Harpagoside B;(-)-Harpagoside B



Compound IDCDAMM00525
Common nameHarpagoside B;(-)-Harpagoside B
IUPAC name[4a-hydroxy-5-methoxy-7-methyl-1-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,5,6,7a-tetrahydrocyclopenta[c]pyran-7-yl] 3-phenylprop-2-enoate
Molecular formulaC25H32O11

Experimental data

Retention time13.46
Adduct[M+H]+
Actual mz509.207
Theoretical mz509.201
Error12.22
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score7.2241

Identifiers and class information

Inchi keyBEHDYQAAWZWDFR-IBXSQOMPNA-N
SmilesO=C(OC1(C)CC(OC)C2(O)C=COC(OC3OC(CO)C(O)C(O)C3O)C21)C=CC=4C=CC=CC4
SuperclassLipids and lipid-like molecules
ClassPrenol lipids

Plant source

  • Piper longum L.

    • 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)13
    Number of reactive functional groups (#rtvFG)3
    Predicted central nervous system activity (CNS)-2
    Molecular weight (mol_MW)508.521
    Computed dipole moment(dipole)3.559
    Total solvent accessible surface area (SASA)788.984
    Hydrophobic component of SASA (FOSA)289.666
    Hydrophilic component of SASA (FISA)202.212
    Pie component of the SASA (PISA)297.105
    Weakly polar component of the SASA (WPSA)0
    Total solvent accesible volume (volume)1475.65
    Number of hydrogen bond donors (donorHB)5
    Number of hydrogen bond acceptors (accptHB)16.35
    Free energy of solvation of dipole (dip^2/V)0.0085843
    Index of cohesive interaction in solids (ACxDN^.5/SA)0.0463377
    Globularity descriptor (glob)0.794485
    Predicted polarizability in cubic angstroms (QPpolrz)47.392
    Predicted hexadecane/gas partition coefficient (QPlogPC16)16.635
    Predicted octanol/gas partition coefficient (QPlogPoct)32.112
    Predicted water/gas partition coefficient (QPlogPw)25.574
    Predicted octanol/water partition coefficient (QPlogPo/w)0.464
    Predicted aqueous solubility (QPlogS)-3.115
    Conformation-independent predicted aqueous solubility (CIQPlogS)-3.569
    Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-6.274
    Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)119.763
    Predicted brain/blood partition coefficient (QPlogBB)-2.356
    Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)49.903
    Predicted skin permeability, log Kp (QPlogKp)-2.952
    PM3 calculated ionization potential (IP(ev))9.518
    PM3 calculated electron affinity (EA(eV))0.923
    Number of likely metabolic reactions (#metab)5
    Prediction of binding to human serum albumin (QPlogKhsa)-0.938
    Predicted qualitative human oral absorption (HumanOralAbsorption)2
    Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)40.945
    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)162.751
    Number of nitrogen and oxygen atoms (#NandO)11
    Number of violations of Lipinski’s rule of five (RuleOfFive)2
    Number of violations of Jorgensen’s rule of three (RuleOfThree)0

