kasugamycin

CHEBI:81419 ·resolve ·ANTIFUNGAL ·EXACT REVIEWED

An amino cyclitol glycoside that is isolated from Streptomyces kasugaensis and exhibits antibiotic and fungicidal properties. — ChEBI

Classification

aminoglycoside antibioticARO:0000016

Strictly broader compounds or drug classes this molecule belongs to.

Label unavailable CHEBI:22479
aminoglycoside antibiotic CHEBI:22507
Label unavailable CHEBI:35359
Label unavailable CHEBI:63367
antibiotic fungicide CHEBI:87114
aminoglycoside antibiotic ARO:0000016

Chemical structure

Computed structure properties
Molecular formula	C14H25N3O9
Charge	0
Average mass	379.366 Da
Monoisotopic mass	379.15908 Da
Source	ChEBI
InChIKey	PVTHJAPFENJVNC-MHRBZPPQSA-N

SMILES

C[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H]2O)[C@@H](N)C[C@@H]1NC(=N)C(=O)O

InChI

InChI=1S/C14H25N3O9/c1-3-5(17-12(16)13(23)24)2-4(15)14(25-3)26-11-9(21)7(19)6(18)8(20)10(11)22/h3-11,14,18-22H,2,15H2,1H3,(H2,16,17)(H,23,24)/t3-,4+,5+,6-,7+,8+,9-,10+,11+,14-/m1/s1

Also called

(1S,2R,3S,4R,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-4-{[carboxy(imino)methyl]amino}-2,3,4,6-tetradeoxy-α-D-arabino-hexopyranoside (EXACT_SYNONYM)— chebi
3-O-[2-amino-4-[(carboxyiminomethyl)amino]-2,3,4,6-tetradeoxy-α-D-arabino-hexopyranosyl]-D-chiro-inositol (EXACT_SYNONYM)— chebi
Kasumin 2L (EXACT_SYNONYM)— chebi
Kasumin L (EXACT_SYNONYM)— chebi
kasugamicin (EXACT_SYNONYM)— aro

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.

Patents and articles

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

wikipedia.en:Kasugamycin

Activity roles

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

fungicide CHEBI:24127
antimicrobial agent CHEBI:33281
antifungal agent CHEBI:35718
antifungal agrochemical CHEBI:86328

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:3001296`	kasugamycin	`antibioticmech:aro-939e110ffd`	2026-08-30
CHEBI	`CHEBI:81419`	kasugamycin	`antibioticmech:chebi-94c20c967b`	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.

30S ribosomal subunit mRNA channel RIBOSOMAL_SUBUNIT DIRECT_BINDING_TARGET

X-ray structures of kasugamycin with the E. coli 70S ribosome and with the 30S subunit directly located two drug-binding sites; paired biochemical experiments tested effects on initiation. Evidence status: PRIMARY_EVIDENCE. Source: PRIMARY_LITERATURE 2006-09 (retrieved 2026-09-02).

Escherichia coli NCBITaxon:562

PMID:16998486 (Primary 3.5-angstrom E. coli 70S cocrystal and biochemical study.)
PMID:16998488 (Primary 30S structural and translation-initiation study.)

Mechanism summary

Mode of action: PROTEIN_SYNTHESIS_INHIBITION host shared target — CURATOR: PMID:16998486 and PMID:16998488 independently report kasugamycin-bound ribosome structures and biochemical analyses. The drug occupies the 30S mRNA path near the P/E-site junction, perturbs the mRNA-tRNA codon-anticodon interaction, and inhibits canonical translation initiation.

Activity spectrum

Measured or curated activity against specific taxa. A number without a method is not an observation — every row here carries an assay.

