Compound ID	CDAMM00389
Common name	Verdamicin
IUPAC name	(2R,3R,4R,5R)-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[[(2S,3R)-3-amino-6-[(1S)-1-aminoethyl]-3,4-dihydro-2H-pyran-2-yl]oxy]-2-hydroxycyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol
Molecular formula	C₂₀H₃₉N₅O₇

Experimental data

Retention time	52.81
Adduct	[M+H]+
Actual mz	462.297
Theoretical mz	462.292
Error	10.32
Ionizaton mode	Positive
Instrument type	LC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score	5.76

Identifiers and class information

Inchi key	XUSXOPRDIDWMFO-JKLNQYLTNA-N
Smiles	OC1C(OCC(O)(C)C1NC)OC2C(O)C(OC3OC(=CCC3N)C(N)C)C(N)CC2N
Superclass	Organic oxygen compounds
Class	Organooxygen compounds

Plant source

Phyllanthus urinaria L.

External sources

HMDB ID
KNApSAcK ID
FooDB ID
DrugBank ID
ChEBI ID
Pubchem Compound ID	512877
PlantCyc ID
UNPD ID	UNPD145731
Coconut ID
LipidMAPS ID
NANPDB ID

Pharmacokinetic properties

Number of descriptor values(#stars)	7
Number of non-conjugated amine groups (#amine)	5
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)	461.557
Computed dipole moment(dipole)	3.62
Total solvent accessible surface area (SASA)	751.134
Hydrophobic component of SASA (FOSA)	464.973
Hydrophilic component of SASA (FISA)	263.874
Pie component of the SASA (PISA)	22.288
Weakly polar component of the SASA (WPSA)	0
Total solvent accesible volume (volume)	1420.07
Number of hydrogen bond donors (donorHB)	12
Number of hydrogen bond acceptors (accptHB)	15.5
Free energy of solvation of dipole (dip^2/V)	0.0092304
Index of cohesive interaction in solids (ACxDN^.5/SA)	0.0714833
Globularity descriptor (glob)	0.81343
Predicted polarizability in cubic angstroms (QPpolrz)	42.543
Predicted hexadecane/gas partition coefficient (QPlogPC16)	16.141
Predicted octanol/gas partition coefficient (QPlogPoct)	40.07
Predicted water/gas partition coefficient (QPlogPw)	33.448
Predicted octanol/water partition coefficient (QPlogPo/w)	-3.852
Predicted aqueous solubility (QPlogS)	2
Conformation-independent predicted aqueous solubility (CIQPlogS)	3.001
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)	-8.288
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)	0.483
Predicted brain/blood partition coefficient (QPlogBB)	-2.082
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)	0.175
Predicted skin permeability, log Kp (QPlogKp)	-9.181
PM3 calculated ionization potential (IP(ev))	8.918
PM3 calculated electron affinity (EA(eV))	-1.192
Number of likely metabolic reactions (#metab)	11
Prediction of binding to human serum albumin (QPlogKhsa)	-1.075
Predicted qualitative human oral absorption (HumanOralAbsorption)	1
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)	0
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)	204.844
Number of nitrogen and oxygen atoms (#NandO)	12
Number of violations of Lipinski’s rule of five (RuleOfFive)	2
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

Target associated diseases

TTD_ID	Disease_ID	Disease name	ICD_11	Uniprot ID	Gene names