    Compound-target network

    Cytoscape Graph

    Protein targets associated with phytocompound

    Uniprot ID Gene name Target name TTD_ID Prediction source
    P00533EGFREpidermal growth factor receptor erbB1T59328SwissTargetPrediction
    P29274ADORA2AAdenosine A2a receptorT77365SwissTargetPrediction
    P30542ADORA1Adenosine A1 receptorT92072SwissTargetPrediction
    P09874PARP1Poly [ADP-ribose] polymerase-1T06273SwissTargetPrediction
    Q8TDS4HCAR2Hydroxycarboxylic acid receptor 2T88185SwissTargetPrediction
    P0DMS8ADORA3Adenosine A3 receptorT36059SwissTargetPrediction
    P42336PIK3CAPI3-kinase p110-alpha subunitT80276SwissTargetPrediction
    P06239LCKTyrosine-protein kinase LCKT12499SwissTargetPrediction
    P13866SLC5A1Sodium/glucose cotransporter 1T54771SwissTargetPrediction
    P08473MMENeprilysinT05409SwissTargetPrediction
    P17612PRKACAcAMP-dependent protein kinase alpha-catalytic subunitT12808SwissTargetPrediction
    P29275ADORA2BAdenosine A2b receptorT86679SwissTargetPrediction
    P35968KDRVascular endothelial growth factor receptor 2T80975SwissTargetPrediction
    P18405SRD5A1Steroid 5-alpha-reductase 1T70309SwissTargetPrediction
    P22894MMP8Matrix metalloproteinase 8T08856SwissTargetPrediction
    P14780MMP9Matrix metalloproteinase 9T54156SwissTargetPrediction
    P03956MMP1Matrix metalloproteinase 1T52450SwissTargetPrediction
    P13726F3Coagulation factor VII/tissue factorT72702SwissTargetPrediction
    P08183ABCB1P-glycoprotein 1T25258SEA
    P00519ABL1Tyrosine-protein kinase ABLT63505SwissTargetPrediction
    P06213INSRInsulin receptorT85435SwissTargetPrediction
    O14965AURKASerine/threonine-protein kinase Aurora-AT87675SwissTargetPrediction
    P11387TOP1DNA topoisomerase IT09826SwissTargetPrediction
    P08238HSP90AB1Heat shock protein HSP 90-betaT96623SwissTargetPrediction
    P07900HSP90AA1Heat shock protein HSP 90-alphaT18477SwissTargetPrediction
    P30556AGTR1Type-1 angiotensin II receptorT74456SwissTargetPrediction
    Q02750MAP2K1Dual specificity mitogen-activated protein kinase kinase 1T99057SwissTargetPrediction
    P53779MAPK10c-Jun N-terminal kinase 3T85421SwissTargetPrediction
    P12931SRCTyrosine-protein kinase SRCT85943SwissTargetPrediction
    P15692VEGFAVascular endothelial growth factor AT20761SEA
    P05230FGF1Acidic fibroblast growth factorT18639SEA
    P09038FGF2Basic fibroblast growth factorT31621SEA
    P04062GBABeta-glucocerebrosidaseT84173SwissTargetPrediction
    P42892ECE1Endothelin-converting enzyme 1T50970SwissTargetPrediction
    Q9NWZ3IRAK4Interleukin-1 receptor-associated kinase 4T55398SwissTargetPrediction
    P11362FGFR1Fibroblast growth factor receptor 1T47101SwissTargetPrediction
    P55263ADKAdenosine kinaseT91661SwissTargetPrediction
    P11142HSPA8Heat shock cognate 71 kDa proteinT12817SwissTargetPrediction
    Q99808SLC29A1Equilibrative nucleoside transporter 1T13491SwissTargetPrediction
    P52789HK2Hexokinase type IIT96685SwissTargetPrediction
    P11021HSPA578 kDa glucose-regulated proteinT77594SwissTargetPrediction
    O43868SLC28A2Sodium/nucleoside cotransporter 2T94627SwissTargetPrediction
    Q9NY91SLC5A4Low affinity sodium-glucose cotransporterT22583SwissTargetPrediction
    P31639SLC5A2Sodium/glucose cotransporter 2T30085SwissTargetPrediction
    P50281MMP14Matrix metalloproteinase 14T65019SwissTargetPrediction
    P14151SELLLeukocyte adhesion molecule-1T60526SEA
    P01112HRASTransforming protein p21/H-Ras-1T71081SwissTargetPrediction
    P17936IGFBP3Insulin-like growth factor binding protein 3T33455SwissTargetPrediction
    P20839IMPDH1Inosine-5'-monophosphate dehydrogenase 1T40111SwissTargetPrediction
    P12268IMPDH2Inosine-5'-monophosphate dehydrogenase 2T89360SwissTargetPrediction
    Q9H244P2RY12Purinergic receptor P2Y12 (by homology)T46937SwissTargetPrediction
    Q06187BTKTyrosine-protein kinase BTKT97719SwissTargetPrediction
    P24530EDNRBEndothelin receptor ET-BT92828SwissTargetPrediction
    P80192MAP3K9Mitogen-activated protein kinase kinase kinase 9T19760SwissTargetPrediction
    P17931LGALS3Galectin-3T72038SwissTargetPrediction and SEA
    P04746AMY2APancreatic alpha-amylaseT86918SEA
    P14679TYRTyrosinaseT97035SEA
    P29317EPHA2Ephrin type-A receptor 2T57278SwissTargetPrediction
    P11166SLC2A1Glucose transporter (by homology)T89458SwissTargetPrediction
    P09382LGALS1Galectin-1T09544SwissTargetPrediction

