Cyclopamine (CHEM003042)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesTargets (2)XML
Record Information
Version1.0
Creation Date2014-08-29 05:04:23 UTC
Update Date2026-04-05 16:31:19 UTC
Accession NumberCHEM003042
Identification
Common NameCyclopamine
ClassSmall Molecule
DescriptionCyclopamine is a naturally occurring chemical that belongs to the group of steroidal jerveratrum alkaloids. It is a teratogen isolated from the corn lily (Veratrum californicum) that causes usually fatal birth defects. It can prevent the fetal brain from dividing into two lobes (holoprosencephaly) and cause the development of a single eye (cyclopia). It does so by inhibiting the hedgehog signaling pathway (Hh). Cyclopamine is useful in studying the role of Hh in normal development, and as a potential treatment for certain cancers in which Hh is overexpressed.
Contaminant Sources
  • T3DB toxins
  • ToxCast & Tox21 Chemicals
Contaminant Type
  • Amine
  • Ether
  • Natural Compound
  • Organic Compound
  • Plant Toxin
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
[3H]-CyclopamineChEMBL
Chemical FormulaC27H41NO2
Average Molecular Mass411.620 g/mol
Monoisotopic Mass411.314 g/mol
CAS Registry Number4449-51-8
IUPAC Name(1'S,2R,2'R,3R,3aS,5'S,6S,7aR,10'S,11'S)-2',3,6,15'-tetramethyl-3a,4,5,6,7,7a-hexahydro-3H-spiro[furo[3,2-b]pyridine-2,14'-tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadecane]-7',15'-dien-5'-ol
Traditional Namecyclopamine
SMILES[H][C@@]12C[C@]([H])(C)CN[C@@]1([H])[C@@]([H])(C)[C@@]1(CC[C@]3([H])C(C[C@@]4([H])[C@@]3([H])CC=C3C[C@@]([H])(O)CC[C@]43C)=C1C)O2
InChI IdentifierInChI=1S/C27H41NO2/c1-15-11-24-25(28-14-15)17(3)27(30-24)10-8-20-21-6-5-18-12-19(29)7-9-26(18,4)23(21)13-22(20)16(27)2/h5,15,17,19-21,23-25,28-29H,6-14H2,1-4H3/t15-,17+,19-,20-,21-,23-,24+,25-,26-,27-/m0/s1
InChI KeyQASFUMOKHFSJGL-LAFRSMQTSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as jerveratrum-type alkaloids. These are steroidal alkaloids with a structure that is based on the jervane ring system. Jerveratrum alkaloids have alkamines with 1-3 oxygen atoms, and occur as such or as monoglycosides.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSteroids and steroid derivatives
Sub ClassSteroidal alkaloids
Direct ParentJerveratrum-type alkaloids
Alternative Parents
Substituents
  • Jerveratrum-type alkaloid
  • Azasteroid
  • Alkaloid or derivatives
  • Piperidine
  • Cyclic alcohol
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Dialkyl ether
  • Secondary aliphatic amine
  • Ether
  • Azacycle
  • Secondary amine
  • Organoheterocyclic compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Amine
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Actin Cytoskeleton
  • Actin Filament
  • Axoneme
  • Cell junction
  • Cell surface
  • Centrosome
  • Clathrin Coated Vesicle
  • Cytosol
  • Endoplasmic reticulum
  • Extracellular
  • Extracellular matrix
  • Focal adhesion
  • Membrane
  • Microtubule
  • Mitochondrial Membrane
  • Mitochondrion
  • Peroxisome
  • Plasma Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
Pathways
NameSMPDB LinkKEGG Link
ApoptosisNot Availablemap04210
Hedgehog Signaling PathwayNot AvailableNot Available
Cell cycleNot Availablemap04110
Notch signaling pathwayNot Availablemap04330
Insulin secretionNot Availablemap04911
Axon guidanceNot Availablemap04360
Rna polymeraseNot Availablemap03020
Nucleotide Excision RepairSMP00478 map03420
Mapk signaling pathwayNot Availablemap04010
EndocytosisNot Availablemap04144
Dna replicationNot Availablemap03030
Base excision repairNot Availablemap03410
ApplicationsNot Available
Biological RolesNot Available
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.0038 g/LALOGPS
logP4.27ALOGPS
logP3.8ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)18.2ChemAxon
pKa (Strongest Basic)10.03ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area41.49 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity122.17 m³·mol⁻¹ChemAxon
Polarizability50.91 ųChemAxon
Number of Rings6ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01ox-1119600000-bba2ea28c0ff0f850252Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00dl-4579200000-4e2e431075c7e5884326Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9010000000-a6d4623d57d584b45a29Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0112900000-a167919b081486158c7dSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03di-0107900000-8cf159fa6dfd830b0d21Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0fxy-9314000000-271f222e1c894052d559Spectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityCyclopamine causes usually fatal birth defects. It can prevent the fetal brain from dividing into two lobes (holoprosencephaly) and cause the development of a single eye (cyclopia). It does so by inhibiting the hedgehog pathway (Hh). Cyclopamine inhibits the Hh by influencing the balance between the active and inactive forms of the smoothened protein. Cyclopamine is useful in studying the role of Hh in normal development, and as a potential treatment for certain cancers in which Hh is overexpressed. Cyclopamine acts as a primary inhibitor of the hedgehog signaling pathway in cells. This pathway named for the ligand for the signal protein, is used by cells to help them react to external chemical signals. The pathway carries out important functions in embryonic development and when it goes awry, deformities can occur. However, errant activation of the pathway can also trigger cancer in adult humans, leading to basal cell carcinoma, medulloblastoma, rhabdomyosarcoma, and prostate, pancreatic and breast cancers. A way of controlling the pathway using cyclopamine could turn this problem on its head and provide a way to treat cancer. (Wikipedia) Cyclopamine inhibits the Hh pathway by binding to and preventing the activation of Smoothened (Smo), preventing downstream target gene regulation. (1)
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesIt is a teratogen isolated from the corn lily (Veratrum californicum) that causes usually fatal birth defects. Cyclopamine is useful in studying the role of Hh in normal development, and as a potential treatment for certain cancers in which Hh is overexpressed.
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsNot Available
TreatmentNot Available
Concentrations
Not Available
DrugBank IDNot Available
HMDB IDNot Available
FooDB IDNot Available
Phenol Explorer IDNot Available
KNApSAcK IDC00002245
BiGG IDNot Available
BioCyc IDNot Available
METLIN IDNot Available
PDB IDNot Available
Wikipedia LinkCyclopamine
Chemspider IDNot Available
ChEBI IDNot Available
PubChem Compound ID442972
Kegg Compound IDC10798
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General ReferencesNot Available