tobramycin

CHEBI:28864 EXACT SEEDED antibacterialenzyme inhibitor

What these status tags mean

Curation status describes a workflow state. SEEDED means the record entered through the source-seeding workflow; it does not imply that no later curation occurred. PROPOSED marks an addition awaiting review; REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record. These are workflow decisions, not independently verified human review. Agent-assisted contributions may appear in the record history.

Grounding describes the identifier mapping: EXACT uses an ontology identity asserted by the source; MINTED keeps a local identifier when no defensible ontology identity is available; REVIEW_NEEDED flags an exact structure whose ontology identity needs adjudication. The grounding note retains any unresolved alternatives. These tags do not establish the strength of producer or activity evidence.

A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring.

Structure

Standard InChIKey	NLVFBUXFDBBNBW-PBSUHMDJSA-N
SMILES	C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H](C[C@@H]([C@H](O3)CN)O)N)N
Stereochemistry	fully defined
Cross-references	pubchem:36294

Filing pathway

Carbohydrates — computed by NPClassifier npclassifier.gnps2.org@2026-09-07, which is why it is pinned rather than recomputed. The gene cluster's asserted class is saccharide, from MIBiG.

Producer organisms 3

A claim that this taxon makes the compound. The basis says what the evidence addressed — a knockout and a database assertion are not the same claim.

Taxon	Basis	Cluster	Evidence
Streptoalloteichus hindustanus NCBITaxon:2017	SOURCE_ASSERTION	mibig:BGC0000719	PMID:16915821
Streptoalloteichus tenebrarius NCBITaxon:1933	SOURCE_ASSERTION	mibig:BGC0000720	PMID:14757238
Streptoalloteichus tenebrarius NCBITaxon:1933	SOURCE_ASSERTION	mibig:BGC0000721	PMID:19362651

Occurrences 12

Somebody found the compound in this organism and cited it. That is not a claim that the organism makes it, and nothing here promotes one to the other.

Taxon	Source	Reference
Streptomyces cremeus NCBITaxon:66881	LOTUS	DOI:10.1007/BF00272160
Streptomyces cremeus NCBITaxon:66881	LOTUS	DOI:10.1007/BF00327918
Streptomyces cremeus NCBITaxon:66881	LOTUS	DOI:10.1007/S00253-010-2908-5
Streptomyces cremeus NCBITaxon:66881	LOTUS	DOI:10.1007/S00284-004-4212-Z
Streptomyces cremeus NCBITaxon:66881	LOTUS	DOI:10.1016/J.BMCL.2004.10.028
Streptomyces cremeus NCBITaxon:66881	LOTUS	DOI:10.1016/S0378-1097(03)00881-4
Streptomyces cremeus NCBITaxon:66881	LOTUS	DOI:10.1023/B:BILE.0000007063.66429.90
Streptomyces cremeus NCBITaxon:66881	LOTUS	DOI:10.1038/JA.2008.111
Streptomyces cremeus NCBITaxon:66881	LOTUS	DOI:10.7164/ANTIBIOTICS.45.1167
Aspergillus fumigatus NCBITaxon:746128	LOTUS	DOI:10.1021/ACS.JNATPROD.8B00382
Serratia plymuthica NCBITaxon:82996	LOTUS	DOI:10.1021/ACS.JNATPROD.7B00565
Streptoalloteichus hindustanus NCBITaxon:2017	LOTUS	DOI:10.1038/JA.2006.51

Biosynthetic gene clusters 3

Accession	Host	Locus evidence	Genome
mibig:BGC0000719	Streptoalloteichus hindustanus NCBITaxon:2017	CLUSTER_UNSTATED	genbank:AB103327.1
mibig:BGC0000720	Streptoalloteichus tenebrarius NCBITaxon:1933	CLUSTER_UNSTATED	genbank:AJ579650.1
mibig:BGC0000721	Streptoalloteichus tenebrarius NCBITaxon:1933	CLUSTER_UNSTATED	genbank:AJ810851.1

A locus claim and a taxon claim are different questions. Heterologous expression settles the first and leaves the second where the isolation report left it.

Mechanism & Biosynthesis Overview

Bioactivities 14

Entries preserve source qualifiers, targets and evidence. Repeated assay names or values are not independent replications; inspect source detail for differences.

