Tomatidine



Compound IDCDAMM02360
Common nameTomatidine
IUPAC name5\',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.02,9.04,8.013,18]icosane-6,2\'-piperidine]-16-ol
Molecular formulaC27H45NO2

Experimental data

Retention time7.53
Adduct[M+H]+
Actual mz416.352
Theoretical mz416.352
Error0.06
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score6.1449

Identifiers and class information

Inchi keyXYNPYHXGMWJBLV-UHFFFAOYNA-N
SmilesOC1CCC2(C)C(CCC3C2CCC4(C)C3CC5OC6(NCC(C)CC6)C(C)C54)C1
SuperclassLipids and lipid-like molecules
ClassSteroids and steroid derivatives

Pharmacokinetic properties

Number of descriptor values(#stars)2
Number of non-conjugated amine groups (#amine)1
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)1
Number of reactive functional groups (#rtvFG)0
Predicted central nervous system activity (CNS)1
Molecular weight (mol_MW)415.658
Computed dipole moment(dipole)3.136
Total solvent accessible surface area (SASA)708.496
Hydrophobic component of SASA (FOSA)643.976
Hydrophilic component of SASA (FISA)64.52
Pie component of the SASA (PISA)0
Weakly polar component of the SASA (WPSA)0
Total solvent accesible volume (volume)1364.66
Number of hydrogen bond donors (donorHB)2
Number of hydrogen bond acceptors (accptHB)3.45
Free energy of solvation of dipole (dip^2/V)0.007208
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0068865
Globularity descriptor (glob)0.839802
Predicted polarizability in cubic angstroms (QPpolrz)47.818
Predicted hexadecane/gas partition coefficient (QPlogPC16)11.754
Predicted octanol/gas partition coefficient (QPlogPoct)20.313
Predicted water/gas partition coefficient (QPlogPw)7.97
Predicted octanol/water partition coefficient (QPlogPo/w)5.25
Predicted aqueous solubility (QPlogS)-6.34
Conformation-independent predicted aqueous solubility (CIQPlogS)-5.136
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-4.85
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)603.889
Predicted brain/blood partition coefficient (QPlogBB)0.292
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)317.3
Predicted skin permeability, log Kp (QPlogKp)-4.675
PM3 calculated ionization potential (IP(ev))9.296
PM3 calculated electron affinity (EA(eV))-2.316
Number of likely metabolic reactions (#metab)2
Prediction of binding to human serum albumin (QPlogKhsa)1.543
Predicted qualitative human oral absorption (HumanOralAbsorption)1
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)94.502
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)44.653
Number of nitrogen and oxygen atoms (#NandO)3
Number of violations of Lipinski’s rule of five (RuleOfFive)1
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
Q99720SIGMAR1Sigma opioid receptorT46360SwissTargetPrediction
Q15125EBPAnti-estrogen binding site (AEBS)T25317SwissTargetPrediction and SEA
Q05586GRIN1Glutamate NMDA receptor; GRIN1/GRIN2BT62276SEA
Q99705MCHR1Melanin-concentrating hormone receptor 1T09572SwissTargetPrediction
P08185SERPINA6Corticosteroid binding globulinT88452SEA
Q9UHC9NPC1L1Niemann-Pick C1-like protein 1T33901SwissTargetPrediction
P28845HSD11B111-beta-hydroxysteroid dehydrogenase 1T65200SwissTargetPrediction
Q8TDU6GPBAR1G-protein coupled bile acid receptor 1T86273SEA
Q13133NR1H3LXR-alphaT52297SwissTargetPrediction
Q15465SHHSonic hedgehog protein (by homology)T12075SwissTargetPrediction
P08183ABCB1P-glycoprotein 1T25258SwissTargetPrediction
P35372OPRM1Mu opioid receptorT47768SwissTargetPrediction
O60674JAK2Tyrosine-protein kinase JAK2T08391SwissTargetPrediction
P32245MC4RMelanocortin receptor 4T72458SwissTargetPrediction
P41143OPRD1Delta opioid receptorT58992SwissTargetPrediction
P51449RORCNuclear receptor ROR-gammaT25307SwissTargetPrediction
P11413G6PDGlucose-6-phosphate 1-dehydrogenaseT63484SEA
P23458JAK1Tyrosine-protein kinase JAK1T62460SwissTargetPrediction
P32246CCR1C-C chemokine receptor type 1T16016SwissTargetPrediction
P52333JAK3Tyrosine-protein kinase JAK3T23172SwissTargetPrediction
P34972CNR2Cannabinoid receptor 2T37693SwissTargetPrediction
Q99835SMOSmoothened homologT66505SwissTargetPrediction
P60568IL2Interleukin-2T61698SEA
P60842EIF4A1Eukaryotic initiation factor 4A-IT86805SEA
Q13224GRIN2BGlutamate [NMDA] receptor subunit epsilon 2T76414SEA
O15399GRIN2DGlutamate [NMDA] receptor subunit epsilon 4T56588SEA
Q14973SLC10A1Bile acid transporterT99189SEA
P38571LIPALysosomal acid lipase/cholesteryl ester hydrolaseT24373SEA
P47870GABRB2GABA(A) receptor beta-2T80387SEA
Q14957GRIN2CGlutamate receptor ionotropic NMDA 2CT72595SEA
O14764GABRDGABA(A) receptor deltaT27376SEA

