IMPPAT Phytochemical information: 
Pygmaeocin A

Pygmaeocin A
Summary

SMILES: O=C1Oc2c(O)c(cc3c2[C@](C1)(C)C1[C@H](C3=O)OC(=O)C1(C)C)C(C)C
InChI: InChI=1S/C20H22O6/c1-8(2)9-6-10-12-15(13(9)22)25-11(21)7-20(12,5)17-16(14(10)23)26-18(24)19(17,3)4/h6,8,16-17,22H,7H2,1-5H3/t16-,17?,20+/m0/s1
InChIKey: BRVFBXOJAHGUQS-YKBQRGLWSA-N
DeepSMILES: O=COccO)cccc6[C@]C%10)C)C[C@H]C6=O))OC=O)C5C)C))))))))))CC)C
Scaffold Graph/Node/Bond level: O=C1CC2c3c(cccc3C(=O)C3OC(=O)CC32)O1
Scaffold Graph/Node level: OC1CC2C3CC(O)OC3C(O)C3CCCC(O1)C32
Scaffold Graph level: CC1CC2C(C)C3CCCC4CC(C)CC(C2C1)C43
Functional groups: cOC(=O)C; cO; cC(=O)C; CC(=O)OC
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Organoheterocyclic compounds
ClassyFire Class: Naphthofurans
NP Classifier Biosynthetic pathway: Terpenoids
NP Classifier Superclass: Diterpenoids
NP Classifier Class: Secoabietane diterpenoids
Synonymous chemical names:
pygmaeocin a
External chemical identifiers:
CID:CID_365926
Chemical structure download


Pygmaeocin A
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 358.39
Log P RDKit 2.85
Topological polar surface area (Å2) RDKit 89.9
Number of hydrogen bond acceptors RDKit 6
Number of hydrogen bond donors RDKit 1
Number of carbon atoms RDKit 20
Number of heavy atoms RDKit 26
Number of heteroatoms RDKit 6
Number of nitrogen atoms RDKit 0
Number of sulfur atoms RDKit 0
Number of chiral carbon atoms RDKit 3
Stereochemical complexity RDKit 0.15
Number of sp hybridized carbon atoms RDKit 0
Number of sp2 hybridized carbon atoms RDKit 9
Number of sp3 hybridized carbon atoms RDKit 11
Shape complexity RDKit 0.55
Number of rotatable bonds RDKit 1
Number of aliphatic carbocycles RDKit 1
Number of aliphatic heterocycles RDKit 2
Number of aliphatic rings RDKit 3
Number of aromatic carbocycles RDKit 1
Number of aromatic heterocycles RDKit 0
Number of aromatic rings RDKit 1
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


Pygmaeocin A
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 Good
GSK 4/400 filter RDKit Good
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.613215


Pygmaeocin A
ADME properties
Property nameToolProperty value
Bioavailability score SwissADME 0.55
Solubility class [ESOL] SwissADME Moderately soluble
Solubility class [Silicos-IT] SwissADME Moderately soluble
Blood Brain Barrier permeation SwissADME No
Gastrointestinal absorption SwissADME High
Log Kp (Skin permeation, cm/s) SwissADME -6.25
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 1
CYP1A2 inhibitor SwissADME No
CYP2C19 inhibitor SwissADME Yes
CYP2C9 inhibitor SwissADME Yes
CYP2D6 inhibitor SwissADME No
CYP3A4 inhibitor SwissADME Yes
P-glycoprotein substrate SwissADME Yes