    Target associated diseases

    TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
    T59328DI0030Angina pectoris[ICD-11: BA40]P00533EGFR
    T59328DI0062Breast cancer[ICD-11: 2C60-2C6Y]P00533EGFR
    T59328DI0095Colorectal cancer[ICD-11: 2B91]P00533EGFR
    T59328DI0121Diabetic foot ulcer[ICD-11: BD54]P00533EGFR
    T59328DI0220Ischemia[ICD-11: 8B10-8B11]P00533EGFR
    T59328DI0238Lung cancer[ICD-11: 2C25]P00533EGFR
    T59328DI0303Non-small-cell lung cancer[ICD-11: 2C25]P00533EGFR
    T59328DI0361Renal cell carcinoma[ICD-11: 2C90]P00533EGFR
    T59328DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P00533EGFR
    T59328DI0420Unspecific body region injury[ICD-11: ND56]P00533EGFR
    T77365DI0319Orthostatic hypotension[ICD-11: BA21]P29274ADORA2A
    T77365DI0331Parkinsonism[ICD-11: 8A00]P29274ADORA2A
    T77365DI0359Radionuclide imaging[ICD-11: N.A.]P29274ADORA2A
    T92072DI0319Orthostatic hypotension[ICD-11: BA21]P30542ADORA1
    T06273DI0006Acquired cutaneous blood vessel malformation[ICD-11: EF20]P09874PARP1
    T06273DI0143Fallopian tube cancer[ICD-11: 2C74]P09874PARP1
    T06273DI0321Ovarian cancer[ICD-11: 2C73]P09874PARP1
    T06273DI0334Peritoneal cancer[ICD-11: 2C51]P09874PARP1
    T88185DI0203Inborn lipid metabolism error[ICD-11: 5C52]Q8TDS4HCAR2
    T36059DI0351Psoriasis[ICD-11: EA90]P0DMS8ADORA3
    T36059DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P0DMS8ADORA3
    T80276DI0062Breast cancer[ICD-11: 2C60-2C6Y]P42336PIK3CA
    T80276DI0151Follicular lymphoma[ICD-11: 2A80]P42336PIK3CA
    T80276DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]P42336PIK3CA
    T12499DI0286Myeloproliferative neoplasm[ICD-11: 2A20]P06239LCK
    T54771DI0120Diabetes mellitus[ICD-11: 5A10]P13866SLC5A1
    T54771DI0175Heart failure[ICD-11: BD10-BD1Z]P13866SLC5A1
    T54771DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P13866SLC5A1
    T05409DI0175Heart failure[ICD-11: BD10-BD1Z]P08473MME
    T12808DI0279Muscular atrophy[ICD-11: 8B61]P17612PRKACA
    T86679DI0180Herpes simplex infection[ICD-11: 1F00]P29275ADORA2B
    T86679DI0397Supraventricular tachyarrhythmia[ICD-11: BC81]P29275ADORA2B
    T80975DI0062Breast cancer[ICD-11: 2C60-2C6Y]P35968KDR
    T80975DI0095Colorectal cancer[ICD-11: 2B91]P35968KDR
    T80975DI0160Gastrointestinal stromal tumour[ICD-11: 2B5B]P35968KDR
    T80975DI0244Malignant digestive organ neoplasm[ICD-11: 2C11]P35968KDR
    T80975DI0361Renal cell carcinoma[ICD-11: 2C90]P35968KDR
    T80975DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P35968KDR
    T80975DI0395Stomach cancer[ICD-11: 2B72]P35968KDR
    T80975DI0403Thrombocytopenia[ICD-11: 3B64]P35968KDR
    T80975DI0407Thyroid cancer[ICD-11: 2D10]P35968KDR
