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lincomycin

CHEBI:6472 EXACT SEEDED antibacterial

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 carbohydrate-containing antibiotic produced by the actinomyces Streptomyces lincolnensis.

Structure

Standard InChIKeyOJMMVQQUTAEWLP-KIDUDLJLSA-N
SMILESCCC[C@@H]1C[C@@H](C(N[C@H]([C@H](O)C)[C@@H]2[C@H](O)[C@H](O)[C@@H](O)[C@@H](SC)O2)=O)N(C)C1
Stereochemistryfully defined
Cross-referencespubchem:3000540, pubchem:9063

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 other, from MIBiG.

Producer organisms 1

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.

TaxonBasisClusterEvidence
Streptomyces lincolnensis
NCBITaxon:1915		 SOURCE_ASSERTION mibig:BGC0000907 PMID:19085073

Occurrences 25

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.

TaxonSourceReference
Streptomyces albidoflavus
NCBITaxon:1886		 LOTUS DOI:10.1128/AAC.02247-16
Streptomyces coelicolor
NCBITaxon:1902		 LOTUS DOI:10.1128/AAC.02247-16
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1002/BIT.260270318
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1007/S002030050578
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1007/S00253-018-8900-1
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1007/S10295-018-2029-1
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1007/S12223-008-0060-8
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1016/J.BBAPAP.2013.12.005
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1016/J.BBRC.2019.08.079
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1016/J.JBIOSC.2012.07.015
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1021/JA00337A038
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1021/JA00337A039
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1023/A:1012034421088
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1046/J.1472-765X.2003.01432.X
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1111/J.1365-2958.1995.TB02338.X
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1111/JAM.12919
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1128/AAC.8.5.526
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1128/AEM.02091-18
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1128/JB.00447-17
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1128/JB.00777-17
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1128/JB.146.2.621-631.1981
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.1186/1475-2859-9-6
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.3389/FMICB.2019.02428
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.3390/IJMS13044797
Streptomyces lincolnensis
NCBITaxon:1915		 LOTUS DOI:10.7164/ANTIBIOTICS.45.1773

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0000907 Streptomyces lincolnensis
NCBITaxon:1915 		CLUSTER_UNSTATED genbank:EU124663.1

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

PRODUCERS & OCCURRENCE 1 producer (0 causal) 25 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 0 curated pathway steps NATURAL PRODUCT lincomycin CHEBI:6472 Carbohydrates TARGETS & BIOACTIVITY 0 molecular targets 3 bioactivities · 0 graphs

Bioactivities 3

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

AssayResultTarget enzymeSource detail
PON Activity Assay from Article 10.3109/14756366.2012.681653: "Impacts of some antibiotics on human serum paraoxonase 1 activity."KI 18300 uM; INACTIVEUniProtKB:P27169
PMID:22591317
assay
PON Activity Assay from Article 10.3109/14756366.2012.681653: "Impacts of some antibiotics on human serum paraoxonase 1 activity."
evidence
  • reference
    PMID:22591317
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1803291, deposited by BindingDB; assay type Confirmatory.
call
INACTIVE
measurement type
KI
value
18300.0
units
uM
target enzyme
UniProtKB:P27169
A screen for compounds that inhibit the activity of LtaS in Staphylococcus aureusACTIVENot 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
DSSTox (FDAMDD) FDA Maximum (Recommended) Daily Dose DatabaseACTIVENot 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

Elsewhere in the fleet

Explore across X-Mech

AntibioticMech (lincomycin) ↗ MediaIngredientMech (CHEBI:6472) ↗ TaxonMech: Streptomyces lincolnensis (NCBITaxon:1915) ↗ PathwayMech (mibig:BGC0000907) ↗

Provenance

Source conceptSourceVersion
BGC0000907MIBIG5
CHEBI:6472CHEBI3-star

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