Rhyncoside D



Compound IDCDAMM01605
Common nameRhyncoside D
IUPAC name2-methyl-6-[[3,4,5-trihydroxy-6-[4-(hydroxymethyl)-2,6-dimethoxyphenoxy]oxan-2-yl]methoxy]oxane-3,4,5-triol
Molecular formulaC21H32O13

Experimental data

Retention time0.36
Adduct[M+Na]+
Actual mz515.171
Theoretical mz515.173
Error3.53
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score7.2761

Identifiers and class information

Inchi keyCLFLQEOCRODKDN-PDFSGIEQNA-N
SmilesOCC1=CC(OC)=C(OC2OC(COC3OC(C)C(O)C(O)C3O)C(O)C(O)C2O)C(OC)=C1
SuperclassOrganic oxygen compounds
ClassOrganooxygen compounds

Pharmacokinetic properties

Number of descriptor values(#stars)4
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)15
Number of reactive functional groups (#rtvFG)2
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)492.476
Computed dipole moment(dipole)11.424
Total solvent accessible surface area (SASA)746.938
Hydrophobic component of SASA (FOSA)438.055
Hydrophilic component of SASA (FISA)265.7
Pie component of the SASA (PISA)43.182
Weakly polar component of the SASA (WPSA)0
Total solvent accesible volume (volume)1412.44
Number of hydrogen bond donors (donorHB)7
Number of hydrogen bond acceptors (accptHB)19.25
Free energy of solvation of dipole (dip^2/V)0.0923906
Index of cohesive interaction in solids (ACxDN^.5/SA)0.068186
Globularity descriptor (glob)0.81507
Predicted polarizability in cubic angstroms (QPpolrz)41.153
Predicted hexadecane/gas partition coefficient (QPlogPC16)15.092
Predicted octanol/gas partition coefficient (QPlogPoct)35.459
Predicted water/gas partition coefficient (QPlogPw)29.522
Predicted octanol/water partition coefficient (QPlogPo/w)-1.728
Predicted aqueous solubility (QPlogS)-1.855
Conformation-independent predicted aqueous solubility (CIQPlogS)-2.129
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-4.73
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)29.941
Predicted brain/blood partition coefficient (QPlogBB)-3.007
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)11.153
Predicted skin permeability, log Kp (QPlogKp)-4.824
PM3 calculated ionization potential (IP(ev))9.12
PM3 calculated electron affinity (EA(eV))-0.06
Number of likely metabolic reactions (#metab)9
Prediction of binding to human serum albumin (QPlogKhsa)-1.404
Predicted qualitative human oral absorption (HumanOralAbsorption)2
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)17.334
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)190.958
Number of nitrogen and oxygen atoms (#NandO)13
Number of violations of Lipinski’s rule of five (RuleOfFive)2
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
P29274ADORA2AAdenosine A2a receptorT77365SwissTargetPrediction
P30542ADORA1Adenosine A1 receptorT92072SwissTargetPrediction
P0DMS8ADORA3Adenosine A3 receptorT36059SwissTargetPrediction
P34913EPHX2Epoxide hydrataseT35734SwissTargetPrediction
Q9ULX7CA14Carbonic anhydrase XIVT31992SwissTargetPrediction
P15121AKR1B1Aldose reductaseT26623SwissTargetPrediction
P29275ADORA2BAdenosine A2b receptorT86679SwissTargetPrediction
Q9BZP6CHIAAcidic mammalian chitinase (by homology)T51597SwissTargetPrediction
P15692VEGFAVascular endothelial growth factor AT20761SEA
P05230FGF1Acidic fibroblast growth factorT18639SEA
P09038FGF2Basic fibroblast growth factorT31621SEA
Q99808SLC29A1Equilibrative nucleoside transporter 1T13491SwissTargetPrediction
P16109SELPP-selectinT10965SEA
P14151SELLLeukocyte adhesion molecule-1T60526SEA
P60568IL2Interleukin-2T61698SEA
Q9NUW8TDP1Tyrosyl-DNA phosphodiesterase 1T33492SwissTargetPrediction and SEA
P20839IMPDH1Inosine-5'-monophosphate dehydrogenase 1T40111SwissTargetPrediction
P04746AMY2APancreatic alpha-amylaseT86918SwissTargetPrediction and SEA
P14679TYRTyrosinaseT97035SwissTargetPrediction
Q9GZQ4NMUR2Neuromedin-U receptor 2T04210SEA
Q9NZ08ERAP1Endoplasmic reticulum aminopeptidase 1T72849SEA
P11717IGF2RInsulin-like growth factor II receptorT59550SEA
Q99417MYCBPMYCBP messenger RNAT37298SEA
P30837ALDH1B1Acetaldehyde dehydrogenaseT99641SEA