7 observations · Browse all observations · Complete record (JSON.gz)

Activity observations
Organism	Activity	MIC	Disk diffusion	Assay	Strain	Sample/genome	Evidence
Escherichia coli NCBITaxon:562	—	50.0 mg/L	—	Liquid-broth dilution in minimal medium; source endpoint below 10% of normalized no-drug culture density	CAG454	—	Evidence Page data (JSON.gz)
Escherichia coli NCBITaxon:562	—	100.0 mg/L	—	Liquid-broth dilution in minimal medium; source endpoint below 10% of normalized no-drug culture density	CAG67776	—	Evidence Page data (JSON.gz)
Escherichia coli NCBITaxon:562	—	100.0 mg/L	—	Liquid-broth dilution in minimal medium; source endpoint below 10% of normalized no-drug culture density	CAG67774	—	Evidence Page data (JSON.gz)
Escherichia coli NCBITaxon:562	—	100.0 mg/L	—	Liquid-broth dilution in minimal medium; source endpoint below 10% of normalized no-drug culture density	CAG67775	—	Evidence Page data (JSON.gz)
Escherichia coli NCBITaxon:562	—	200.0 mg/L	—	Liquid-broth dilution in minimal medium; source endpoint below 10% of normalized no-drug culture density	CAG67781	—	Evidence Page data (JSON.gz)
Escherichia coli NCBITaxon:562	—	200.0 mg/L	—	Liquid-broth dilution in minimal medium; source endpoint below 10% of normalized no-drug culture density	CAG67780	—	Evidence Page data (JSON.gz)
Escherichia coli NCBITaxon:562	—	200.0 mg/L	—	Liquid-broth dilution in minimal medium; source endpoint below 10% of normalized no-drug culture density	CAG67788	—	Evidence Page data (JSON.gz)

Resistance mechanisms

9 source-backed resistance determinants or associations, with ARO grounding where reported. Grouped by reported mechanism type.

