Skimmin



Compound IDCDAMM00333
Common nameSkimmin
IUPAC name7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-2-one
Molecular formulaC15H16O8

Experimental data

Retention time40.297
Adduct[M+H]+
Actual mz325.095
Theoretical mz325.092
Error10.17
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score7.22

Identifiers and class information

Inchi keyVPAOSFFTKWUGAD-TYKRLAFXNA-N
SmilesO=C1OC=2C=C(OC3OC(CO)C(O)C(O)C3O)C=CC2C=C1
SuperclassPhenylpropanoids and polyketides
ClassCoumarins and derivatives

Plant source

  • Pedalium murex 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)7
    Number of reactive functional groups (#rtvFG)2
    Predicted central nervous system activity (CNS)-2
    Molecular weight (mol_MW)324.287
    Computed dipole moment(dipole)3.147
    Total solvent accessible surface area (SASA)547.431
    Hydrophobic component of SASA (FOSA)115.827
    Hydrophilic component of SASA (FISA)243.154
    Pie component of the SASA (PISA)188.45
    Weakly polar component of the SASA (WPSA)0
    Total solvent accesible volume (volume)943.666
    Number of hydrogen bond donors (donorHB)4
    Number of hydrogen bond acceptors (accptHB)11.75
    Free energy of solvation of dipole (dip^2/V)0.0104959
    Index of cohesive interaction in solids (ACxDN^.5/SA)0.0429278
    Globularity descriptor (glob)0.849926
    Predicted polarizability in cubic angstroms (QPpolrz)28.917
    Predicted hexadecane/gas partition coefficient (QPlogPC16)10.908
    Predicted octanol/gas partition coefficient (QPlogPoct)22.011
    Predicted water/gas partition coefficient (QPlogPw)19.86
    Predicted octanol/water partition coefficient (QPlogPo/w)-1.028
    Predicted aqueous solubility (QPlogS)-1.984
    Conformation-independent predicted aqueous solubility (CIQPlogS)-2.099
    Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-4.859
    Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)48.986
    Predicted brain/blood partition coefficient (QPlogBB)-2.102
    Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)18.988
    Predicted skin permeability, log Kp (QPlogKp)-4.665
    PM3 calculated ionization potential (IP(ev))9.221
    PM3 calculated electron affinity (EA(eV))0.87
    Number of likely metabolic reactions (#metab)4
    Prediction of binding to human serum albumin (QPlogKhsa)-0.96
    Predicted qualitative human oral absorption (HumanOralAbsorption)2
    Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)51.174
    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)143.251
    Number of nitrogen and oxygen atoms (#NandO)8
    Number of violations of Lipinski’s rule of five (RuleOfFive)0
    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
    P29274ADORA2AAdenosine A2a receptorT77365SwissTargetPrediction
    P30542ADORA1Adenosine A1 receptorT92072SwissTargetPrediction
    O43570CA12Carbonic anhydrase XIIT16987SwissTargetPrediction and SEA
    Q16790CA9Carbonic anhydrase IXT64567SwissTargetPrediction and SEA
    Q07820MCL1Induced myeloid leukemia cell differentiation protein Mcl-1T14912SwissTargetPrediction
    P0DMS8ADORA3Adenosine A3 receptorT36059SwissTargetPrediction
    P00915CA1Carbonic anhydrase IT13201SwissTargetPrediction and SEA
    P00918CA2Carbonic anhydrase IIT20401SwissTargetPrediction and SEA
    P10253GAALysosomal alpha-glucosidase (by homology)T31514SwissTargetPrediction
    P27487DPP4Dipeptidyl peptidase IVT31391SwissTargetPrediction
    P43166CA7Carbonic anhydrase VIIT37541SwissTargetPrediction and SEA
    P23280CA6Carbonic anhydrase VIT06569SEA
    Q9ULX7CA14Carbonic anhydrase XIVT31992SEA
    P22748CA4Carbonic anhydrase IVT53378SEA
    P27338MAOBMonoamine oxidase BT83011SEA
    P00491PNPPurine nucleoside phosphorylaseT78198SwissTargetPrediction
    P24941CDK2Cyclin-dependent kinase 2T70176SwissTargetPrediction
    P01375TNFTNF-alphaT20178SwissTargetPrediction
    P24385CCND1Cyclin-dependent kinase 4/cyclin D1T12355SwissTargetPrediction
    P32320CDACytidine deaminase (by homology)T79027SEA
    P00813ADAAdenosine deaminaseT03661SwissTargetPrediction
    P15692VEGFAVascular endothelial growth factor AT20761SEA
    P05230FGF1Acidic fibroblast growth factorT18639SEA
    P09038FGF2Basic fibroblast growth factorT31621SEA
    P04062GBABeta-glucocerebrosidaseT84173SwissTargetPrediction
    P28482MAPK1MAP kinase ERK2T58970SwissTargetPrediction
    P55263ADKAdenosine kinaseT91661SwissTargetPrediction
    P11142HSPA8Heat shock cognate 71 kDa proteinT12817SwissTargetPrediction
    P06493CDK1Cyclin-dependent kinase 1/cyclin B1T49898SwissTargetPrediction
    P04406GAPDHGlyceraldehyde-3-phosphate dehydrogenase liverT39321SwissTargetPrediction
    P52789HK2Hexokinase type IIT96685SwissTargetPrediction
    P11021HSPA578 kDa glucose-regulated proteinT77594SwissTargetPrediction
    P23526AHCYAdenosylhomocysteinaseT68698SwissTargetPrediction
    P01112HRASTransforming protein p21/H-Ras-1T71081SEA
    P60568IL2Interleukin-2T61698SwissTargetPrediction and SEA
    P30837ALDH1B1Acetaldehyde dehydrogenaseT99641SwissTargetPrediction
    P17931LGALS3Galectin-3T72038SEA
    P14679TYRTyrosinaseT97035SEA
    Q9GZQ4NMUR2Neuromedin-U receptor 2T04210SEA
    P47989XDHXanthine dehydrogenaseT40954SEA
    P22001KCNA3Voltage-gated potassium channel subunit Kv1.3T76914SEA
    P63316TNNC1Troponin, cardiac muscleT12966SEA
    P09382LGALS1Galectin-1T09544SEA
    P01111NRASGTPase NRasT35486SEA
    Q9NZ08ERAP1Endoplasmic reticulum aminopeptidase 1T72849SEA
    Q15391P2RY14Purinergic receptor P2Y14T16555SEA
    P05231IL6Interleukin-6T32578SEA
    O15427SLC16A3Monocarboxylate transporter 4T31788SEA
    P30837ALDH1B1Acetaldehyde dehydrogenaseT99641SEA
    P19429TNNI3Cardiac troponin IT20186SEA
    P45379TNNT2Cardiac muscle troponin TT05887SEA

