compound 4 [PMID: 39046805]   Click here for help

GtoPdb Ligand ID: 13528

Compound class: Natural product
Comment: Compound 4 is a phytochemical that has been isolated from the buds of the tropical plant tropical Cleistocalyx operculatus (also known as C. nervosum Kosterm). It is reported as an inhibitor of protein tyrosine phosphatase non-receptor type 1 (PTPN1, PTP1B) [1]. The structure shown here represents the racemic mixture of enantiomers.
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 4
Hydrogen bond donors 2
Rotatable bonds 7
Topological polar surface area 66.76
Molecular weight 434.57
XLogP 6.16
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 CC(=CCCC1=CCC(C(C1)C2=CC=CC=C2)C(=O)C3=C(C(=C(C(=C3O)C)O)C)OC)C
Isomeric SMILES COC1=C(C(=O)C2CC=C(CCC=C(C)C)CC2C3=CC=CC=C3)C(O)=C(C)C(O)=C1C
InChI InChI=1S/C28H34O4/c1-17(2)10-9-11-20-14-15-22(23(16-20)21-12-7-6-8-13-21)27(31)24-26(30)18(3)25(29)19(4)28(24)32-5/h6-8,10,12-14,22-23,29-30H,9,11,15-16H2,1-5H3
InChI Key NDZMOXYPYAVMQI-UHFFFAOYSA-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/)
Bioactivity Comments
Racemic 4 inhibits PTP1B by ~70% (at 10 μM concentration) [1].