cyclopamine   Click here for help

GtoPdb Ligand ID: 10328

Synonyms: 11-Deoxyjervine
PDB Ligand
Compound class: Natural product or derivative
Comment: Cyclopamine is a SMO antagonist that acts as a potent inhibitor of the Hedgehog (Hh) signaling pathway [1]. It is a natural product present in the roots and rhizomes of Veratrum californicum (corn lily). Multiple structures with alternative stereochemistry are recorded in online chemistry resources.
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species

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2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 3
Hydrogen bond donors 2
Rotatable bonds 0
Topological polar surface area 41.49
Molecular weight 411.31
XLogP 3.65
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES OC1CCC2(C(=CCC3C2CC2=C(C)C4(CCC32)OC2C(C4C)NCC(C2)C)C1)C
Isomeric SMILES O[C@H]1CC[C@]2(C(=CC[C@@H]3[C@@H]2CC2=C(C)[C@]4(CC[C@@H]32)O[C@H]2[C@H]([C@H]4C)NC[C@H](C2)C)C1)C
InChI InChI=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 Key QASFUMOKHFSJGL-LAFRSMQTSA-N
Classification Click here for help
Compound class Natural product or derivative
Synonyms Click here for help
11-Deoxyjervine
Database Links Click here for help
Specialist databases
GPCRdb Ligand cyclopamine
Other databases
BindingDB Ligand 50232973
ChEMBL Ligand CHEMBL254129
GtoPdb PubChem SID 381745009
PubChem CID 442972
RCSB PDB Ligand CY8
Search Google for chemical match using the InChIKey QASFUMOKHFSJGL-LAFRSMQTSA-N
Search Google for chemicals with the same backbone QASFUMOKHFSJGL
UniChem Compound Search for chemical match using the InChIKey QASFUMOKHFSJGL-LAFRSMQTSA-N
UniChem Connectivity Search for chemical match using the InChIKey QASFUMOKHFSJGL-LAFRSMQTSA-N

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Tocris
Cyclopamine (links to external site)
Cat. No. 1623