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sclareol   Click here for help

GtoPdb Ligand ID: 13431

PDB Ligand
Compound class: Natural product
Comment: Sclareol is a diterpenoid compound that was initally isolated from the sage plant Salvia sclarea. It has proposed anti-inflammatory, antimicrobial and pro-apoptotic/anti-proliferative bioactivities [2], but its molecular mechanism(s) and molecular target(s) are still to be fully established.
An X-ray structure of sclareol in complex with the human pregnane X receptor (PXR) has been resolved (RCSB PDB ID 8CF9), and in silico docking simulations have revealed potential interactions with cyclooxygenase (COX)-1 and COX-2 which could contribute towards observed in vivo anti-inflammatory action [1].

sclareol is commercially available from our sponsors

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 Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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 2
Hydrogen bond donors 2
Rotatable bonds 4
Topological polar surface area 40.46
Molecular weight 308.5
XLogP 5.99
No. Lipinski's rules broken 1

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES C=C[C@@](C)(CC[C@@H]1[C@@]2(C)CCCC(C)(C)[C@@H]2CC[C@@]1(C)O)O
Isomeric SMILES C[C@]12CCCC([C@@H]1CC[C@@]([C@@H]2CC[C@](C)(C=C)O)(C)O)(C)C
InChI InChI=1S/C20H36O2/c1-7-18(4,21)13-9-16-19(5)12-8-11-17(2,3)15(19)10-14-20(16,6)22/h7,15-16,21-22H,1,8-14H2,2-6H3/t15-,16+,18-,19-,20+/m0/s1
InChI Key XVULBTBTFGYVRC-HHUCQEJWSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Classification Click here for help
Compound class Natural product
IUPAC Name Click here for help
(1R,2R,4aS,8aS)-1-[(3R)-3-hydroxy-3-methylpent-4-enyl]-2,5,5,8a-tetramethyl-3,4,4a,6,7,8-hexahydro-1H-naphthalen-2-ol
Database Links Click here for help
ChEBI CHEBI:9053
ChEMBL Ligand CHEMBL294740
GtoPdb PubChem SID 500839841
LIPID MAPS LMPR0104030010
PubChem CID 163263
RCSB PDB Ligand UK6
Search Google for chemical match using the InChIKey XVULBTBTFGYVRC-HHUCQEJWSA-N
Search Google for chemicals with the same backbone XVULBTBTFGYVRC
UniChem Compound Search for chemical match using the InChIKey XVULBTBTFGYVRC-HHUCQEJWSA-N
UniChem Connectivity Search for chemical match using the InChIKey XVULBTBTFGYVRC-HHUCQEJWSA-N

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MedChemExpress
Sclareol (links to external site)
Cat. No. HY-N0128