Cyclopamine



Compound IDCDAMM00274
Common nameCyclopamine
IUPAC name(3S,3\'R,3\'aS,6\'S,6aS,6bS,7\'aR,9R,11aS,11bR)-3\',6\',10,11b-tetramethylspiro[2,3,4,6,6a,6b,7,8,11,11a-decahydro-1H-benzo[a]fluorene-9,2\'-3a,4,5,6,7,7a-hexahydro-3H-furo[3,2-b]pyridine]-3-ol
Molecular formulaC27H41NO2

Experimental data

Retention time60.179
Adduct[M+H]+
Actual mz412.326
Theoretical mz412.321
Error11.14
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score7.53

Identifiers and class information

Inchi keyCQLRUIIRRZYHHS-UHFFFAOYSA-N
SmilesCC1CC2C(C(C3(O2)CCC4C5CC=C6CC(CCC6(C5CC4=C3C)C)O)C)NC1
SuperclassPhenylpropanoids and polyketides
ClassFlavonoids

Pharmacokinetic properties

Number of descriptor values(#stars)0
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)411.626
Computed dipole moment(dipole)3.309
Total solvent accessible surface area (SASA)716.444
Hydrophobic component of SASA (FOSA)616.574
Hydrophilic component of SASA (FISA)66.684
Pie component of the SASA (PISA)33.187
Weakly polar component of the SASA (WPSA)0
Total solvent accesible volume (volume)1356.41
Number of hydrogen bond donors (donorHB)2
Number of hydrogen bond acceptors (accptHB)3.95
Free energy of solvation of dipole (dip^2/V)0.0080727
Index of cohesive interaction in solids (ACxDN^.5/SA)0.007797
Globularity descriptor (glob)0.827135
Predicted polarizability in cubic angstroms (QPpolrz)47.804
Predicted hexadecane/gas partition coefficient (QPlogPC16)11.95
Predicted octanol/gas partition coefficient (QPlogPoct)20.597
Predicted water/gas partition coefficient (QPlogPw)8.722
Predicted octanol/water partition coefficient (QPlogPo/w)5.017
Predicted aqueous solubility (QPlogS)-6.319
Conformation-independent predicted aqueous solubility (CIQPlogS)-5.123
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-5.214
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)576.018
Predicted brain/blood partition coefficient (QPlogBB)0.252
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)301.501
Predicted skin permeability, log Kp (QPlogKp)-4.598
PM3 calculated ionization potential (IP(ev))9.313
PM3 calculated electron affinity (EA(eV))-0.885
Number of likely metabolic reactions (#metab)7
Prediction of binding to human serum albumin (QPlogKhsa)1.425
Predicted qualitative human oral absorption (HumanOralAbsorption)1
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)92.77
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)44.058
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)2

Compound-target network

Cytoscape Graph

Protein targets associated with phytocompound

Uniprot ID Gene name Target name TTD_ID Prediction source
Q9Y5N1HRH3Histamine H3 receptorT64765SwissTargetPrediction
P00797RENReninT61622SwissTargetPrediction
P14416DRD2Dopamine D2 receptorT67162SwissTargetPrediction
Q15125EBPAnti-estrogen binding site (AEBS)T25317SwissTargetPrediction and SEA
P27487DPP4Dipeptidyl peptidase IVT31391SwissTargetPrediction
P31645SLC6A4Serotonin transporter (by homology)T27812SwissTargetPrediction
P50406HTR6Serotonin 6 (5-HT6) receptorT16691SwissTargetPrediction
Q99705MCHR1Melanin-concentrating hormone receptor 1T09572SwissTargetPrediction
P10275ARAndrogen ReceptorT11211SEA
Q92731ESR2Estrogen receptor betaT80896SEA
P08185SERPINA6Corticosteroid binding globulinT88452SEA
Q9UHC9NPC1L1Niemann-Pick C1-like protein 1T33901SEA
P28845HSD11B111-beta-hydroxysteroid dehydrogenase 1T65200SwissTargetPrediction
P03372ESR1Estrogen receptor alphaT02506SEA
Q13133NR1H3LXR-alphaT52297SEA
Q15465SHHSonic hedgehog protein (by homology)T12075SwissTargetPrediction and SEA
Q9UM73ALKALK tyrosine kinase receptorT56418SwissTargetPrediction
P35462DRD3Dopamine D3 receptorT02551SwissTargetPrediction
P41145OPRK1Kappa Opioid receptorT60693SwissTargetPrediction
P06213INSRInsulin receptorT85435SwissTargetPrediction
P35270SPRSubstance-P receptorT47094SwissTargetPrediction
P11413G6PDGlucose-6-phosphate 1-dehydrogenaseT63484SEA
P05093CYP17A1Cytochrome P450 17A1T89041SEA
P31749AKT1Serine/threonine-protein kinase AKTT67619SwissTargetPrediction
P32246CCR1C-C chemokine receptor type 1T16016SwissTargetPrediction
P52333JAK3Tyrosine-protein kinase JAK3T23172SwissTargetPrediction
P04062GBABeta-glucocerebrosidaseT84173SwissTargetPrediction
P41146OPRL1Nociceptin receptorT52921SwissTargetPrediction
Q99835SMOSmoothened homologT66505SwissTargetPrediction and SEA
P31751AKT2Serine/threonine-protein kinase AKT2T94621SwissTargetPrediction
Q9Y243AKT3Serine/threonine-protein kinase AKTT71266SwissTargetPrediction
P60568IL2Interleukin-2T61698SEA
Q08881ITKTyrosine-protein kinase ITK/TSKT77537SwissTargetPrediction
P21452TACR2Neurokinin 2 receptorT52790SwissTargetPrediction
P53634CTSCDipeptidyl peptidase IT70490SwissTargetPrediction

