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fidaxomicin   Click here for help

GtoPdb Ligand ID: 10909

Synonyms: Dificid® | Dificlir® | lipiarmycin A3 | OPT-80 | PAR-101 | tiacumicin B
Approved drug PDB Ligand
fidaxomicin is an approved drug (EMA & FDA (2011))
Compound class: Natural product
Comment: Fidaxomicin is a narrow-spectrum macrolide antibacterial. It was isolated from the hamdenensis subspecies of soil-dwelling actinomycete Dactylosporangium aurantiacum [5] and is chemically and structurally identical to lipiarmycin A3 [2,4].
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 16
Hydrogen bond donors 7
Rotatable bonds 15
Topological polar surface area 266.66
Molecular weight 1056.43
XLogP 5.76
No. Lipinski's rules broken 4

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 CO[C@@H]1[C@H](OC/C/2=C\C=C\C[C@H](O)/C(=C/[C@H](CC)[C@H](/C(=C/C(=C/C[C@H](OC2=O)[C@H](O)C)/C)/C)O[C@@H]2OC(C)(C)[C@H]([C@@H]([C@@H]2O)O)OC(=O)C(C)C)/C)O[C@@H]([C@H]([C@@H]1O)OC(=O)c1c(O)c(Cl)c(c(c1CC)Cl)O)C
Isomeric SMILES CO[C@@H]1[C@H](OC/C/2=C\C=C\C[C@H](O)/C(=C/[C@H](CC)[C@H](/C(=C/C(=C/C[C@H](OC2=O)[C@H](O)C)/C)/C)O[C@@H]2OC(C)(C)[C@H]([C@@H]([C@@H]2O)O)OC(=O)C(C)C)/C)O[C@@H]([C@H]([C@@H]1O)OC(=O)c1c(O)c(Cl)c(c(c1CC)Cl)O)C
InChI InChI=1S/C52H74Cl2O18/c1-13-30-22-26(6)33(56)18-16-15-17-31(23-66-51-45(65-12)42(61)44(29(9)67-51)69-49(64)35-32(14-2)36(53)39(58)37(54)38(35)57)48(63)68-34(28(8)55)20-19-25(5)21-27(7)43(30)70-50-41(60)40(59)46(52(10,11)72-50)71-47(62)24(3)4/h15-17,19,21-22,24,28-30,33-34,40-46,50-51,55-61H,13-14,18,20,23H2,1-12H3/b16-15+,25-19+,26-22+,27-21+,31-17+/t28-,29-,30+,33+,34+,40-,41+,42+,43+,44-,45+,46+,50-,51-/m1/s1
InChI Key ZVGNESXIJDCBKN-UUEYKCAUSA-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. Chen C, Doll NK, Casadei G, Bremner JB, Lewis K, Kelso MJ. (2014)
Diarylacylhydrazones: Clostridium-selective antibacterials with activity against stationary-phase cells.
Bioorg Med Chem Lett, 24 (2): 595-600. [PMID:24360560]
2. Coronelli C, White RJ, Lancini GC, Parenti F. (1975)
Lipiarmycin, a new antibiotic from Actinoplanes. II. Isolation, chemical, biological and biochemical characterization.
J Antibiot (Tokyo), 28 (4): 253-9. [PMID:807545]
3. Karlowsky JA, Laing NM, Zhanel GG. (2008)
In vitro activity of OPT-80 tested against clinical isolates of toxin-producing Clostridium difficile.
Antimicrob Agents Chemother, 52 (11): 4163-5. [PMID:18725442]
4. Serra S, Malpezzi L, Bedeschi A, Fuganti C, Fonte P. (2017)
Final Demonstration of the Co-Identity of Lipiarmycin A3 and Tiacumicin B (Fidaxomicin) through Single Crystal X-ray Analysis.
Antibiotics (Basel), 6 (1). [PMID:28208717]
5. Theriault RJ, Karwowski JP, Jackson M, Girolami RL, Sunga GN, Vojtko CM, Coen LJ. (1987)
Tiacumicins, a novel complex of 18-membered macrolide antibiotics. I. Taxonomy, fermentation and antibacterial activity.
J Antibiot (Tokyo), 40 (5): 567-74. [PMID:3610815]