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T46360DI0105Cough[ICD-11: MD12]Q99720SIGMAR1
T25317DI0366Rheumatoid arthritis[ICD-11: FA20]Q15125EBP
T62276DI0046Bacterial infection[ICD-11: 1A00-1C4Z]Q05586GRIN1
T62276DI0182HIV-infected patients with tuberculosis[ICD-11: 1B10-1B14]Q05586GRIN1
T09572DI0308Obesity[ICD-11: 5B80-5B81]Q99705MCHR1
T88452DI0037Asthma[ICD-11: CA23]P08185SERPINA6
T88452DI0339Postoperative inflammation[ICD-11: 1A00-CA43]P08185SERPINA6
T88452DI0362Respiratory system disease[ICD-11: CB40-CB7Z]P08185SERPINA6
T33901DI0188Hyper-lipoproteinaemia[ICD-11: 5C80]Q9UHC9NPC1L1
T65200DI0210Influenza[ICD-11: 1E30-1E32]P28845HSD11B1
T65200DI0239Lupus erythematosus[ICD-11: 4A40]P28845HSD11B1
T65200DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P28845HSD11B1
T86273DI0417Type 2 diabetes mellitus[ICD-11: 5A11]Q8TDU6GPBAR1
T52297DI0117Depression[ICD-11: 6A70-6A7Z]Q13133NR1H3
T25258DI0238Lung cancer[ICD-11: 2C25]P08183ABCB1
T47768DI0013Acute pain[ICD-11: MG31]P35372OPRM1
T47768DI0059Bowel habit change[ICD-11: ME05]P35372OPRM1
T47768DI0087Chronic pain[ICD-11: MG30]P35372OPRM1
T47768DI0101Corneal disease[ICD-11: 9A76-9A78]P35372OPRM1
T47768DI0105Cough[ICD-11: MD12]P35372OPRM1
T47768DI0117Depression[ICD-11: 6A70-6A7Z]P35372OPRM1
T47768DI0124Digestive system disease[ICD-11: DE2Z]P35372OPRM1
T47768DI0218Irritable bowel syndrome[ICD-11: DD91]P35372OPRM1
T47768DI0228Large intestine motility disorder[ICD-11: DB32]P35372OPRM1
T47768DI0317Opioid use disorder[ICD-11: 6C43]P35372OPRM1
T47768DI0324Pain[ICD-11: MG30-MG3Z]P35372OPRM1
T47768DI0349Pruritus[ICD-11: EC90]P35372OPRM1
T47768DI0374Sensation disturbance[ICD-11: MB40]P35372OPRM1
T08391DI0039Atopic eczema[ICD-11: EA80]O60674JAK2
T08391DI0286Myeloproliferative neoplasm[ICD-11: 2A20]O60674JAK2
T08391DI0366Rheumatoid arthritis[ICD-11: FA20]O60674JAK2
T08391DI0404Thrombocytosis[ICD-11: 3B63]O60674JAK2
T72458DI0192Hypoactive sexual desire dysfunction[ICD-11: HA00]P32245MC4R
T72458DI0228Large intestine motility disorder[ICD-11: DB32]P32245MC4R
T72458DI0308Obesity[ICD-11: 5B80-5B81]P32245MC4R
T58992DI0059Bowel habit change[ICD-11: ME05]P41143OPRD1
T58992DI0218Irritable bowel syndrome[ICD-11: DD91]P41143OPRD1
T58992DI0324Pain[ICD-11: MG30-MG3Z]P41143OPRD1
T25307DI0042Autoimmune disease[ICD-11: 4A40-4A45]P51449RORC
