actinonin

naturalproductmech:mibig-30a67209ce MINTED SEEDED enzyme inhibitor

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	XJLATMLVMSFZBN-VYDXJSESSA-N
SMILES	[H][C@@](CCCCC)(CC(=O)NO)C(=O)N[C@@]([H])(C(C)C)C(=O)N1CCC[C@H]1CO
Stereochemistry	fully defined
Cross-references	npatlas:NPA07269, pubchem:443600

Filing pathway

Amino acids and peptides — 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 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 sp. strain ATCC 14903 NCBITaxon:1931	SOURCE_ASSERTION	mibig:BGC0001442	PMID:13900478

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 NCBITaxon:1883	LOTUS	DOI:10.1039/P19750000819
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.3389/FMICB.2016.01467

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0001442	Streptomyces sp. strain ATCC 14903 NCBITaxon:1931	CLUSTER_UNSTATED	genbank:KY906183.1

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

Causal graph — bioactivity 2 nodes, 1 edge

Actinonin inhibits Arabidopsis thaliana peptide deformylase 1B captured in the actinonin-bound PDB 3PN4 structure.

Subject	Predicate	Object	Notes	Evidence
actinonin	inhibits	Arabidopsis thaliana peptide deformylase 1B	PubChem BioAssay AID 977610 maps this exact Standard InChIKey to an active 0.14 uM Ki row for PDB 3PN4 chain A; PDBe maps 3PN4_A to Arabidopsis thaliana UniProtKB:Q9FUZ2, and RCSB reports BB2 actinonin with the record's Standard InChIKey as a 3PN4 non-polymer ligand. Chain A is an AtPDF1B construct containing UniProt residues 83-273 with a two-residue expression tag.	DOI:10.1371/journal.pbio.1001066 DOI:10.2210/pdb3pn4/pdb reference DOI:10.1371/journal.pbio.1001066 evidence type PRIMARY_EXPERIMENT snippet we explored the precise inhibitory mechanism of actinonin on Arabidopsis thaliana PDF1B notes Fieulaine et al. solved PDB 3PN4 among Arabidopsis thaliana PDF1B structures trapping actinonin-bound conformational states. reference DOI:10.2210/pdb3pn4/pdb evidence type DATABASE_ASSERTION notes RCSB PDB identifies 3PN4 as an Arabidopsis thaliana AtPDF1B crystal structure with BB2 actinonin, and PDBe maps chain A to UniProtKB:Q9FUZ2.

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

Bioactivities 25

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

Explore across X-Mech

AntibioticMech (actinonin) ↗ MediaIngredientMech (naturalproductmech:mibig-30a67209ce) ↗ TaxonMech: Streptomyces sp. strain ATCC 14903 (NCBITaxon:1931) ↗ PathwayMech (mibig:BGC0001442) ↗

