pederin

CHEBI:78591 EXACT SEEDED cytotoxic

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 polyketide and carboxamide produced by a (Pseudomonas) bacterial endosymbiont of certain rove beetles (genus Paederus). Pederin is the agent responsible for the vesicant effects (linear or Paederus dermatitis) when the beetle is crushed against the skin. It is a powerful inhibitor of protein biosynthesis and mitosis and a potent antitumour agent.

Structure

Standard InChIKey	ZNEZZONMADKYTB-VRCUBXEUSA-N
SMILES	C[C@H]1[C@H](O[C@](CC1=C)([C@@H](C(=O)N[C@H]([C@@H]2C[C@H](C([C@H](O2)C[C@@H](COC)OC)(C)C)O)OC)O)OC)C
Stereochemistry	fully defined
Cross-references	pubchem:5381287, npatlas:NPA020381

Filing pathway

Polyketides — 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 pks, nrps, from MIBiG.

Producer organisms 0

None. The compound has a characterized gene cluster whose host NCBI does not name, which for an uncultured symbiont is the honest state — see the discussion below.

Occurrences 1

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
Pseudomonas aeruginosa NCBITaxon:287	LOTUS	DOI:10.1128/JB.186.5.1280-1286.2004

Biosynthetic gene clusters 3

Accession	Host	Locus evidence	Genome
mibig:BGC0000255	not named	CLUSTER_UNSTATED	genbank:AY850690.1
mibig:BGC0001108	not named	CLUSTER_DEMONSTRATED	genbank:AY328023.1
mibig:BGC0001109	not named	CLUSTER_UNSTATED	genbank:DD161836.1

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 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 (pederin) ↗ MediaIngredientMech (CHEBI:78591) ↗ PathwayMech (mibig:BGC0000255) ↗ PathwayMech (mibig:BGC0001108) ↗ PathwayMech (mibig:BGC0001109) ↗

Open questions 2

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000255, BGC0001108, BGC0001109. Confirm they describe the same compound rather than an upstream cross-reference error.

unnamed-producer — No producer claim is written from BGC0000255, which gives NCBITaxon:77133 (uncultured bacterium — shared by every unplaced bacterium); BGC0001108, which gives NCBITaxon:77133 (uncultured bacterium — shared by every unplaced bacterium); BGC0001109, which gives NCBITaxon:12908 (NCBI's bin for unclassified sequences), because the taxon names no single organism. The cluster is kept: a characterized locus is an origin assertion whether or not its host has a name, and for a compound from an uncultured symbiont that is the honest state. Name the producer if the primary literature does.

Provenance

Source concept	Source	Version
BGC0000255	MIBIG	5
BGC0001108	MIBIG	5
BGC0001109	MIBIG	4
CHEBI:78591	CHEBI	3-star