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T64765DI0392Somnolence[ICD-11: MG42]Q9Y5N1HRH3
T61622DI0190Hypertension[ICD-11: BA00-BA04]P00797REN
T67162DI0022Allergic/hypersensitivity disorder[ICD-11: 4A80-4A8Z]P14416DRD2
T67162DI0025Alzheimer disease[ICD-11: 8A20]P14416DRD2
T67162DI0037Asthma[ICD-11: CA23]P14416DRD2
T67162DI0040Attention deficit hyperactivity disorder[ICD-11: 6A05]P14416DRD2
T67162DI0051Bipolar disorder[ICD-11: 6A60]P14416DRD2
T67162DI0063Breathing abnormality[ICD-11: MD11]P14416DRD2
T67162DI0070Cardiovascular disease[ICD-11: BA00-BE2Z]P14416DRD2
T67162DI0073Cerebral ischaemia[ICD-11: 8B1Z]P14416DRD2
T67162DI0117Depression[ICD-11: 6A70-6A7Z]P14416DRD2
T67162DI0124Digestive system disease[ICD-11: DE2Z]P14416DRD2
T67162DI0137Essential hypertension[ICD-11: BA00]P14416DRD2
T67162DI0142Faecal incontinence[ICD-11: ME07]P14416DRD2
T67162DI0156Gangrene[ICD-11: MC85]P14416DRD2
T67162DI0166Glaucoma[ICD-11: 9C61]P14416DRD2
T67162DI0175Heart failure[ICD-11: BD10-BD1Z]P14416DRD2
T67162DI0185Hyperaemia[ICD-11: 9A61-9B7Y]P14416DRD2
T67162DI0190Hypertension[ICD-11: BA00-BA04]P14416DRD2
T67162DI0196Hypotension[ICD-11: BA20-BA21]P14416DRD2
T67162DI0205Inborn porphyrin/heme metabolism error[ICD-11: 5C58]P14416DRD2
T67162DI0214Insomnia[ICD-11: 7A00-7A0Z]P14416DRD2
T67162DI0222Itching[ICD-11: 1F28-1G07]P14416DRD2
T67162DI0264Migraine[ICD-11: 8A80]P14416DRD2
T67162DI0293Nausea/vomiting[ICD-11: MD90]P14416DRD2
T67162DI0324Pain[ICD-11: MG30-MG3Z]P14416DRD2
T67162DI0331Parkinsonism[ICD-11: 8A00]P14416DRD2
T67162DI0337Pituitary gland disorder[ICD-11: 5A60-5A61]P14416DRD2
T67162DI0340Postpartum haemorrhage[ICD-11: JA43]P14416DRD2
T67162DI0354Psychotic disorder[ICD-11: 6A20-6A25]P14416DRD2
T67162DI0356Pulmonary hypertension[ICD-11: BB01]P14416DRD2
T67162DI0370Schizophrenia[ICD-11: 6A20]P14416DRD2
T67162DI0396Substance abuse[ICD-11: 6C40]P14416DRD2
T67162DI0408Thyrotoxicosis[ICD-11: 5A02]P14416DRD2
T67162DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P14416DRD2
T25317DI0366Rheumatoid arthritis[ICD-11: FA20]Q15125EBP
T31391DI0009Acute diabete complication[ICD-11: 5A2Y]P27487DPP4
T31391DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P27487DPP4
T27812DI0033Anxiety disorder[ICD-11: 6B00-6B0Z]P31645SLC6A4
T27812DI0040Attention deficit hyperactivity disorder[ICD-11: 6A05]P31645SLC6A4
T27812DI0087Chronic pain[ICD-11: MG30]P31645SLC6A4
T27812DI0096concerning food/fluid intake symptom[ICD-11: MG43]P31645SLC6A4
T27812DI0101Corneal disease[ICD-11: 9A76-9A78]P31645SLC6A4
T27812DI0105Cough[ICD-11: MD12]P31645SLC6A4
T27812DI0117Depression[ICD-11: 6A70-6A7Z]P31645SLC6A4
T27812DI0264Migraine[ICD-11: 8A80]P31645SLC6A4
T27812DI0301Nicotine use disorder[ICD-11: 6C4A]P31645SLC6A4
T27812DI0308Obesity[ICD-11: 5B80-5B81]P31645SLC6A4
T27812DI0324Pain[ICD-11: MG30-MG3Z]P31645SLC6A4
