130649CYP2E11571BindingDB, ChEMBL, NPASS
TAR_EXP_000280ENSG00000160868CYP3A41576BindingDB, ChEMBL, NPASS
TAR_EXP_000491ENSG00000186318BACE123621BindingDB, ChEMBL, NPASS
TAR_EXP_000390ENSG00000142208AKT1207ChEMBL
TAR_EXP_000132ENSG00000137491SLCO2B111309ChEMBL, NPASS
TAR_EXP_000281ENSG00000106258CYP3A51577ChEMBL, NPASS
TAR_EXP_001631ENSG00000165409TSHR7253ChEMBL, NPASS
TAR_EXP_000097ENSG00000108468CBX110951NPASS