epothilone B   Click here for help

GtoPdb Ligand ID: 13600

Synonyms: EPO-906 | EPO906 | patupilone
PDB Ligand
Compound class: Synthetic organic
Comment: Epothilone B is a macrolide from plant (Sorangium cellulosum, a soil-dwelling Gram-negative myxobacterium), Aspergillus fumigatus [3] and insect (Apis cerana, Asiatic honey bee) sources. It mimics the microtubule binding activity of taxoid drugs such as paclitaxel (taxol) [1,5], but is active in [4] paclitaxel resistant cells. It acts to stabilise microtubules, which induces mitotic arrest and cell death.

epothilone B 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 7
Hydrogen bond donors 2
Rotatable bonds 2
Topological polar surface area 134.02
Molecular weight 507.68
XLogP 2.14
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@H]1CCC[C@]2(C)[C@H](C[C@@H](/C(=C/C3=CSC(=N3)C)/C)OC(=O)C[C@@H](C(C)(C)C(=O)[C@H](C)[C@H]1O)O)O2
Isomeric SMILES C[C@H]1CCC[C@@]2([C@@H](O2)C[C@H](OC(=O)C[C@@H](C(C(=O)[C@@H]([C@H]1O)C)(C)C)O)/C(=C/C3=CSC(=N3)C)/C)C
InChI InChI=1S/C27H41NO6S/c1-15-9-8-10-27(7)22(34-27)12-20(16(2)11-19-14-35-18(4)28-19)33-23(30)13-21(29)26(5,6)25(32)17(3)24(15)31/h11,14-15,17,20-22,24,29,31H,8-10,12-13H2,1-7H3/b16-11+/t15-,17+,20-,21-,22-,24-,27+/m0/s1
InChI Key QXRSDHAAWVKZLJ-PVYNADRNSA-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/)
References
1. Bollag DM, McQueney PA, Zhu J, Hensens O, Koupal L, Liesch J, Goetz M, Lazarides E, Woods CM. (1995)
Epothilones, a new class of microtubule-stabilizing agents with a taxol-like mechanism of action.
Cancer Res, 55 (11): 2325-33. [PMID:7757983]
2. Buey RM, Calvo E, Barasoain I, Pineda O, Edler MC, Matesanz R, Cerezo G, Vanderwal CD, Day BW, Sorensen EJ et al.. (2007)
Cyclostreptin binds covalently to microtubule pores and lumenal taxoid binding sites.
Nat Chem Biol, 3 (2): 117-25. [PMID:17206139]
3. El-Sayed ASA, Shindia A, Ammar H, Seadawy MG, Khashana SA. (2024)
Bioprocessing of Epothilone B from Aspergillus fumigatus under solid state fermentation: Antiproliferative activity, tubulin polymerization and cell cycle analysis.
BMC Microbiol, 24 (1): 43. [PMID:38291363]
4. Kowalski RJ, Giannakakou P, Hamel E. (1997)
Activities of the microtubule-stabilizing agents epothilones A and B with purified tubulin and in cells resistant to paclitaxel (Taxol(R)).
J Biol Chem, 272 (4): 2534-41. [PMID:8999970]
5. Muhlradt PF, Sasse F. (1997)
Epothilone B stabilizes microtubuli of macrophages like taxol without showing taxol-like endotoxin activity.
Cancer Res, 57 (16): 3344-6. [PMID:9269992]