fidaxomicin

CHEBI:68590 ·resolve ·ANTIBACTERIAL ·EXACT REVIEWED

An 18-membered macrolide that is a fermentation product obtained from the Actinomycete Dactylosporangium aurantiacum. A narrow spectrum antibiotic used for treatment of Clostridium difficile-related infections. — ChEBI

Classification

macrocyclic antibioticARO:3001318

Strictly broader compounds or drug classes this molecule belongs to.

Label unavailable CHEBI:24400
macrolide antibiotic CHEBI:25105
Label unavailable CHEBI:33308
Label unavailable CHEBI:33853
Label unavailable CHEBI:36683
macrocyclic antibiotic ARO:3001318

Chemical structure

Computed structure properties
Molecular formula	C52H74Cl2O18
Charge	0
Average mass	1058.052 Da
Monoisotopic mass	1056.42522 Da
Source	ChEBI
InChIKey	ZVGNESXIJDCBKN-KFGPIHIUSA-N

SMILES

CCc1c(Cl)c(O)c(Cl)c(O)c1C(=O)O[C@H]1[C@H](O)[C@H](OC)[C@H](OC/C2=C\C=C\C[C@H](O)/C(C)=C/[C@H](CC)[C@@H](O[C@@H]3OC(C)(C)[C@@H](OC(=O)C(C)C)[C@H](O)[C@@H]3O)/C(C)=C/C(C)=C/CC([C@@H](C)O)OC2=O)O[C@@H]1C

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

Also called

Dificid (BRAND_NAME)— chebi
Lipiarmicin (EXACT_SYNONYM)— chebi
Lipiarmycin (EXACT_SYNONYM)— chebi
OPT 80 (EXACT_SYNONYM)— chebi
OPT-80 (EXACT_SYNONYM)— chebi
PAR 101 (EXACT_SYNONYM)— chebi
PAR-101 (EXACT_SYNONYM)— chebi
Tiacumicin B (EXACT_SYNONYM)— chebi

Cross-references

Identifiers for this same structure in other resources. An accession that lands on two different structures in this corpus is withheld from both rather than shown here, since it names at most one of them.

Drug registries

Identifiers that name a drug rather than a structure. One of these can cover a parent compound, its salts and its stereoisomers, which this corpus keeps as separate records, so it is not an equivalence of structure.

kegg.drug:D09394

Patents and articles

Documents about this compound. A patent covers a class and an article covers a topic; neither identifies a structure.

Activity roles

Every antimicrobial role a source asserts for this compound — the unreduced evidence behind its antimicrobial_class.

antimicrobial agent CHEBI:33281
antibacterial drug CHEBI:36047

Source concepts

Every upstream concept that resolved to this record. The merge is the product: this is what shows ChEBI and CARD are describing the same structure.

Upstream concepts merged into this record
Source	Native ID	Label	Minted CURIE	Version
ARO	`ARO:3001319`	fidaxomicin	`antibioticmech:aro-1169c528a5`	2026-08-30
CHEBI	`CHEBI:68590`	fidaxomicin	`antibioticmech:chebi-ff9b90ceb4`	2026-08-30

Molecular targets

The molecular entity or process this compound acts on. Each target carries evidence — this is a mechanistic claim, not a classification.

antibiotic sensitive RNA polymerase switch region PROTEIN_COMPLEX DIRECT_BINDING_TARGET

ARO:3003439

CARD/ARO database assertion; target organism, strain, and assay are not specified. The RNA polymerase switch region is asserted as the target site. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3003439 (CARD/ARO asserts targeted_by_antibiotic ARO:3001319 (fidaxomicin); database assertion, not a primary citation.)

bacterial RNA polymerase PROTEIN_COMPLEX DIRECT_BINDING_TARGET

A cryo-EM structure directly observed fidaxomicin bound to C. difficile RNA polymerase; biochemical and genetic tests identified a residue that sensitizes the enzyme and contributes to narrow-spectrum activity. Evidence status: PRIMARY_EVIDENCE. Source: PRIMARY_LITERATURE 2022-04 (retrieved 2026-09-02).

Clostridioides difficile NCBITaxon:1496

Organism-specific examples
Protein	Gene	Organism	Entry
DNA-directed RNA polymerase subunit beta `UniProtKB:Q18CF4` RNA polymerase beta subunit forming part of the fidaxomicin-binding clamp cleft in the C. difficile cryo-EM complex (PMID:35388215, PDB 7L7B; strain 630 reference proteome context).	rpoB	Clostridioides difficile (strain 630) `NCBITaxon:272563`	REVIEWED
DNA-directed RNA polymerase subunit beta' `UniProtKB:Q18CF3` RNA polymerase beta' subunit contributing the lineage-specific fidaxomicin-sensitizing residue in the C. difficile cryo-EM complex (PMID:35388215, PDB 7L7B; strain 630 reference proteome context).	rpoC	Clostridioides difficile (strain 630) `NCBITaxon:272563`	REVIEWED

PMID:35388215 (Primary C. difficile RNAP-fidaxomicin structure and selectivity study (DOI:10.1038/s41586-022-04545-z).)

Mechanism summary

Mode of action: NUCLEIC_ACID_SYNTHESIS_INHIBITION host shared target — CURATOR: PMID:35388215 resolved fidaxomicin bound to Clostridioides difficile RNA polymerase and combined structural, biochemical, genetic, and bioinformatic evidence to identify a single sensitizing residue absent from many gut commensals. These data support bacterial transcription inhibition and explain an important determinant of narrow-spectrum activity.

Record-level evidence

PMID:35388215 (Primary exact-fidaxomicin C. difficile RNA-polymerase structure and selectivity study.)

Curation history

SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Seeded from data/raw/ inventories (ARO, CHEBI)
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
Re-seeded from updated data/raw/ inventories
REVIEWED 2026-09-03 · codex · LLM-assisted
Verified exact ChEBI/CARD identity, structure, antibacterial role, class, FDA provenance, and retained CARD target assertion; curator-confirmed transcription inhibition and added the directly bound C. difficile RNAP complex.
RESEEDED_FROM_SOURCES 2026-09-10 · seed_from_sources
Re-seeded from updated data/raw/ inventories
CURATED_UNIPROT_PROTEIN_EXAMPLES 2026-10-18 · antigravity · LLM-assisted
Added curated Clostridioides difficile strain 630 RpoB (Q18CF4) and RpoC (Q18CF3) UniProtKB protein examples on the PRIMARY_LITERATURE bacterial RNA polymerase molecular target.

Provenance

Seeded by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record (YAML).

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