REDUCED_PERMEABILITY 6

REDUCED_PERMEABILITY
Determinant	ARO ID	Organism	Gene families	Evidence
opp and dpp loss associated with kasugamycin resistance in laboratory E. coli MG1655-derived laboratory subject. Reduced uptake is an operon-level interpretation supported by a translation-inhibition proxy, not direct drug flux measured in this derivative. The result belongs to the combined genotype; no component is assigned its full effect. Operon deletions are not single-gene or single-protein assignments. No clinical category or derivative genome is assigned.	—	Escherichia coli `NCBITaxon:562` strain CAG67781	—	PMID:27355376 (Table 2 and Table S2 identify the measured genotype; Figure 4A provides separate operon-level uptake-proxy evidence.) DOI:10.1371/journal.pgen.1006902 (Correction reviewed. Corrected Figure 3 used; Table 2 and Table S2 remain unchanged.) Liquid-broth dilution MIC assay
opp loss associated with kasugamycin resistance in laboratory E. coli MG1655-derived laboratory subject. Reduced uptake is an operon-level interpretation supported by a translation-inhibition proxy, not direct drug flux measured in this derivative. Operon deletions are not single-gene or single-protein assignments. No clinical category or derivative genome is assigned.	—	Escherichia coli `NCBITaxon:562` strain CAG67776	—	PMID:27355376 (Table 2 and Table S2 identify the measured genotype; Figure 4A provides separate operon-level uptake-proxy evidence.) DOI:10.1371/journal.pgen.1006902 (Correction reviewed. Corrected Figure 3 used; Table 2 and Table S2 remain unchanged.) Liquid-broth dilution MIC assay
oppA and dppA loss associated with kasugamycin resistance in laboratory E. coli MG1655-derived laboratory subject. Reduced uptake is an operon-level interpretation supported by a translation-inhibition proxy, not direct drug flux measured in this derivative. The result belongs to the combined genotype; no component is assigned its full effect. Reference protein context (reference-only): UniProtKB:P23843, UniProtKB:P23847. No exact experimental protein accession is assigned. No clinical category or derivative genome is assigned.	—	Escherichia coli `NCBITaxon:562` strain CAG67780	oppA, dppA	PMID:27355376 (Table 2 and Table S2 identify the measured genotype; Figure 4A provides separate operon-level uptake-proxy evidence.) DOI:10.1371/journal.pgen.1006902 (Correction reviewed. Corrected Figure 3 used; Table 2 and Table S2 remain unchanged.) https://www.uniprot.org/uniprotkb/P23843/entry (Reference-only UniProtKB:P23843 (oppA); UniProtKB reviewed (Swiss-Prot), entry version 171, sequence version 2, release 2026_03; retrieved 2026-10-12. Reference organism NCBITaxon:83333, not an experimental subject assignment. Not an exact tested allele, altered protein, strain or genome identifier, and not independent phenotype or mechanism evidence. A component reference does not assign the effect of a combined genotype to that component. UniProt Consortium, CC BY 4.0.) https://www.uniprot.org/uniprotkb/P23847/entry (Reference-only UniProtKB:P23847 (dppA); UniProtKB reviewed (Swiss-Prot), entry version 195, sequence version 1, release 2026_03; retrieved 2026-10-12. Reference organism NCBITaxon:83333, not an experimental subject assignment. Not an exact tested allele, altered protein, strain or genome identifier, and not independent phenotype or mechanism evidence. A component reference does not assign the effect of a combined genotype to that component. UniProt Consortium, CC BY 4.0.) Liquid-broth dilution MIC assay
oppA loss associated with kasugamycin resistance in laboratory E. coli MG1655-derived laboratory subject. Reduced uptake is an operon-level interpretation supported by a translation-inhibition proxy, not direct drug flux measured in this derivative. Reference protein context (reference-only): UniProtKB:P23843. No exact experimental protein accession is assigned. No clinical category or derivative genome is assigned.	—	Escherichia coli `NCBITaxon:562` strain CAG67774	oppA	PMID:27355376 (Table 2 and Table S2 identify the measured genotype; Figure 4A provides separate operon-level uptake-proxy evidence.) DOI:10.1371/journal.pgen.1006902 (Correction reviewed. Corrected Figure 3 used; Table 2 and Table S2 remain unchanged.) https://www.uniprot.org/uniprotkb/P23843/entry (Reference-only UniProtKB:P23843 (oppA); UniProtKB reviewed (Swiss-Prot), entry version 171, sequence version 2, release 2026_03; retrieved 2026-10-12. Reference organism NCBITaxon:83333, not an experimental subject assignment. Not an exact tested allele, altered protein, strain or genome identifier, and not independent phenotype or mechanism evidence. A component reference does not assign the effect of a combined genotype to that component. UniProt Consortium, CC BY 4.0.) Liquid-broth dilution MIC assay
oppB and dppB loss associated with kasugamycin resistance in laboratory E. coli MG1655-derived laboratory subject. Reduced uptake is an operon-level interpretation supported by a translation-inhibition proxy, not direct drug flux measured in this derivative. The result belongs to the combined genotype; no component is assigned its full effect. Reference protein context (reference-only): UniProtKB:P0AFH2, UniProtKB:P0AEF8. No exact experimental protein accession is assigned. No clinical category or derivative genome is assigned.	—	Escherichia coli `NCBITaxon:562` strain CAG67788	oppB, dppB	PMID:27355376 (Table 2 and Table S2 identify the measured genotype; Figure 4A provides separate operon-level uptake-proxy evidence.) DOI:10.1371/journal.pgen.1006902 (Correction reviewed. Corrected Figure 3 used; Table 2 and Table S2 remain unchanged.) https://www.uniprot.org/uniprotkb/P0AFH2/entry (Reference-only UniProtKB:P0AFH2 (oppB); UniProtKB reviewed (Swiss-Prot), entry version 126, sequence version 1, release 2026_03; retrieved 2026-10-12. Reference organism NCBITaxon:83333, not an experimental subject assignment. Not an exact tested allele, altered protein, strain or genome identifier, and not independent phenotype or mechanism evidence. A component reference does not assign the effect of a combined genotype to that component. UniProt Consortium, CC BY 4.0.) https://www.uniprot.org/uniprotkb/P0AEF8/entry (Reference-only UniProtKB:P0AEF8 (dppB); UniProtKB reviewed (Swiss-Prot), entry version 136, sequence version 1, release 2026_03; retrieved 2026-10-12. Reference organism NCBITaxon:83333, not an experimental subject assignment. Not an exact tested allele, altered protein, strain or genome identifier, and not independent phenotype or mechanism evidence. A component reference does not assign the effect of a combined genotype to that component. UniProt Consortium, CC BY 4.0.) Liquid-broth dilution MIC assay
oppB loss associated with kasugamycin resistance in laboratory E. coli MG1655-derived laboratory subject. Reduced uptake is an operon-level interpretation supported by a translation-inhibition proxy, not direct drug flux measured in this derivative. Reference protein context (reference-only): UniProtKB:P0AFH2. No exact experimental protein accession is assigned. No clinical category or derivative genome is assigned.	—	Escherichia coli `NCBITaxon:562` strain CAG67775	oppB	PMID:27355376 (Table 2 and Table S2 identify the measured genotype; Figure 4A provides separate operon-level uptake-proxy evidence.) DOI:10.1371/journal.pgen.1006902 (Correction reviewed. Corrected Figure 3 used; Table 2 and Table S2 remain unchanged.) https://www.uniprot.org/uniprotkb/P0AFH2/entry (Reference-only UniProtKB:P0AFH2 (oppB); UniProtKB reviewed (Swiss-Prot), entry version 126, sequence version 1, release 2026_03; retrieved 2026-10-12. Reference organism NCBITaxon:83333, not an experimental subject assignment. Not an exact tested allele, altered protein, strain or genome identifier, and not independent phenotype or mechanism evidence. A component reference does not assign the effect of a combined genotype to that component. UniProt Consortium, CC BY 4.0.) Liquid-broth dilution MIC assay

