lomaiviticin D

naturalproductmech:mibig-591a288508 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	RKAAVHMHEYQQIN-QLNCNNILSA-N
SMILES	O=C1C2=C(C([H])=C3C2=C(O)C4=C(O)C=CC(O)=C4C3=O)[C@@H](O[C@H]5O[C@@H](C)[C@@H](N(C)C)[C@@H](O)C5)[C@](O[C@@H]6O[C@@H](C)[C@H](O)[C@@H](OC)C6)(CC)C1C7[C@@](O[C@@H]8O[C@@H](C)[C@H](OC)[C@@H](OC)C8)(CC)[C@H](O[C@H]9O[C@@H](C)[C@H](N(C)C)[C@@H](O)C9)C(C(C(C(C%10=C(O)C=CC(O)=C%10%11)=O)C%12C%11=O)=[N+]=[N-])=C%12C7=O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers

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, saccharide, 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
Salinispora tropica CNB-440 NCBITaxon:369723	BGC_CHARACTERIZED	mibig:BGC0000241	PMID:23649992

Occurrences 0

None cited.

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000241	Salinispora tropica CNB-440 NCBITaxon:369723	CLUSTER_DEMONSTRATED	genbank:CP000667.1

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.

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	Strop_2223 beta-ketoacyl synthase UniProtKB:A4X724		ungrounded → ungrounded	DOI:10.1002/cbic.201300147

Step 1: This curates the S. tropica CNB-440 Strop_2223/ABP54674.1 beta-ketoacyl synthase as a knockout-supported type II PKS enzyme in the ST_pks2/lom scaffold-biosynthesis branch that produces lomaiviticins, including lomaiviticin D. UniProtKB A4X724 resolves to Strop_2223 in the CNB-440 genome; the exact Strop_2223 substrate/product pair and its minimal-PKS partner are left unresolved. Exact-product identity remains disputed (issue #976). The two deposited D encodings differ by two hydrogens and connectivity. The experiments do not adjudicate which exact D encoding is correct; the 2021 A-C revision is not automatically evidence for revising D.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 3 nodes, 2 edges

Partial S. tropica lomaiviticin D biosynthesis graph for the knockout-supported Strop_2223 type II PKS scaffold branch. Exact-product identity is unresolved; see the curator identity discussion.

Subject	Predicate	Object	Notes	Evidence
Strop_2223 beta-ketoacyl synthase	is required for	lomaiviticin type II PKS scaffold biosynthesis	Kersten et al. knocked out strop2223 and MIBiG v5 maps that locus to ABP54674.1; the edge stops at scaffold biosynthesis because the exact condensation reaction was not assayed in vitro.	DOI:10.1002/cbic.201300147 https://mibig.secondarymetabolites.org/repository/BGC0000241.5/index.html https://www.ncbi.nlm.nih.gov/protein/ABP54674.1 https://www.uniprot.org/uniprotkb/A4X724 reference DOI:10.1002/cbic.201300147 evidence type PRIMARY_EXPERIMENT snippet lomaiviticins A, D and E notes Kersten et al. inactivated the S. tropica CNB-440 strop2223 beta-ketosynthase, found that the mutant extract was inactive in the DNA-interference assay, and used LC-MS profiling of wild-type and mutant extracts to identify lomaiviticins, including lomaiviticin D, as ST_pks2/lom products. reference https://mibig.secondarymetabolites.org/repository/BGC0000241.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Scaffold biosynthesis notes MIBiG BGC0000241.5 lists lomaiviticin D among the Salinispora tropica CNB-440 products and annotates Strop_2223/ABP54674.1 as a beta-ketoacyl synthase with scaffold-biosynthesis function and knockout evidence. reference https://www.ncbi.nlm.nih.gov/protein/ABP54674.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet beta-ketoacyl synthase notes NCBI Protein ABP54674.1 is the 423 aa Salinispora tropica CNB-440 Strop_2223 product. reference https://www.uniprot.org/uniprotkb/A4X724 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Beta-ketoacyl-acyl-carrier-protein synthase I notes UniProtKB A4X724 resolves to the 423 aa S. tropica CNB-440 Strop_2223 entry and cross-references the CP000667 chromosome.
lomaiviticin type II PKS scaffold biosynthesis	contributes to	lomaiviticin D	LC-MS comparison connected ST_pks2 with the lomaiviticin family and identified lomaiviticin D among the wild-type S. tropica CNB-440 products; this graph does not claim a complete route from the type II PKS scaffold to the fully tailored glycoside. Exact-product identity remains disputed (issue #976). The two deposited D encodings differ by two hydrogens and connectivity. The experiments do not adjudicate which exact D encoding is correct; the 2021 A-C revision is not automatically evidence for revising D.	DOI:10.1002/cbic.201300147 https://mibig.secondarymetabolites.org/repository/BGC0000241.5/index.html DOI:10.1021/ja3074984 reference DOI:10.1002/cbic.201300147 evidence type PRIMARY_EXPERIMENT snippet lomaiviticins A, D and E notes Kersten et al. inactivated the S. tropica CNB-440 strop2223 beta-ketosynthase, found that the mutant extract was inactive in the DNA-interference assay, and used LC-MS profiling of wild-type and mutant extracts to identify lomaiviticins, including lomaiviticin D, as ST_pks2/lom products. reference https://mibig.secondarymetabolites.org/repository/BGC0000241.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Scaffold biosynthesis notes MIBiG BGC0000241.5 lists lomaiviticin D among the Salinispora tropica CNB-440 products and annotates Strop_2223/ABP54674.1 as a beta-ketoacyl synthase with scaffold-biosynthesis function and knockout evidence. reference DOI:10.1021/ja3074984 evidence type CURATOR_INFERENCE notes Only the isolation abstract was inspected; full text returned 403. Exact D structure adjudication remains incomplete.

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

Explore across X-Mech

AntibioticMech (lomaiviticin D) ↗ MediaIngredientMech (naturalproductmech:mibig-591a288508) ↗ TaxonMech: Salinispora tropica CNB-440 (NCBITaxon:369723) ↗ PathwayMech (mibig:BGC0000241) ↗

Open questions 1

curator-lomaiviticin-identity-conflict — Which exact structure is supported for this source product?

Provenance

Source concept	Source	Version
BGC0000241	MIBIG	5

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