IMPPAT Phytochemical information: 
Pelargonidin 3-rhamnoside

Pelargonidin 3-rhamnoside
Summary

SMILES: Oc1ccc(cc1)c1[o+]c2cc(O)cc(c2cc1O[C@@H]1OC(C)[C@@H](C([C@@H]1O)O)O)O
InChI: InChI=1S/C21H20O9/c1-9-17(25)18(26)19(27)21(28-9)30-16-8-13-14(24)6-12(23)7-15(13)29-20(16)10-2-4-11(22)5-3-10/h2-9,17-19,21,25-27H,1H3,(H2-,22,23,24)/p+1/t9?,17-,18?,19-,21-/m0/s1
InChIKey: RFOBAKWGJRIIMU-NXNGTVNRSA-O
DeepSMILES: Occcccc6))c[o+]cccO)ccc6cc%10O[C@@H]OCC)[C@@H]C[C@@H]6O))O))O)))))))))O
Scaffold Graph/Node/Bond level: c1ccc(-c2[o+]c3ccccc3cc2OC2CCCCO2)cc1
Scaffold Graph/Node level: C1CCC(C2OC3CCCCC3CC2OC2CCCCO2)CC1
Scaffold Graph level: C1CCC(CC2CC3CCCCC3CC2C2CCCCC2)CC1
Functional groups: cO; c[o+]c; cO[C@@H](C)OC; CO
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Phenylpropanoids and polyketides
ClassyFire Class: Flavonoids
ClassyFire Subclass: Flavonoid glycosides
Synonymous chemical names:
3-rhamnosides of pelargonidin
External chemical identifiers:
CID:CID_44256696
Chemical structure download


Pelargonidin 3-rhamnoside
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 417.39
Log P RDKit 1.7
Topological polar surface area (Å2) RDKit 151.14
Number of hydrogen bond acceptors RDKit 8
Number of hydrogen bond donors RDKit 6
Number of carbon atoms RDKit 21
Number of heavy atoms RDKit 30
Number of heteroatoms RDKit 9
Number of nitrogen atoms RDKit 0
Number of sulfur atoms RDKit 0
Number of chiral carbon atoms RDKit 5
Stereochemical complexity RDKit 0.24
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 3
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 1
Number of aliphatic rings RDKit 1
Number of aromatic carbocycles RDKit 2
Number of aromatic heterocycles RDKit 1
Number of aromatic rings RDKit 3
Total number of rings RDKit 4
Number of saturated carbocycles RDKit 0
Number of saturated heterocycles RDKit 1
Number of saturated rings RDKit 1
Number of Smallest Set of Smallest Rings (SSSR) RDKit 4


Pelargonidin 3-rhamnoside
Drug-likeness properties
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 1
Lipinski’s rule of 5 RDKit Passed
Number of Ghose rule violations RDKit 0
Ghose rule RDKit Passed
Veber rule RDKit Bad
Egan rule RDKit Bad
GSK 4/400 rule RDKit Bad
Pfizer 3/75 rule RDKit Good
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.35


Pelargonidin 3-rhamnoside
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 No
Gastrointestinal absorption SwissADME Low
Log Kp (Skin permeation, cm/s) SwissADME -8.14
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 1
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