    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
    T16987DI0046Bacterial infection[ICD-11: 1A00-1C4Z]O43570CA12
    T16987DI0372Seborrhoeic dermatitis[ICD-11: EA81]O43570CA12
    T64567DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]Q16790CA9
    T14912DI0012Acute myeloid leukaemia[ICD-11: 2A60]Q07820MCL1
    T14912DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]Q07820MCL1
    T14912DI0250Mature B-cell lymphoma[ICD-11: 2A85]Q07820MCL1
    T14912DI0252Melanoma[ICD-11: 2C30]Q07820MCL1
    T14912DI0274Multiple myeloma[ICD-11: 2A83]Q07820MCL1
    T14912DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]Q07820MCL1
    T36059DI0351Psoriasis[ICD-11: EA90]P0DMS8ADORA3
    T36059DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P0DMS8ADORA3
    T13201DI0166Glaucoma[ICD-11: 9C61]P00915CA1
    T13201DI0372Seborrhoeic dermatitis[ICD-11: EA81]P00915CA1
    T20401DI0046Bacterial infection[ICD-11: 1A00-1C4Z]P00918CA2
    T20401DI0137Essential hypertension[ICD-11: BA00]P00918CA2
    T20401DI0166Glaucoma[ICD-11: 9C61]P00918CA2
    T20401DI0175Heart failure[ICD-11: BD10-BD1Z]P00918CA2
    T20401DI0214Insomnia[ICD-11: 7A00-7A0Z]P00918CA2
    T20401DI0372Seborrhoeic dermatitis[ICD-11: EA81]P00918CA2
    T31514DI0201Inborn carbohydrate metabolism error[ICD-11: 5C51]P10253GAA
    T31391DI0009Acute diabete complication[ICD-11: 5A2Y]P27487DPP4
    T31391DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P27487DPP4
    T06569DI0046Bacterial infection[ICD-11: 1A00-1C4Z]P23280CA6
    T06569DI0372Seborrhoeic dermatitis[ICD-11: EA81]P23280CA6
    T31992DI0046Bacterial infection[ICD-11: 1A00-1C4Z]Q9ULX7CA14
    T31992DI0204Inborn metabolism deficiency[ICD-11: 5C50-5C59]Q9ULX7CA14
    T53378DI0046Bacterial infection[ICD-11: 1A00-1C4Z]P22748CA4
    T53378DI0166Glaucoma[ICD-11: 9C61]P22748CA4
    T53378DI0372Seborrhoeic dermatitis[ICD-11: EA81]P22748CA4
    T83011DI0115Dementia[ICD-11: 6D80-6D8Z]P27338MAOB
    T83011DI0117Depression[ICD-11: 6A70-6A7Z]P27338MAOB
    T83011DI0190Hypertension[ICD-11: BA00-BA04]P27338MAOB
    T83011DI0243Malaria[ICD-11: 1F40-1F45]P27338MAOB
    T83011DI0264Migraine[ICD-11: 8A80]P27338MAOB
    T83011DI0331Parkinsonism[ICD-11: 8A00]P27338MAOB
    T78198DI0120Diabetes mellitus[ICD-11: 5A10]P00491PNP
    T78198DI0167Gout[ICD-11: FA25]P00491PNP
    T78198DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]P00491PNP
    T78198DI0283Mycosis fungoides[ICD-11: 2B01]P00491PNP
    T78198DI0351Psoriasis[ICD-11: EA90]P00491PNP
    T70176DI0060Brain cancer[ICD-11: 2A00]P24941CDK2
    T70176DI0062Breast cancer[ICD-11: 2C60-2C6Y]P24941CDK2
    T70176DI0238Lung cancer[ICD-11: 2C25]P24941CDK2
    T70176DI0241Lymphoma[ICD-11: 2A80-2A86]P24941CDK2
    T70176DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]P24941CDK2
    T70176DI0303Non-small-cell lung cancer[ICD-11: 2C25]P24941CDK2
    T70176DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P24941CDK2