ANTIBIOTIC_INACTIVATION 2

ANTIBIOTIC_INACTIVATION
Determinant	ARO ID	Organism	Gene families	Evidence
AAC(2')-IIa	ARO:3004628	not organism-specific	—	ARO:3004628 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3001296 (kasugamycin); database assertion, not a primary citation.)
AAC(2')-IIb	ARO:3003988	not organism-specific	—	ARO:3003988 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3001296 (kasugamycin); database assertion, not a primary citation.)

ANTIBIOTIC_TARGET_ALTERATION 1

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
Escherichia coli 16S rRNA (rrsC) mutation conferring resistance to kasugamicin	ARO:3003333	not organism-specific	—	ARO:3003333 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3001296 (kasugamycin); database assertion, not a primary citation.)

Record-level evidence

PMID:16998486 (Primary ribosome cocrystal study.)
PMID:16998488 (Primary structural and biochemical mechanism 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
REVIEWED 2026-09-02 · codex · LLM-assisted
Verified exact ChEBI identity, structure, roles, and filing class; curator-confirmed protein-synthesis inhibition and added the directly bound bacterial 30S mRNA-channel target with two primary studies.
RESEEDED_FROM_SOURCES 2026-09-10 · seed_from_sources
Re-seeded from updated data/raw/ inventories
CURATED_RESISTANCE_EVIDENCE 2026-10-12 · codex · LLM-assisted
Added six genotype-specific laboratory resistance claims and seven MIC observations from corrected-paper Table 2. Preserved operon and combined-genotype scope, the measured comparator, all three CARD assertions and prior curation. Normalized ug/mL to mg/L without inferring clinical categories or assigning experimental proteins/genomes.
GROUNDED_RESISTANCE_REFERENCE_CITATIONS 2026-10-14 · codex · LLM-assisted
Added qualified UniProt evidence citations for reference proteins already verified in the research dossier. Preserved all biological assertions, experimental identity fields, activities and existing evidence. Reference citations are not tested alleles, altered proteins or independent resistance evidence; no strain TaxID, genome, variant or quantitative endpoint added. Whole-record review remains open.

Provenance

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

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