    T70309DI0347Prostate disease[ICD-11: GA91]P18405SRD5A1
    T08856DI0366Rheumatoid arthritis[ICD-11: FA20]P22894MMP8
    T54156DI0219Ischaemic/haemorrhagic stroke[ICD-11: 8B20]P14780MMP9
    T54156DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P14780MMP9
    T54156DI0395Stomach cancer[ICD-11: 2B72]P14780MMP9
    T54156DI0419Ulcerative colitis[ICD-11: DD71]P14780MMP9
    T52450DI0238Lung cancer[ICD-11: 2C25]P03956MMP1
    T72702DI0075Cervical cancer[ICD-11: 2C77]P13726F3
    T25258DI0238Lung cancer[ICD-11: 2C25]P08183ABCB1
    T63505DI0062Breast cancer[ICD-11: 2C60-2C6Y]P00519ABL1
    T63505DI0220Ischemia[ICD-11: 8B10-8B11]P00519ABL1
    T63505DI0250Mature B-cell lymphoma[ICD-11: 2A85]P00519ABL1
    T63505DI0306Nutritional deficiency[ICD-11: 5B50-5B71]P00519ABL1
    T85435DI0009Acute diabete complication[ICD-11: 5A2Y]P06213INSR
    T85435DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P06213INSR
    T87675DI0009Acute diabete complication[ICD-11: 5A2Y]O14965AURKA
    T87675DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]O14965AURKA
    T09826DI0046Bacterial infection[ICD-11: 1A00-1C4Z]P11387TOP1
    T09826DI0095Colorectal cancer[ICD-11: 2B91]P11387TOP1
    T09826DI0238Lung cancer[ICD-11: 2C25]P11387TOP1
    T09826DI0321Ovarian cancer[ICD-11: 2C73]P11387TOP1
    T09826DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P11387TOP1
    T96623DI0062Breast cancer[ICD-11: 2C60-2C6Y]P08238HSP90AB1
    T96623DI0238Lung cancer[ICD-11: 2C25]P08238HSP90AB1
    T96623DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]P08238HSP90AB1
    T96623DI0249Mature B-cell leukaemia[ICD-11: 2A82]P08238HSP90AB1
    T96623DI0286Myeloproliferative neoplasm[ICD-11: 2A20]P08238HSP90AB1
    T96623DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P08238HSP90AB1
    T96623DI0395Stomach cancer[ICD-11: 2B72]P08238HSP90AB1
    T18477DI0015Acute upper respiratory infection[ICD-11: CA07]P07900HSP90AA1
    T18477DI0037Asthma[ICD-11: CA23]P07900HSP90AA1
    T74456DI0137Essential hypertension[ICD-11: BA00]P30556AGTR1
    T74456DI0190Hypertension[ICD-11: BA00-BA04]P30556AGTR1
    T74456DI0373Secondary hypertension[ICD-11: BA04]P30556AGTR1
    T74456DI0425Urinary system clinical symptom[ICD-11: MF8Y]P30556AGTR1
    T99057DI0262Metastatic tumour[ICD-11: 2D50-2E2Z]Q02750MAP2K1
    T99057DI0336Phakomatoses/hamartoneoplastic syndrome[ICD-11: LD2D]Q02750MAP2K1
    T85421DI0125Dissociative neurological symptom disorder[ICD-11: 6B60]P53779MAPK10
    T85943DI0062Breast cancer[ICD-11: 2C60-2C6Y]P12931SRC
    T85943DI0220Ischemia[ICD-11: 8B10-8B11]P12931SRC
    T85943DI0286Myeloproliferative neoplasm[ICD-11: 2A20]P12931SRC
    T85943DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P12931SRC