    T70176DI0406Thymoma[ICD-11: 2C27]P24941CDK2
    T20178DI0035Arterial occlusive disease[ICD-11: BD40]P01375TNF
    T20178DI0274Multiple myeloma[ICD-11: 2A83]P01375TNF
    T20178DI0351Psoriasis[ICD-11: EA90]P01375TNF
    T20178DI0366Rheumatoid arthritis[ICD-11: FA20]P01375TNF
    T12355DI0286Myeloproliferative neoplasm[ICD-11: 2A20]P24385CCND1
    T79027DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P32320CDA
    T03661DI0016Adaptive immunity immunodeficiency[ICD-11: 4A01]P00813ADA
    T03661DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]P00813ADA
    T03661DI0249Mature B-cell leukaemia[ICD-11: 2A82]P00813ADA
    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
    T58970DI0036Arteries/arterioles disorder[ICD-11: BD52]P28482MAPK1
    T58970DI0252Melanoma[ICD-11: 2C30]P28482MAPK1
    T58970DI0326Pancreatic cancer[ICD-11: 2C10]P28482MAPK1
    T58970DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P28482MAPK1
    T91661DI0134Epilepsy/seizure[ICD-11: 8A61-8A6Z]P55263ADK
    T49898DI0062Breast cancer[ICD-11: 2C60-2C6Y]P06493CDK1
    T49898DI0238Lung cancer[ICD-11: 2C25]P06493CDK1
    T49898DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]P06493CDK1
    T49898DI0250Mature B-cell lymphoma[ICD-11: 2A85]P06493CDK1
    T49898DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P06493CDK1
    T39321DI0279Muscular atrophy[ICD-11: 8B61]P04406GAPDH
    T39321DI0280Muscular dystrophy[ICD-11: 8C70]P04406GAPDH
    T96685DI0133Epidermal dysplasias[ICD-11: EK90]P52789HK2
    T77594DI0252Melanoma[ICD-11: 2C30]P11021HSPA5
    T77594DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P11021HSPA5
    T61698DI0275Multiple sclerosis[ICD-11: 8A40]P60568IL2
    T61698DI0361Renal cell carcinoma[ICD-11: 2C90]P60568IL2
    T99641DI0396Substance abuse[ICD-11: 6C40]P30837ALDH1B1
    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
    T97035DI0007Acquired hypermelanosis[ICD-11: ED60]P14679TYR
    T97035DI0008Acquired hypomelanotic disorder[ICD-11: ED63]P14679TYR
    T40954DI0206Inborn purine/pyrimidine/nucleotide metabolism error[ICD-11: 5C55]P47989XDH
    T40954DI0266Mineral deficiency[ICD-11: 5B5K]P47989XDH
    T76914DI0198Idiopathic inflammatory myopathy[ICD-11: 4A41]P22001KCNA3
    T76914DI0351Psoriasis[ICD-11: EA90]P22001KCNA3
    T76914DI0352Psoriatic arthritis[ICD-11: FA21]P22001KCNA3
    T12966DI0006Acquired cutaneous blood vessel malformation[ICD-11: EF20]P63316TNNC1
    T12966DI0175Heart failure[ICD-11: BD10-BD1Z]P63316TNNC1
    T35486DI0095Colorectal cancer[ICD-11: 2B91]P01111NRAS
    T35486DI0172Head and neck cancer[ICD-11: 2D42]P01111NRAS
    T35486DI0238Lung cancer[ICD-11: 2C25]P01111NRAS
    T35486DI0326Pancreatic cancer[ICD-11: 2C10]P01111NRAS
    T35486DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P01111NRAS
    T32578DI0028Anemia[ICD-11: 3A00-3A9Z]P05231IL6
    T99641DI0396Substance abuse[ICD-11: 6C40]P30837ALDH1B1

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