5-dimethylallylindole-3-acetonitrile

naturalproductmech:mibig-380600c810 MINTED SEEDED

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 InChIKey	OTLRZZMUVKJCDO-UHFFFAOYSA-N
SMILES	CC(C)=CCC1=CC2=C(C=C1)[NH]C=C2CC#N
Stereochemistry	fully defined
Cross-references	npatlas:NPA032817

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 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.

Taxon	Basis	Cluster	Evidence
Streptomyces coelicolor A3(2) NCBITaxon:100226	SOURCE_ASSERTION	mibig:BGC0002128	PMID:23430264

Occurrences 2

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 albidoflavus NCBITaxon:1886	LOTUS	DOI:10.1074/JBC.M112.436451
Streptomyces coelicolor NCBITaxon:1902	LOTUS	DOI:10.1074/JBC.M112.436451

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0002128	Streptomyces coelicolor A3(2) NCBITaxon:100226	CLUSTER_DEMONSTRATED	genbank:AL645882.2

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.

Biosynthesis curated

Written by a curator with claim-level evidence on each step; not derived from a source. This is what the rest of the record exists to support.

Step	Enzyme	Reaction	Substrate → product	Evidence
1	SCO7467 5-dimethylallyltryptophan synthase UniProtKB:Q9ADJ2		CHEBI:16828 + CHEBI:16057 → ungrounded	DOI:10.1074/jbc.M112.436451
2	SCO7468 flavin-dependent monooxygenase UniProtKB:Q8CJJ9		ungrounded → ungrounded	DOI:10.1074/jbc.M112.436451

Step 1: SCO7467 prenylates L-tryptophan at C-5 with dimethylallyl diphosphate to form 5-dimethylallyl-L-tryptophan. The 5-DMAT product is left out of the structured product field because no exact stable chemical CURIE was selected.

Step 2: SCO7468 converts 5-DMAT into 5-dimethylallylindole-3-acetaldoxime. Both the 5-DMAT substrate and 5-DMAIAOx product are left out of the structured substrate and product fields because no exact stable chemical CURIEs were selected.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 7 nodes, 6 edges

Partial Streptomyces coelicolor A3(2) graph for SCO7467 prenylation of L-tryptophan, SCO7468 aldoxime formation, and the proposed dehydration to 5-dimethylallylindole-3-acetonitrile.

