Cucurbitacin A



Compound IDCDAMM02580
Common nameCucurbitacin A
IUPAC name[6-[2,16-dihydroxy-9-(hydroxymethyl)-4,4,13,14-tetramethyl-3,11-dioxo-2,7,8,10,12,15,16,17-octahydro-1H-cyclopenta[a]phenanthren-17-yl]-6-hydroxy-2-methyl-5-oxohept-3-en-2-yl] acetate
Molecular formulaC32H46O9

Experimental data

Retention time13.41
Adduct[M+NH4]+
Actual mz592.354
Theoretical mz592.348
Error10.6
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score6.2857

Identifiers and class information

Inchi keyIHTCCHVMPGDDSL-JEWXSFAPNA-N
SmilesO=C(OC(C=CC(=O)C(O)(C)C1C(O)CC2(C)C3CC=C4C(CC(O)C(=O)C4(C)C)C3(C(=O)CC12C)CO)(C)C)C
SuperclassLipids and lipid-like molecules
ClassSteroids and steroid derivatives

Pharmacokinetic properties

Number of descriptor values(#stars)0
Number of non-conjugated amine groups (#amine)0
Number of amidine and guanidine groups (#amidine)0
Number of carboxylic acid groups (#acid)0
Number of non-conjugated amide groups (#amide)0
Number of rotatable bonds (#rotor)10
Number of reactive functional groups (#rtvFG)2
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)574.71
Computed dipole moment(dipole)11.587
Total solvent accessible surface area (SASA)856.84
Hydrophobic component of SASA (FOSA)610.794
Hydrophilic component of SASA (FISA)232.384
Pie component of the SASA (PISA)13.662
Weakly polar component of the SASA (WPSA)0
Total solvent accesible volume (volume)1724.46
Number of hydrogen bond donors (donorHB)3
Number of hydrogen bond acceptors (accptHB)12.85
Free energy of solvation of dipole (dip^2/V)0.0778558
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0259755
Globularity descriptor (glob)0.811647
Predicted polarizability in cubic angstroms (QPpolrz)56.568
Predicted hexadecane/gas partition coefficient (QPlogPC16)16.464
Predicted octanol/gas partition coefficient (QPlogPoct)31.468
Predicted water/gas partition coefficient (QPlogPw)18.3
Predicted octanol/water partition coefficient (QPlogPo/w)2.948
Predicted aqueous solubility (QPlogS)-5.49
Conformation-independent predicted aqueous solubility (CIQPlogS)-5.826
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-4.645
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)61.973
Predicted brain/blood partition coefficient (QPlogBB)-2.391
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)24.483
Predicted skin permeability, log Kp (QPlogKp)-4.794
PM3 calculated ionization potential (IP(ev))9.611
PM3 calculated electron affinity (EA(eV))0.275
Number of likely metabolic reactions (#metab)7
Prediction of binding to human serum albumin (QPlogKhsa)0.335
Predicted qualitative human oral absorption (HumanOralAbsorption)2
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)63.324
Solvent-accessible surface area of fluorine atoms (SAFluorine)0
Solvent-accessible surface area of amide oxygen atoms (SAamideO)0
Van der Waals surface area (PSA)173.651
Number of nitrogen and oxygen atoms (#NandO)9
Number of violations of Lipinski’s rule of five (RuleOfFive)1
Number of violations of Jorgensen’s rule of three (RuleOfThree)1

Compound-target network

Cytoscape Graph

Protein targets associated with phytocompound

Uniprot ID Gene name Target name TTD_ID Prediction source
P20701ITGALIntercellular adhesion molecule (ICAM-1), Integrin alpha-L/beta-2T35640SwissTargetPrediction and SEA
P40763STAT3Signal transducer and activator of transcription 3T29130SwissTargetPrediction

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T35640DI0351Psoriasis[ICD-11: EA90]P20701ITGAL
T35640DI0436Visual system disease[ICD-11: 9E1Z]P20701ITGAL
T29130DI0351Psoriasis[ICD-11: EA90]P40763STAT3

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