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T77365DI0319Orthostatic hypotension[ICD-11: BA21]P29274ADORA2A
T77365DI0331Parkinsonism[ICD-11: 8A00]P29274ADORA2A
T77365DI0359Radionuclide imaging[ICD-11: N.A.]P29274ADORA2A
T92072DI0319Orthostatic hypotension[ICD-11: BA21]P30542ADORA1
T36059DI0351Psoriasis[ICD-11: EA90]P0DMS8ADORA3
T36059DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P0DMS8ADORA3
T35734DI0086Chronic obstructive pulmonary disease[ICD-11: CA22]P34913EPHX2
T35734DI0190Hypertension[ICD-11: BA00-BA04]P34913EPHX2
T31992DI0046Bacterial infection[ICD-11: 1A00-1C4Z]Q9ULX7CA14
T31992DI0204Inborn metabolism deficiency[ICD-11: 5C50-5C59]Q9ULX7CA14
T26623DI0298Neuropathy[ICD-11: 8C0Z]P15121AKR1B1
T26623DI0366Rheumatoid arthritis[ICD-11: FA20]P15121AKR1B1
T86679DI0180Herpes simplex infection[ICD-11: 1F00]P29275ADORA2B
T86679DI0397Supraventricular tachyarrhythmia[ICD-11: BC81]P29275ADORA2B
T20761DI0095Colorectal cancer[ICD-11: 2B91]P15692VEGFA
T20761DI0365Retinopathy[ICD-11: 9B71]P15692VEGFA
T20761DI0430Vascular system developmental anomaly[ICD-11: LA90]P15692VEGFA
T18639DI0081Chronic arterial occlusive disease[ICD-11: BD4Z]P05230FGF1
T18639DI0102Coronary atherosclerosis[ICD-11: BA52]P05230FGF1
T31621DI0005Acne vulgaris[ICD-11: ED80]P09038FGF2
T13491DI0030Angina pectoris[ICD-11: BA40]Q99808SLC29A1
T10965DI0088Circulatory system disease[ICD-11: BE2Z]P16109SELP
T10965DI0381Sickle-cell disorder[ICD-11: 3A51]P16109SELP
T60526DI0037Asthma[ICD-11: CA23]P14151SELL
T60526DI0088Circulatory system disease[ICD-11: BE2Z]P14151SELL
T61698DI0275Multiple sclerosis[ICD-11: 8A40]P60568IL2
T61698DI0361Renal cell carcinoma[ICD-11: 2C90]P60568IL2
T40111DI0062Breast cancer[ICD-11: 2C60-2C6Y]P20839IMPDH1
T40111DI0179Hepatitis virus infection[ICD-11: 1E50-1E51]P20839IMPDH1
T40111DI0250Mature B-cell lymphoma[ICD-11: 2A85]P20839IMPDH1
T40111DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P20839IMPDH1
T40111DI0413Transplant rejection[ICD-11: NE84]P20839IMPDH1
T86918DI0110Cystic fibrosis[ICD-11: CA25]P04746AMY2A
T86918DI0328Pancreatic malfunction[ICD-11: DC30-DC3Z]P04746AMY2A
T97035DI0007Acquired hypermelanosis[ICD-11: ED60]P14679TYR
T97035DI0008Acquired hypomelanotic disorder[ICD-11: ED63]P14679TYR
T59550DI0146Fibrosis[ICD-11: GA14-GC01]P11717IGF2R
T59550DI0368Sarcoidosis[ICD-11: 4B20]P11717IGF2R
T37298DI0235Liver cancer[ICD-11: 2C12]Q99417MYCBP
T99641DI0396Substance abuse[ICD-11: 6C40]P30837ALDH1B1

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