Compound ID	CDAMM02658
Common name	Gentioside
IUPAC name	1-hydroxy-7-methoxy-3-[3,4,5-trihydroxy-6-[(3,4,5-trihydroxyoxan-2-yl)oxymethyl]oxan-2-yl]oxyxanthen-9-one
Molecular formula	C₂₅H₂₈O₁₄

Experimental data

Retention time	5.29
Adduct	[M+H]+
Actual mz	553.161
Theoretical mz	553.155
Error	11.07
Ionizaton mode	Positive
Instrument type	LC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score	7.3644

Identifiers and class information

Inchi key	DNIDCQUDANKQTL-LWAOGCTDNA-N
Smiles	O=C1C2=CC(OC)=CC=C2OC3=CC(OC4OC(COC5OCC(O)C(O)C5O)C(O)C(O)C4O)=CC(O)=C13
Superclass	Organoheterocyclic compounds
Class	Benzopyrans

Plant source

Convolvulus prostratus Forssk.

External sources

HMDB ID	HMDB0030872
KNApSAcK ID	C00030375
FooDB ID	FDB002833
DrugBank ID
ChEBI ID
Pubchem Compound ID	15559485
PlantCyc ID
UNPD ID	UNPD180228
Coconut ID	CNP0252565
LipidMAPS ID
NANPDB ID

Pharmacokinetic properties

Number of descriptor values(#stars)	2
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)	13
Number of reactive functional groups (#rtvFG)	2
Predicted central nervous system activity (CNS)	-2
Molecular weight (mol_MW)	552.488
Computed dipole moment(dipole)	2.553
Total solvent accessible surface area (SASA)	756.963
Hydrophobic component of SASA (FOSA)	298.77
Hydrophilic component of SASA (FISA)	282.393
Pie component of the SASA (PISA)	175.8
Weakly polar component of the SASA (WPSA)	0
Total solvent accesible volume (volume)	1445.26
Number of hydrogen bond donors (donorHB)	6
Number of hydrogen bond acceptors (accptHB)	19.05
Free energy of solvation of dipole (dip^2/V)	0.0045112
Index of cohesive interaction in solids (ACxDN^.5/SA)	0.0616447
Globularity descriptor (glob)	0.816685
Predicted polarizability in cubic angstroms (QPpolrz)	45.017
Predicted hexadecane/gas partition coefficient (QPlogPC16)	16.205
Predicted octanol/gas partition coefficient (QPlogPoct)	34.431
Predicted water/gas partition coefficient (QPlogPw)	29.341
Predicted octanol/water partition coefficient (QPlogPo/w)	-1.367
Predicted aqueous solubility (QPlogS)	-2.223
Conformation-independent predicted aqueous solubility (CIQPlogS)	-3.717
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)	-5.337
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)	20.795
Predicted brain/blood partition coefficient (QPlogBB)	-3.043
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)	7.521
Predicted skin permeability, log Kp (QPlogKp)	-4.857
PM3 calculated ionization potential (IP(ev))	8.919
PM3 calculated electron affinity (EA(eV))	0.634
Number of likely metabolic reactions (#metab)	8
Prediction of binding to human serum albumin (QPlogKhsa)	-1.269
Predicted qualitative human oral absorption (HumanOralAbsorption)	1
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)	3.656
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)	216.959
Number of nitrogen and oxygen atoms (#NandO)	14
Number of violations of Lipinski’s rule of five (RuleOfFive)	3
Number of violations of Jorgensen’s rule of three (RuleOfThree)	2

Compound-target network

Cytoscape Graph

Protein targets associated with phytocompound

Uniprot ID	Gene name	Target name	TTD_ID	Prediction source
O43570	CA12	Carbonic anhydrase XII	T16987	SEA
P43166	CA7	Carbonic anhydrase VII	T37541	SEA
P22748	CA4	Carbonic anhydrase IV	T53378	SEA
P60568	IL2	Interleukin-2	T61698	SEA
Q9NUW8	TDP1	Tyrosyl-DNA phosphodiesterase 1	T33492	SEA
Q9UNQ0	ABCG2	ATP-binding cassette sub-family G member 2	T56556	SEA
P14679	TYR	Tyrosinase	T97035	SEA
Q9GZQ4	NMUR2	Neuromedin-U receptor 2	T04210	SEA
P47989	XDH	Xanthine dehydrogenase	T40954	SEA
Q16678	CYP1B1	Cytochrome P450 1B1	T92521	SEA
P16152	CBR1	Carbonyl reductase [NADPH] 1	T70518	SEA
Q9NZ08	ERAP1	Endoplasmic reticulum aminopeptidase 1	T72849	SEA
P30837	ALDH1B1	Acetaldehyde dehydrogenase	T99641	SEA
Q9UK17	KCND3	Voltage-gated potassium channel Kv4.3	T74500	SEA

Target associated diseases

TTD_ID	Disease_ID	Disease name	ICD_11	Uniprot ID	Gene names
T16987	DI0046	Bacterial infection	[ICD-11: 1A00-1C4Z]	O43570	CA12
T16987	DI0372	Seborrhoeic dermatitis	[ICD-11: EA81]	O43570	CA12
T53378	DI0046	Bacterial infection	[ICD-11: 1A00-1C4Z]	P22748	CA4
T53378	DI0166	Glaucoma	[ICD-11: 9C61]	P22748	CA4
T53378	DI0372	Seborrhoeic dermatitis	[ICD-11: EA81]	P22748	CA4
T61698	DI0275	Multiple sclerosis	[ICD-11: 8A40]	P60568	IL2
T61698	DI0361	Renal cell carcinoma	[ICD-11: 2C90]	P60568	IL2
T56556	DI0218	Irritable bowel syndrome	[ICD-11: DD91]	Q9UNQ0	ABCG2
T56556	DI0366	Rheumatoid arthritis	[ICD-11: FA20]	Q9UNQ0	ABCG2
T97035	DI0007	Acquired hypermelanosis	[ICD-11: ED60]	P14679	TYR
T97035	DI0008	Acquired hypomelanotic disorder	[ICD-11: ED63]	P14679	TYR
T40954	DI0206	Inborn purine/pyrimidine/nucleotide metabolism error	[ICD-11: 5C55]	P47989	XDH
T40954	DI0266	Mineral deficiency	[ICD-11: 5B5K]	P47989	XDH
T70518	DI0037	Asthma	[ICD-11: CA23]	P16152	CBR1
T99641	DI0396	Substance abuse	[ICD-11: 6C40]	P30837	ALDH1B1
T74500	DI0004	Acidosis	[ICD-11: 5C73]	Q9UK17	KCND3