Provenance

Source concept	Source	Version
BGC0001442	MIBIG	5

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

Assay	Result	Target enzyme	Source detail
Experimentally measured binding affinity data (IC50) for protein-ligand complexes derived from PDB	IC50 0.01 uM; ACTIVE	Not recorded	PMID:23407310 assay Experimentally measured binding affinity data (IC50) for protein-ligand complexes derived from PDB evidence reference PMID:23407310 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977608, deposited by Shanghai Institute of Organic Chemistry; assay type Other. call ACTIVE measurement type IC50 value 0.01 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB	KD 0.0045 uM; ACTIVE	Not recorded	pubchem.aid:977611 assay Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB evidence reference pubchem.aid:977611 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977611, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 3M6P_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KD value 0.0045 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB	KD 0.048 uM; ACTIVE	Not recorded	pubchem.aid:977611 assay Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB evidence reference pubchem.aid:977611 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977611, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 3M6Q_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KD value 0.048 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB	KD 0.032 uM; ACTIVE	Not recorded	pubchem.aid:977611 assay Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB evidence reference pubchem.aid:977611 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977611, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 3M6R_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KD value 0.032 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB	KD 0.395 uM; ACTIVE	Not recorded	PMID:24531459 assay Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB evidence reference PMID:24531459 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977611, deposited by Shanghai Institute of Organic Chemistry; assay type Other. call ACTIVE measurement type KD value 0.395 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB	KI 0.14 uM; ACTIVE	Not recorded	PMID:21629676 assay Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB evidence reference PMID:21629676 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977610, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 3PN4_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KI value 0.14 units uM activity class ENZYME_INHIBITOR
Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB	KI 0.0003 uM; ACTIVE	Not recorded	PMID:12951107 assay Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB evidence reference PMID:12951107 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977610, deposited by Shanghai Institute of Organic Chemistry; assay type Other. call ACTIVE measurement type KI value 0.0003 units uM activity class ENZYME_INHIBITOR
Inhibitors of Regulator of G Protein Signaling (RGS) 4: qHTS	OTHER 2.6654 uM; NOT_DETERMINED	Not recorded	pubchem.aid:504845 assay Inhibitors of Regulator of G Protein Signaling (RGS) 4: qHTS evidence reference pubchem.aid:504845 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 504845, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. Target accession ABC94591 was left ungrounded because PubChem did not provide a UniProtKB accession. call NOT_DETERMINED measurement type OTHER value 2.6654 units uM
Nrf2 qHTS screen for inhibitors: Validation	OTHER 16.3601 uM; ACTIVE	Not recorded	pubchem.aid:493153 assay Nrf2 qHTS screen for inhibitors: Validation evidence reference pubchem.aid:493153 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 493153, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. call ACTIVE measurement type OTHER value 16.3601 units uM
Nrf2 qHTS screen for inhibitors: Validation	OTHER 16.3601 uM; ACTIVE	Not recorded	pubchem.aid:493153 assay Nrf2 qHTS screen for inhibitors: Validation evidence reference pubchem.aid:493153 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 493153, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. Target accession NP_001138884 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type OTHER value 16.3601 units uM
Primary qHTS assay for inhibitors of alpha-synuclein gene (SNCA) expression	OTHER 3.5481 uM; NOT_DETERMINED	Not recorded	pubchem.aid:1671194 assay Primary qHTS assay for inhibitors of alpha-synuclein gene (SNCA) expression evidence reference pubchem.aid:1671194 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1671194, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 3.5481 units uM
Primary qHTS assay for inhibitors of alpha-synuclein gene (SNCA) expression	OTHER 3.5481 uM; NOT_DETERMINED	UniProtKB:P37840	pubchem.aid:1671194 assay Primary qHTS assay for inhibitors of alpha-synuclein gene (SNCA) expression evidence reference pubchem.aid:1671194 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1671194, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 3.5481 units uM target enzyme UniProtKB:P37840
Primary qHTS assay for inhibitors of human arachidonate 12S-lipoxygenase (ALOX12): Round 2	OTHER 12.5893 uM; NOT_DETERMINED	Not recorded	pubchem.aid:1671190 assay Primary qHTS assay for inhibitors of human arachidonate 12S-lipoxygenase (ALOX12): Round 2 evidence reference pubchem.aid:1671190 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1671190, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 12.5893 units uM
