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congocidine

naturalproductmech:mibig-0a89c3541b MINTED SEEDED antiparasitic

Grounding review: No 3-star ChEBI entry shares this structure, so the record keeps a content-hashed identifier.
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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

Structure

Standard InChIKeyIDBIFFKSXLYUOT-UHFFFAOYSA-N
SMILESCN1C=C(C=C1C(=O)NC2=CN(C(=C2)C(=O)NCCC(=N)N)C)NC(=O)CN=C(N)N
Stereochemistryfully defined
Cross-referencespubchem:4461, npatlas:NPA018236

Filing pathway

Alkaloids — 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 nrps, from MIBiG.

Producer organisms 2

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 netropsis
NCBITaxon:55404		 BGC_CHARACTERIZED mibig:BGC0001147 PMID:25415678
Streptomyces ambofaciens ATCC 23877
NCBITaxon:278992		 SOURCE_ASSERTION mibig:BGC0000327 PMID:17074905

Occurrences 6

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 ambofaciens
NCBITaxon:1889		 LOTUS DOI:10.1002/JOBM.200410529
Streptomyces ambofaciens
NCBITaxon:1889		 LOTUS DOI:10.1016/J.CHEMBIOL.2009.03.010
Streptomyces ambofaciens
NCBITaxon:1889		 LOTUS DOI:10.1099/MIC.0.29161-0
Streptomyces ambofaciens
NCBITaxon:1889		 LOTUS DOI:10.1128/JB.01269-10
Streptomyces ambofaciens
NCBITaxon:1889		 LOTUS DOI:10.1371/JOURNAL.PONE.0099077
Streptomyces netropsis
NCBITaxon:55404		 LOTUS DOI:10.1021/JA01145A113

Biosynthetic gene clusters 2

AccessionHostLocus evidenceGenome
mibig:BGC0001147 Streptomyces netropsis
NCBITaxon:55404 		CLUSTER_DEMONSTRATED genbank:KJ634466.1
mibig:BGC0000327 Streptomyces ambofaciens ATCC 23877
NCBITaxon:278992 		CLUSTER_UNSTATED genbank:AM238664.2

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 2 producers (1 causal) 6 cited occurrences BIOSYNTHETIC LOCUS 2 gene clusters 0 curated pathway steps NATURAL PRODUCT congocidine naturalproductmech:mibig-0a89c3541b Alkaloids TARGETS & BIOACTIVITY 4 molecular targets 4 bioactivities · 1 graph

Causal graph — bioactivity 4 nodes, 4 edges

Congocidine/netropsin inhibition of recombinant Plasmodium falciparum 3D7 PfUDN ATPase and DNA-unwinding activities.

SubjectPredicateObjectNotesEvidence
P. falciparum PfUDN fragment has activity PfUDN ssDNA-dependent ATPase activity The expressed PfUDN construct spans amino acids 35-727 of the 1441 aa P. falciparum 3D7 Q8I3W6 DNA 3'-5' helicase.
DOI:10.1371/journal.pone.0049385
  • reference
    DOI:10.1371/journal.pone.0049385
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    possess ssDNA-dependent ATPase and DNA helicase activities in vitro
    notes
    Q8I3W6 resolves in UniProtKB to PF3D7_0514100 from P. falciparum isolate 3D7 and annotates a UvrD-like helicase ATP-binding domain over amino acids 35-727.
P. falciparum PfUDN fragment has activity PfUDN DNA unwinding activity The expressed PfUDN construct spans amino acids 35-727 of the 1441 aa P. falciparum 3D7 Q8I3W6 DNA 3'-5' helicase.
DOI:10.1371/journal.pone.0049385
  • reference
    DOI:10.1371/journal.pone.0049385
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    possess ssDNA-dependent ATPase and DNA helicase activities in vitro
    notes
    The authors showed ATP-dependent 3' to 5' DNA unwinding by purified PfUDN.
congocidine inhibits PfUDN ssDNA-dependent ATPase activity PubChem AID 1802684 and BindingDB capture the netropsin 3.1 uM IC50 against P. falciparum DNA helicase [35-727].
DOI:10.1186/1471-2091-15-9
  • reference
    DOI:10.1186/1471-2091-15-9
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    we screened the effect of various DNA interacting compounds on the ATPase and helicase activity of PfUDN
congocidine inhibits PfUDN DNA unwinding activity PubChem AID 1802685 and BindingDB capture the netropsin 4.7 uM IC50 against P. falciparum DNA helicase [35-727].
DOI:10.1186/1471-2091-15-9
  • reference
    DOI:10.1186/1471-2091-15-9
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    we screened the effect of various DNA interacting compounds on the ATPase and helicase activity of PfUDN

Every edge carries its own citation; an uncited edge is refused by the corpus tests.