    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
    T84173DI0257Metabolic disorder[ICD-11: 5C50-5D2Z]P04062GBA
    T55398DI0039Atopic eczema[ICD-11: EA80]Q9NWZ3IRAK4
    T55398DI0109Cutaneous lupus erythematosus[ICD-11: EB50-EB5Z]Q9NWZ3IRAK4
    T55398DI0241Lymphoma[ICD-11: 2A80-2A86]Q9NWZ3IRAK4
    T55398DI0339Postoperative inflammation[ICD-11: 1A00-CA43]Q9NWZ3IRAK4
    T55398DI0351Psoriasis[ICD-11: EA90]Q9NWZ3IRAK4
    T55398DI0366Rheumatoid arthritis[ICD-11: FA20]Q9NWZ3IRAK4
    T47101DI0095Colorectal cancer[ICD-11: 2B91]P11362FGFR1
    T47101DI0199Idiopathic interstitial pneumonitis[ICD-11: CB03]P11362FGFR1
    T47101DI0235Liver cancer[ICD-11: 2C12]P11362FGFR1
    T47101DI0403Thrombocytopenia[ICD-11: 3B64]P11362FGFR1
    T91661DI0134Epilepsy/seizure[ICD-11: 8A61-8A6Z]P55263ADK
    T13491DI0030Angina pectoris[ICD-11: BA40]Q99808SLC29A1
    T96685DI0133Epidermal dysplasias[ICD-11: EK90]P52789HK2
    T77594DI0252Melanoma[ICD-11: 2C30]P11021HSPA5
    T77594DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P11021HSPA5
    T22583DI0009Acute diabete complication[ICD-11: 5A2Y]Q9NY91SLC5A4
    T22583DI0417Type 2 diabetes mellitus[ICD-11: 5A11]Q9NY91SLC5A4
    T30085DI0120Diabetes mellitus[ICD-11: 5A10]P31639SLC5A2
    T30085DI0175Heart failure[ICD-11: BD10-BD1Z]P31639SLC5A2
    T30085DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P31639SLC5A2
    T65019DI0178Hepatic fibrosis/cirrhosis[ICD-11: DB93]P50281MMP14
    T60526DI0037Asthma[ICD-11: CA23]P14151SELL
    T60526DI0088Circulatory system disease[ICD-11: BE2Z]P14151SELL
    T33455DI0115Dementia[ICD-11: 6D80-6D8Z]P17936IGFBP3
    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
    T89360DI0413Transplant rejection[ICD-11: NE84]P12268IMPDH2
    T46937DI0287Myocardial infarction[ICD-11: BA41-BA43]Q9H244P2RY12
    T46937DI0405Thrombosis[ICD-11: DB61-GB90]Q9H244P2RY12
    T97719DI0231Leukaemia[ICD-11: 2A60-2B33]Q06187BTK
    T92828DI0070Cardiovascular disease[ICD-11: BA00-BE2Z]P24530EDNRB
    T92828DI0356Pulmonary hypertension[ICD-11: BB01]P24530EDNRB
    T19760DI0037Asthma[ICD-11: CA23]P80192MAP3K9
    T72038DI0190Hypertension[ICD-11: BA00-BA04]P17931LGALS3
    T72038DI0199Idiopathic interstitial pneumonitis[ICD-11: CB03]P17931LGALS3
    T72038DI0252Melanoma[ICD-11: 2C30]P17931LGALS3
    T72038DI0302Non-alcoholic fatty liver disease[ICD-11: DB92]P17931LGALS3
    T72038DI0351Psoriasis[ICD-11: EA90]P17931LGALS3
    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
    T57278DI0060Brain cancer[ICD-11: 2A00]P29317EPHA2
    T57278DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P29317EPHA2
    T89458DI0384Skin disease[ICD-11: EA00-EM0Z]P11166SLC2A1

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