T16691DI0025Alzheimer disease[ICD-11: 8A20]P50406HTR6
T16691DI0370Schizophrenia[ICD-11: 6A20]P50406HTR6
T09572DI0308Obesity[ICD-11: 5B80-5B81]Q99705MCHR1
T11211DI0005Acne vulgaris[ICD-11: ED80]P10275AR
T11211DI0012Acute myeloid leukaemia[ICD-11: 2A60]P10275AR
T11211DI0021Alcoholic liver disease[ICD-11: DB94]P10275AR
T11211DI0062Breast cancer[ICD-11: 2C60-2C6Y]P10275AR
T11211DI0086Chronic obstructive pulmonary disease[ICD-11: CA22]P10275AR
T11211DI0145Female pelvic pain[ICD-11: GA34]P10275AR
T11211DI0194Hypo-osmolality/hyponatraemia[ICD-11: 5C72]P10275AR
T11211DI0237Low bone mass disorder[ICD-11: FB83]P10275AR
T11211DI0247Mammary tumour[ICD-11: 2C60-2C6Z]P10275AR
T11211DI0346Prostate cancer[ICD-11: 2C82]P10275AR
T11211DI0401Testicular dysfunction[ICD-11: 5A81]P10275AR
T80896DI0062Breast cancer[ICD-11: 2C60-2C6Y]Q92731ESR2
T80896DI0108Cushing syndrome[ICD-11: 5A70]Q92731ESR2
T80896DI0254Menopausal disorder[ICD-11: GA30]Q92731ESR2
T80896DI0432Vasomotor/allergic rhinitis[ICD-11: CA08]Q92731ESR2
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
T02506DI0106COVID-19[ICD-11: 1D6Y]P03372ESR1
T52297DI0117Depression[ICD-11: 6A70-6A7Z]Q13133NR1H3
T56418DI0238Lung cancer[ICD-11: 2C25]Q9UM73ALK
T56418DI0251Mature T-cell lymphoma[ICD-11: 2A90]Q9UM73ALK
T56418DI0303Non-small-cell lung cancer[ICD-11: 2C25]Q9UM73ALK
T02551DI0051Bipolar disorder[ICD-11: 6A60]P35462DRD3
T02551DI0331Parkinsonism[ICD-11: 8A00]P35462DRD3
T60693DI0304Non-specific cutaneous vascular symptom[ICD-11: ME64]P41145OPRK1
T60693DI0324Pain[ICD-11: MG30-MG3Z]P41145OPRK1
T60693DI0349Pruritus[ICD-11: EC90]P41145OPRK1
T85435DI0009Acute diabete complication[ICD-11: 5A2Y]P06213INSR
T85435DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P06213INSR
T47094DI0117Depression[ICD-11: 6A70-6A7Z]P35270SPR
T47094DI0293Nausea/vomiting[ICD-11: MD90]P35270SPR
T63484DI0086Chronic obstructive pulmonary disease[ICD-11: CA22]P11413G6PD
T89041DI0346Prostate cancer[ICD-11: 2C82]P05093CYP17A1
T67619DI0062Breast cancer[ICD-11: 2C60-2C6Y]P31749AKT1
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
T84173DI0257Metabolic disorder[ICD-11: 5C50-5D2Z]P04062GBA
T52921DI0039Atopic eczema[ICD-11: EA80]P41146OPRL1
T52921DI0117Depression[ICD-11: 6A70-6A7Z]P41146OPRL1
T52921DI0173Headache[ICD-11: 8A80-8A84]P41146OPRL1
T52921DI0175Heart failure[ICD-11: BD10-BD1Z]P41146OPRL1
T66505DI0047Basal cell carcinoma[ICD-11: 2C32]Q99835SMO
T66505DI0085Chronic myelomonocytic leukaemia[ICD-11: 2A40]Q99835SMO
T66505DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]Q99835SMO
T71266DI0062Breast cancer[ICD-11: 2C60-2C6Y]Q9Y243AKT3
T61698DI0275Multiple sclerosis[ICD-11: 8A40]P60568IL2
T61698DI0361Renal cell carcinoma[ICD-11: 2C90]P60568IL2
T52790DI0218Irritable bowel syndrome[ICD-11: DD91]P21452TACR2
T70490DI0064Bronchiectasis[ICD-11: CA24]P53634CTSC

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