Assay	Result	Target enzyme	Source detail
BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: AML-191 cell line	OTHER 7.4219 uM; INACTIVE	Not recorded	pubchem.aid:2202236 assay BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: AML-191 cell line evidence reference pubchem.aid:2202236 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 2202236, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. call INACTIVE measurement type OTHER value 7.4219 units uM
BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: AML-194 cell line	OTHER 20.9177 uM; NOT_DETERMINED	Not recorded	pubchem.aid:2202237 assay BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: AML-194 cell line evidence reference pubchem.aid:2202237 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 2202237, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 20.9177 units uM
BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: HNT-34 cell line	OTHER 23.47 uM; NOT_DETERMINED	Not recorded	pubchem.aid:2202234 assay BET inhibitor-based combinations targeting novel dependencies in MECOM-rearranged (r) AML: HNT-34 cell line evidence reference pubchem.aid:2202234 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 2202234, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 23.47 units uM
Validation qHTS for agonist of cAMP-regulated guanine nucleotide exchange factor 4 (EPAC2)	OTHER 0.7943 uM; INACTIVE	Not recorded	pubchem.aid:1645887 assay Validation qHTS for agonist of cAMP-regulated guanine nucleotide exchange factor 4 (EPAC2) evidence reference pubchem.aid:1645887 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645887, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. call INACTIVE measurement type OTHER value 0.7943 units uM
Validation qHTS for agonist of cAMP-regulated guanine nucleotide exchange factor 4 (EPAC2)	OTHER 0.7943 uM; INACTIVE	UniProtKB:Q8WZA2	pubchem.aid:1645887 assay Validation qHTS for agonist of cAMP-regulated guanine nucleotide exchange factor 4 (EPAC2) evidence reference pubchem.aid:1645887 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1645887, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. call INACTIVE measurement type OTHER value 0.7943 units uM target enzyme UniProtKB:Q8WZA2
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) drug resistant MV4-11 cells	OTHER 18.6429 uM; ACTIVE	Not recorded	pubchem.aid:1963824 assay Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) drug resistant MV4-11 cells evidence reference pubchem.aid:1963824 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1963824, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. call ACTIVE measurement type OTHER value 18.6429 units uM
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) drug resistant MV4-11 cells	OTHER 18.6429 uM; ACTIVE	UniProtKB:P43405	pubchem.aid:1963824 assay Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) drug resistant MV4-11 cells evidence reference pubchem.aid:1963824 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1963824, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. call ACTIVE measurement type OTHER value 18.6429 units uM target enzyme UniProtKB:P43405
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) naive MV4-11 cells	OTHER 2.9547 uM; NOT_DETERMINED	Not recorded	pubchem.aid:1963823 assay Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) naive MV4-11 cells evidence reference pubchem.aid:1963823 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1963823, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 2.9547 units uM
Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) naive MV4-11 cells	OTHER 2.9547 uM; NOT_DETERMINED	UniProtKB:P43405	pubchem.aid:1963823 assay Viability qHTS for spleen associated tyrosine kinase inhibitor (SYKi) naive MV4-11 cells evidence reference pubchem.aid:1963823 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1963823, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 2.9547 units uM target enzyme UniProtKB:P43405
qHTS assay for small molecule agonists of the p53 signaling pathway - cell viability	OTHER 1.0124 uM; INACTIVE	Not recorded	pubchem.aid:651633 assay qHTS assay for small molecule agonists of the p53 signaling pathway - cell viability evidence reference pubchem.aid:651633 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 651633, deposited by 824; assay type Confirmatory. Source endpoint: Potency. call INACTIVE measurement type OTHER value 1.0124 units uM
A screen for compounds that inhibit the activity of LtaS in Staphylococcus aureus	ACTIVE	Not recorded	pubchem.aid:720641 assay A screen for compounds that inhibit the activity of LtaS in Staphylococcus aureus evidence reference pubchem.aid:720641 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 720641, deposited by ICCB-Longwood/NSRB Screening Facility, Harvard Medical School; assay type Other. Target accession NP_371243 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE activity class ANTIBACTERIAL
Cell-based high throughput primary assay to identify activators of GPR151	ACTIVE	UniProtKB:Q8TDV0	pubchem.aid:1508602 assay Cell-based high throughput primary assay to identify activators of GPR151 evidence reference pubchem.aid:1508602 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1508602, deposited by The Scripps Research Institute Molecular Screening Center; assay type Screening. call ACTIVE target enzyme UniProtKB:Q8TDV0
DSSTox (FDAMDD) FDA Maximum (Recommended) Daily Dose Database	ACTIVE	Not recorded	pubchem.aid:1195 assay DSSTox (FDAMDD) FDA Maximum (Recommended) Daily Dose Database evidence reference pubchem.aid:1195 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1195, deposited by EPA DSSTox; assay type Other. call ACTIVE
High Throughput Screen to Identify Inhibitors of Mycobacterium tuberculosis H37Rv	ACTIVE	Not recorded	pubchem.aid:1332 assay High Throughput Screen to Identify Inhibitors of Mycobacterium tuberculosis H37Rv evidence reference pubchem.aid:1332 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1332, deposited by Southern Research Institute; assay type Confirmatory. call ACTIVE activity class ENZYME_INHIBITOR

Elsewhere in the fleet

AntibioticMech — CHEBI:28864 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (tobramycin) ↗ MediaIngredientMech (CHEBI:28864) ↗ TaxonMech: Streptoalloteichus hindustanus (NCBITaxon:2017) ↗ TaxonMech: Streptoalloteichus tenebrarius (NCBITaxon:1933) ↗ TaxonMech: Streptoalloteichus tenebrarius (NCBITaxon:1933) ↗ PathwayMech (mibig:BGC0000719) ↗ PathwayMech (mibig:BGC0000720) ↗ PathwayMech (mibig:BGC0000721) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000719, BGC0000720, BGC0000721. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0000719	MIBIG	5
BGC0000720	MIBIG	3
BGC0000721	MIBIG	4
CHEBI:28864	CHEBI	3-star

This page is generated from data/natural_products/carbohydrates/tobramycin.yaml, which is generated from the committed inventories. Neither is edited by hand.