Subject	Predicate	Object	Notes	Evidence
L-tryptophan	is C-5-prenylated by	SCO7467	SCO7467 accepts L-tryptophan as the indole substrate for C-5 prenylation.	DOI:10.1074/jbc.M112.436451 https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk https://www.uniprot.org/uniprotkb/Q9ADJ2 reference DOI:10.1074/jbc.M112.436451 evidence type PRIMARY_EXPERIMENT snippet SCO7467 catalyzes the prenylation of L-tryptophan notes Izumikawa et al. introduced SCO7467 and SCO7468 into Streptomyces lividans, overproduced 5-DMAIAN, and biochemically assigned recombinant SCO7467 to C-5 prenylation of L-tryptophan to 5-DMAT. reference https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0002128.3 places SCO7467 in the Streptomyces coelicolor A3(2) locus, annotates it as the rule-based indole_PTase core biosynthetic CDS, and cross-references protein CAC36059.1 and UniProtKB:Q9ADJ2. reference https://www.uniprot.org/uniprotkb/Q9ADJ2 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes UniProtKB:Q9ADJ2 is the unreviewed Streptomyces coelicolor A3(2) prenyltransferase entry cross-referenced to EMBL AL645882 protein CAC36059.1.
dimethylallyl diphosphate	donates dimethylallyl to	SCO7467	SCO7467 transfers a dimethylallyl group from DMAPP onto L-tryptophan.	DOI:10.1074/jbc.M112.436451 https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk https://www.uniprot.org/uniprotkb/Q9ADJ2 reference DOI:10.1074/jbc.M112.436451 evidence type PRIMARY_EXPERIMENT snippet SCO7467 catalyzes the prenylation of L-tryptophan notes Izumikawa et al. introduced SCO7467 and SCO7468 into Streptomyces lividans, overproduced 5-DMAIAN, and biochemically assigned recombinant SCO7467 to C-5 prenylation of L-tryptophan to 5-DMAT. reference https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0002128.3 places SCO7467 in the Streptomyces coelicolor A3(2) locus, annotates it as the rule-based indole_PTase core biosynthetic CDS, and cross-references protein CAC36059.1 and UniProtKB:Q9ADJ2. reference https://www.uniprot.org/uniprotkb/Q9ADJ2 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes UniProtKB:Q9ADJ2 is the unreviewed Streptomyces coelicolor A3(2) prenyltransferase entry cross-referenced to EMBL AL645882 protein CAC36059.1.
SCO7467	forms	5-dimethylallyl-L-tryptophan	The SCO7467 prenyltransferase reaction forms the ungrounded intermediate 5-DMAT.	DOI:10.1074/jbc.M112.436451 https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk https://www.uniprot.org/uniprotkb/Q9ADJ2 reference DOI:10.1074/jbc.M112.436451 evidence type PRIMARY_EXPERIMENT snippet SCO7467 catalyzes the prenylation of L-tryptophan notes Izumikawa et al. introduced SCO7467 and SCO7468 into Streptomyces lividans, overproduced 5-DMAIAN, and biochemically assigned recombinant SCO7467 to C-5 prenylation of L-tryptophan to 5-DMAT. reference https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0002128.3 places SCO7467 in the Streptomyces coelicolor A3(2) locus, annotates it as the rule-based indole_PTase core biosynthetic CDS, and cross-references protein CAC36059.1 and UniProtKB:Q9ADJ2. reference https://www.uniprot.org/uniprotkb/Q9ADJ2 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes UniProtKB:Q9ADJ2 is the unreviewed Streptomyces coelicolor A3(2) prenyltransferase entry cross-referenced to EMBL AL645882 protein CAC36059.1.
5-dimethylallyl-L-tryptophan	is converted by	SCO7468	SCO7468 accepts 5-DMAT for aldoxime formation with NADPH, FAD, and oxygen.	DOI:10.1074/jbc.M112.436451 https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk https://www.uniprot.org/uniprotkb/Q8CJJ9 reference DOI:10.1074/jbc.M112.436451 evidence type PRIMARY_EXPERIMENT snippet SCO7468 then catalyzes the conversion of 5-DMAT notes Izumikawa et al. biochemically assigned recombinant SCO7468 as the FMO enzyme that converts 5-DMAT into the aldoxime intermediate 5-DMAIAOx. reference https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0002128.3 places SCO7468 next to SCO7467 in the Streptomyces coelicolor A3(2) locus, annotates it as an FMO-like biosynthetic-additional CDS, and cross-references protein CAD55403.1 and UniProtKB:Q8CJJ9. reference https://www.uniprot.org/uniprotkb/Q8CJJ9 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes UniProtKB:Q8CJJ9 is the unreviewed Streptomyces coelicolor A3(2) flavin-binding monooxygenase entry cross-referenced to EMBL AL645882 protein CAD55403.1.
SCO7468	forms	5-dimethylallylindole-3-acetaldoxime	The SCO7468 FMO reaction forms the ungrounded aldoxime intermediate 5-DMAIAOx.	DOI:10.1074/jbc.M112.436451 https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk https://www.uniprot.org/uniprotkb/Q8CJJ9 reference DOI:10.1074/jbc.M112.436451 evidence type PRIMARY_EXPERIMENT snippet SCO7468 then catalyzes the conversion of 5-DMAT notes Izumikawa et al. biochemically assigned recombinant SCO7468 as the FMO enzyme that converts 5-DMAT into the aldoxime intermediate 5-DMAIAOx. reference https://mibig.secondarymetabolites.org/repository/BGC0002128.3/BGC0002128.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0002128.3 places SCO7468 next to SCO7467 in the Streptomyces coelicolor A3(2) locus, annotates it as an FMO-like biosynthetic-additional CDS, and cross-references protein CAD55403.1 and UniProtKB:Q8CJJ9. reference https://www.uniprot.org/uniprotkb/Q8CJJ9 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes UniProtKB:Q8CJJ9 is the unreviewed Streptomyces coelicolor A3(2) flavin-binding monooxygenase entry cross-referenced to EMBL AL645882 protein CAD55403.1.
5-dimethylallylindole-3-acetaldoxime	is proposed to dehydrate to	5-dimethylallylindole-3-acetonitrile	Izumikawa et al. proposed dehydration of 5-DMAIAOx as the terminal unassigned conversion to 5-DMAIAN.	DOI:10.1074/jbc.M112.436451 reference DOI:10.1074/jbc.M112.436451 evidence type PRIMARY_EXPERIMENT snippet dehydration of 5-DMAIAOx presumably occurs to yield 5-DMAIAN notes The source observed 5-DMAIAN after heterologous expression of SCO7467 and SCO7468 and proposed, but did not assign an enzyme for, the aldoxime dehydration.

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

Explore across X-Mech

AntibioticMech (5-dimethylallylindole-3-acetonitrile) ↗ MediaIngredientMech (naturalproductmech:mibig-380600c810) ↗ TaxonMech: Streptomyces coelicolor A3(2) (NCBITaxon:100226) ↗ PathwayMech (mibig:BGC0002128) ↗

Provenance

Source concept	Source	Version
BGC0002128	MIBIG	3

This page is generated from data/natural_products/alkaloids/5-dimethylallylindole-3-acetonitrile.yaml, which is generated from the committed inventories. Neither is edited by hand.