Primary qHTS assay for inhibitors of human arachidonate 12S-lipoxygenase (ALOX12): Round 2	OTHER 12.5893 uM; NOT_DETERMINED	UniProtKB:P18054	pubchem.aid:1671190 assay Primary qHTS assay for inhibitors of human arachidonate 12S-lipoxygenase (ALOX12): Round 2 evidence reference pubchem.aid:1671190 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1671190, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 12.5893 units uM target enzyme UniProtKB:P18054
Primary qHTS to identify anti-liver cancer compounds using libraries of approved drugs and bioactive compounds	OTHER 11.2202 uM; NOT_DETERMINED	Not recorded	pubchem.aid:2202548 assay Primary qHTS to identify anti-liver cancer compounds using libraries of approved drugs and bioactive compounds evidence reference pubchem.aid:2202548 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 2202548, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 11.2202 units uM
Quantitative high throughput screen for delayed death inhibitors of the malarial parasite plastid, 48 hour incubation	OTHER 2.9362 uM; ACTIVE	Not recorded	pubchem.aid:488752 assay Quantitative high throughput screen for delayed death inhibitors of the malarial parasite plastid, 48 hour incubation evidence reference pubchem.aid:488752 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 488752, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. call ACTIVE measurement type OTHER value 2.9362 units uM activity class ENZYME_INHIBITOR
Quantitative high throughput screen for delayed death inhibitors of the malarial parasite plastid, 96 hour incubation	OTHER 1.1689 uM; ACTIVE	Not recorded	pubchem.aid:488745 assay Quantitative high throughput screen for delayed death inhibitors of the malarial parasite plastid, 96 hour incubation evidence reference pubchem.aid:488745 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 488745, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. call ACTIVE measurement type OTHER value 1.1689 units uM activity class ENZYME_INHIBITOR
Total Fluorescence Counterscreen for Inhibitors of the Interaction of Thyroid Hormone Receptor and Steroid Receptor Coregulator 2	OTHER 2.2387 uM; NOT_DETERMINED	Not recorded	pubchem.aid:1479 assay Total Fluorescence Counterscreen for Inhibitors of the Interaction of Thyroid Hormone Receptor and Steroid Receptor Coregulator 2 evidence reference pubchem.aid:1479 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1479, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. Target accession NP_001121649 was left ungrounded because PubChem did not provide a UniProtKB accession. call NOT_DETERMINED measurement type OTHER value 2.2387 units uM
Validation qHTS for agonist of cAMP-regulated guanine nucleotide exchange factor 4 (EPAC2)	OTHER 25.1189 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 25.1189 units uM
Validation qHTS for agonist of cAMP-regulated guanine nucleotide exchange factor 4 (EPAC2)	OTHER 25.1189 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 25.1189 units uM target enzyme UniProtKB:Q8WZA2
Validation screen for small molecules that induce genotoxicity in human embryonic kidney (HEK293T) cells expressing luciferase-tagged ELG1	OTHER 9.1962 uM; INACTIVE	Not recorded	pubchem.aid:493106 assay Validation screen for small molecules that induce genotoxicity in human embryonic kidney (HEK293T) cells expressing luciferase-tagged ELG1 evidence reference pubchem.aid:493106 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 493106, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. Target accession AAH15051 was left ungrounded because PubChem did not provide a UniProtKB accession. call INACTIVE measurement type OTHER value 9.1962 units uM
Validation screen for small molecules that inhibit ELG1-dependent DNA repair in human embryonic kidney (HEK293T) cells expressing luciferase-tagged ELG1	OTHER 3.6611 uM; NOT_DETERMINED	Not recorded	pubchem.aid:493107 assay Validation screen for small molecules that inhibit ELG1-dependent DNA repair in human embryonic kidney (HEK293T) cells expressing luciferase-tagged ELG1 evidence reference pubchem.aid:493107 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 493107, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. Target accession AAH15051 was left ungrounded because PubChem did not provide a UniProtKB accession. call NOT_DETERMINED measurement type OTHER value 3.6611 units uM
qHTS Assay for Antagonists of the Neuropeptide S Receptor: cAMP Signal Transduction	OTHER 31.6228 uM; NOT_DETERMINED	Not recorded	pubchem.aid:1461 assay qHTS Assay for Antagonists of the Neuropeptide S Receptor: cAMP Signal Transduction evidence reference pubchem.aid:1461 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1461, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. Target accession NP_997055 was left ungrounded because PubChem did not provide a UniProtKB accession. call NOT_DETERMINED measurement type OTHER value 31.6228 units uM
qHTS Assay for Inhibitors of GCN5L2	OTHER 39.8107 uM; NOT_DETERMINED	Not recorded	pubchem.aid:504327 assay qHTS Assay for Inhibitors of GCN5L2 evidence reference pubchem.aid:504327 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 504327, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. Target accession NP_066564 was left ungrounded because PubChem did not provide a UniProtKB accession. call NOT_DETERMINED measurement type OTHER value 39.8107 units uM
qHTS Assay for Inhibitors of Histone Lysine Methyltransferase G9a	OTHER 9.4662 uM; ACTIVE	Not recorded	pubchem.aid:504332 assay qHTS Assay for Inhibitors of Histone Lysine Methyltransferase G9a evidence reference pubchem.aid:504332 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 504332, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. Target accession CAQ07474 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type OTHER value 9.4662 units uM activity class ENZYME_INHIBITOR notes 35 further PubChem assay results are in data/raw/pubchem_bioassay.tsv but not written here.