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

Assay	Result	Target enzyme	Source detail
NCI In Vivo Anticancer Drug Screen. Data for tumor model P388 Leukemia (intraperitoneal) in CD2F1 (CDF1) mice	ACTIVE	Not recorded	pubchem.aid:330 assay NCI In Vivo Anticancer Drug Screen. Data for tumor model P388 Leukemia (intraperitoneal) in CD2F1 (CDF1) mice evidence reference pubchem.aid:330 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 330, deposited by DTP/NCI; assay type Other. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the 786-0 Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794775 assay NCI human tumor cell line growth inhibition assay. Data for the 786-0 Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794775 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794775, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the 786-0 Renal cell line	ACTIVE	Not recorded	pubchem.aid:137 assay NCI human tumor cell line growth inhibition assay. Data for the 786-0 Renal cell line evidence reference pubchem.aid:137 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 137, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the A498 Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794774 assay NCI human tumor cell line growth inhibition assay. Data for the A498 Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794774 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794774, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the A498 Renal cell line	ACTIVE	Not recorded	pubchem.aid:129 assay NCI human tumor cell line growth inhibition assay. Data for the A498 Renal cell line evidence reference pubchem.aid:129 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 129, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the A549/ATCC Non-Small Cell Lung cell line	ACTIVE	Not recorded	pubchem.aid:19 assay NCI human tumor cell line growth inhibition assay. Data for the A549/ATCC Non-Small Cell Lung cell line evidence reference pubchem.aid:19 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 19, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the A549/ATCC Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794740 assay NCI human tumor cell line growth inhibition assay. Data for the A549/ATCC Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794740 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794740, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the ACHN Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794771 assay NCI human tumor cell line growth inhibition assay. Data for the ACHN Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794771 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794771, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the ACHN Renal cell line	ACTIVE	Not recorded	pubchem.aid:139 assay NCI human tumor cell line growth inhibition assay. Data for the ACHN Renal cell line evidence reference pubchem.aid:139 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 139, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the BT-549 Breast cell line	ACTIVE	Not recorded	pubchem.aid:89 assay NCI human tumor cell line growth inhibition assay. Data for the BT-549 Breast cell line evidence reference pubchem.aid:89 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 89, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the BT-549 Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794793 assay NCI human tumor cell line growth inhibition assay. Data for the BT-549 Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794793 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794793, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the CAKI-1 Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794772 assay NCI human tumor cell line growth inhibition assay. Data for the CAKI-1 Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794772 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794772, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the CAKI-1 Renal cell line	ACTIVE	Not recorded	pubchem.aid:131 assay NCI human tumor cell line growth inhibition assay. Data for the CAKI-1 Renal cell line evidence reference pubchem.aid:131 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 131, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the CCRF-CEM Leukemia cell line	ACTIVE	Not recorded	pubchem.aid:119 assay NCI human tumor cell line growth inhibition assay. Data for the CCRF-CEM Leukemia cell line evidence reference pubchem.aid:119 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 119, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the CCRF-CEM Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794778 assay NCI human tumor cell line growth inhibition assay. Data for the CCRF-CEM Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794778 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794778, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the COLO 205 Colon cell line	ACTIVE	Not recorded	pubchem.aid:67 assay NCI human tumor cell line growth inhibition assay. Data for the COLO 205 Colon cell line evidence reference pubchem.aid:67 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 67, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the COLO 205 Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794742 assay NCI human tumor cell line growth inhibition assay. Data for the COLO 205 Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794742 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794742, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the DU-145 Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794760 assay NCI human tumor cell line growth inhibition assay. Data for the DU-145 Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794760 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794760, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the DU-145 Prostate cell line	ACTIVE	Not recorded	pubchem.aid:43 assay NCI human tumor cell line growth inhibition assay. Data for the DU-145 Prostate cell line evidence reference pubchem.aid:43 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 43, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the EKVX Non-Small Cell Lung cell line	ACTIVE	Not recorded	pubchem.aid:21 assay NCI human tumor cell line growth inhibition assay. Data for the EKVX Non-Small Cell Lung cell line evidence reference pubchem.aid:21 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 21, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the EKVX Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794765 assay NCI human tumor cell line growth inhibition assay. Data for the EKVX Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794765 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794765, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the HCC-2998 Colon cell line	ACTIVE	Not recorded	pubchem.aid:77 assay NCI human tumor cell line growth inhibition assay. Data for the HCC-2998 Colon cell line evidence reference pubchem.aid:77 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 77, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the HCT-116 Colon cell line	ACTIVE	Not recorded	pubchem.aid:79 assay NCI human tumor cell line growth inhibition assay. Data for the HCT-116 Colon cell line evidence reference pubchem.aid:79 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 79, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the HCT-116 Non-Small Cell Lung cell line, single concentration	ACTIVE	Not recorded	pubchem.aid:1794798 assay NCI human tumor cell line growth inhibition assay. Data for the HCT-116 Non-Small Cell Lung cell line, single concentration evidence reference pubchem.aid:1794798 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1794798, deposited by DTP/NCI; assay type Screening. call ACTIVE activity class CYTOTOXIC
NCI human tumor cell line growth inhibition assay. Data for the HCT-15 Colon cell line	ACTIVE	Not recorded	pubchem.aid:71 assay NCI human tumor cell line growth inhibition assay. Data for the HCT-15 Colon cell line evidence reference pubchem.aid:71 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 71, deposited by DTP/NCI; assay type Confirmatory. call ACTIVE activity class CYTOTOXIC notes 92 further PubChem assay results are in data/raw/pubchem_bioassay.tsv but not written here.