Molecular targets 4

TargetTarget organismMeasurementEvidence
DNA helicase [35-727]
PROTEIN BINDS		 Plasmodium falciparum
NCBITaxon:5833		 IC50 3100 nM
PMID:24707807
  • reference
    PMID:24707807
    evidence type
    DATABASE_ASSERTION
    notes
    BindingDB own-curated affinity; measured at pH 8.0000, 37.00 C C; qualifier EQUAL.
DNA helicase [35-727]
PROTEIN BINDS		 Plasmodium falciparum
NCBITaxon:5833		 IC50 4700 nM
PMID:24707807
  • reference
    PMID:24707807
    evidence type
    DATABASE_ASSERTION
    notes
    BindingDB own-curated affinity; measured at pH 8.0000, 37.00 C C; qualifier EQUAL.
Plasminogen
PROTEIN BINDS
UniProtKB:P00747		 Homo sapiens
NCBITaxon:9606		 IC50 40000 nM
PMID:20429779
  • reference
    PMID:20429779
    evidence type
    DATABASE_ASSERTION
    notes
    BindingDB own-curated affinity; qualifier EQUAL.
Urokinase-type plasminogen activator
PROTEIN BINDS
UniProtKB:P00749		 Homo sapiens
NCBITaxon:9606		 IC50 30000 nM
PMID:20429779
  • reference
    PMID:20429779
    evidence type
    DATABASE_ASSERTION
    notes
    BindingDB own-curated affinity; qualifier EQUAL.

Bioactivities 4

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

AssayResultTarget enzymeSource detail
Antiamidolytic Assay from Article 10.3109/14756360903389872: "Carbocyclic potential DNA minor groove binders and their biological evaluation."IC50 40 uM; INACTIVEUniProtKB:P00747
PMID:20429779
assay
Antiamidolytic Assay from Article 10.3109/14756360903389872: "Carbocyclic potential DNA minor groove binders and their biological evaluation."
evidence
  • reference
    PMID:20429779
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1802946, deposited by BindingDB; assay type Confirmatory.
call
INACTIVE
measurement type
IC50
value
40.0
units
uM
target enzyme
UniProtKB:P00747
Antiamidolytic Assay from Article 10.3109/14756360903389872: "Carbocyclic potential DNA minor groove binders and their biological evaluation."IC50 30 uM; INACTIVEUniProtKB:P00749
PMID:20429779
assay
Antiamidolytic Assay from Article 10.3109/14756360903389872: "Carbocyclic potential DNA minor groove binders and their biological evaluation."
evidence
  • reference
    PMID:20429779
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1802946, deposited by BindingDB; assay type Confirmatory.
call
INACTIVE
measurement type
IC50
value
30.0
units
uM
target enzyme
UniProtKB:P00749
DNA Helicase Assay from Article 10.1186/1471-2091-15-9: "Plasmodium falciparum UvrD activities are downregulated by DNA-interacting compounds and its dsRNA inhibits malaria parasite growth."IC50 4.7 uM; ACTIVENot recorded
PMID:24707807
assay
DNA Helicase Assay from Article 10.1186/1471-2091-15-9: "Plasmodium falciparum UvrD activities are downregulated by DNA-interacting compounds and its dsRNA inhibits malaria parasite growth."
evidence
  • reference
    PMID:24707807
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1802685, deposited by BindingDB; assay type Confirmatory.
call
ACTIVE
measurement type
IC50
value
4.7
units
uM
activity class
ANTIPARASITIC
DNA-Dependent ATPase Assay from Article 10.1186/1471-2091-15-9: "Plasmodium falciparum UvrD activities are downregulated by DNA-interacting compounds and its dsRNA inhibits malaria parasite growth."IC50 3.1 uM; ACTIVENot recorded
PMID:24707807
assay
DNA-Dependent ATPase Assay from Article 10.1186/1471-2091-15-9: "Plasmodium falciparum UvrD activities are downregulated by DNA-interacting compounds and its dsRNA inhibits malaria parasite growth."
evidence
  • reference
    PMID:24707807
    evidence type
    DATABASE_ASSERTION
    notes
    PubChem BioAssay AID 1802684, deposited by BindingDB; assay type Confirmatory.
call
ACTIVE
measurement type
IC50
value
3.1
units
uM
activity class
ANTIPARASITIC

Explore across X-Mech

AntibioticMech (congocidine) ↗ MediaIngredientMech (naturalproductmech:mibig-0a89c3541b) ↗ TaxonMech: Streptomyces netropsis (NCBITaxon:55404) ↗ TaxonMech: Streptomyces ambofaciens ATCC 23877 (NCBITaxon:278992) ↗ PathwayMech (mibig:BGC0001147) ↗ PathwayMech (mibig:BGC0000327) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000327, BGC0001147. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source conceptSourceVersion
BGC0001147MIBIG4
BGC0000327MIBIG5

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