T25307DI0107Crohn disease[ICD-11: DD70]P51449RORC
T25307DI0238Lung cancer[ICD-11: 2C25]P51449RORC
T25307DI0275Multiple sclerosis[ICD-11: 8A40]P51449RORC
T25307DI0351Psoriasis[ICD-11: EA90]P51449RORC
T25307DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P51449RORC
T63484DI0086Chronic obstructive pulmonary disease[ICD-11: CA22]P11413G6PD
T62460DI0039Atopic eczema[ICD-11: EA80]P23458JAK1
T62460DI0286Myeloproliferative neoplasm[ICD-11: 2A20]P23458JAK1
T62460DI0366Rheumatoid arthritis[ICD-11: FA20]P23458JAK1
T62460DI0404Thrombocytosis[ICD-11: 3B63]P23458JAK1
T16016DI0120Diabetes mellitus[ICD-11: 5A10]P32246CCR1
T16016DI0366Rheumatoid arthritis[ICD-11: FA20]P32246CCR1
T23172DI0023Alopecia[ICD-11: ED70]P52333JAK3
T23172DI0039Atopic eczema[ICD-11: EA80]P52333JAK3
T23172DI0286Myeloproliferative neoplasm[ICD-11: 2A20]P52333JAK3
T23172DI0366Rheumatoid arthritis[ICD-11: FA20]P52333JAK3
T37693DI0040Attention deficit hyperactivity disorder[ICD-11: 6A05]P34972CNR2
T37693DI0214Insomnia[ICD-11: 7A00-7A0Z]P34972CNR2
T66505DI0047Basal cell carcinoma[ICD-11: 2C32]Q99835SMO
T66505DI0085Chronic myelomonocytic leukaemia[ICD-11: 2A40]Q99835SMO
T66505DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]Q99835SMO
T61698DI0275Multiple sclerosis[ICD-11: 8A40]P60568IL2
T61698DI0361Renal cell carcinoma[ICD-11: 2C90]P60568IL2
T86805DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P60842EIF4A1
T76414DI0024Alpha-1-antitrypsin deficiency[ICD-11: 5C5A]Q13224GRIN2B
T56588DI0296Neurodegenerative disorder[ICD-11: 8A20-8A23]O15399GRIN2D
T99189DI0179Hepatitis virus infection[ICD-11: 1E50-1E51]Q14973SLC10A1
T24373DI0132Enzyme deficiency[ICD-11: 5C51-5C57]P38571LIPA
T80387DI0117Depression[ICD-11: 6A70-6A7Z]P47870GABRB2
T80387DI0214Insomnia[ICD-11: 7A00-7A0Z]P47870GABRB2
T80387DI0256Mental/behavioural/neurodevelopmental disorder[ICD-11: 6E20-6E8Z]P47870GABRB2
T80387DI0411Tonus and reflex abnormality[ICD-11: MB47]P47870GABRB2
T72595DI0296Neurodegenerative disorder[ICD-11: 8A20-8A23]Q14957GRIN2C
T27376DI0117Depression[ICD-11: 6A70-6A7Z]O14764GABRD
T27376DI0214Insomnia[ICD-11: 7A00-7A0Z]O14764GABRD
T27376DI0256Mental/behavioural/neurodevelopmental disorder[ICD-11: 6E20-6E8Z]O14764GABRD

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