streptolydigin

CHEBI:45773 ·resolve ·ANTIMICROBIAL_UNSPECIFIED ·EXACT REVIEWED

A monocarboxylic acid amide that is a broad-spectrum antibiotic produced by Streptomyces lydicus. — ChEBI

Classification

Strictly broader compounds or drug classes this molecule belongs to.

• Label unavailable CHEBI:133131
• Label unavailable CHEBI:21731
• Label unavailable CHEBI:27171
• Label unavailable CHEBI:29347
• Label unavailable CHEBI:33823
• Label unavailable CHEBI:35990
• Label unavailable CHEBI:38275
• Label unavailable CHEBI:59779

Chemical structure

SMILES

[H][C@]1([C@H](C)/C=C(C)/C=C/C(O)=C2\C(=O)N([C@@H]3CC[C@H](O)[C@H](C)O3)[C@@]([H])([C@H](C)C(=O)NC)C2=O)O[C@@]2(C)O[C@H](C=C[C@@]23CO3)[C@@H]1C

InChI

InChI=1S/C32H44N2O9/c1-16(14-17(2)28-18(3)23-12-13-32(15-40-32)31(6,42-23)43-28)8-9-22(36)25-27(37)26(19(4)29(38)33-7)34(30(25)39)24-11-10-21(35)20(5)41-24/h8-9,12-14,17-21,23-24,26,28,35-36H,10-11,15H2,1-7H3,(H,33,38)/b9-8+,16-14+,25-22+/t17-,18+,19+,20+,21+,23-,24+,26+,28-,31-,32-/m1/s1

Also called

• (2S)-2-{(2S,4E)-4-{(2E,4E,6R)-6-[(1R,2R,5R,6S,7R)-1,6-dimethylspiro[8,9-dioxabicyclo[3.3.1]non-3-ene-2,2'-oxiran]-7-yl]-1-hydroxy-4-methylhepta-2,4-dien-1-ylidene}-1-[(2S,5S,6S)-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]-3,5-dioxopyrrolidin-2-yl}-N-methylpropanamide (EXACT_SYNONYM)— chebi
• Antibiotic D-45 (EXACT_SYNONYM)— chebi
• NSC 3360 (EXACT_SYNONYM)— chebi

Cross-references

Identifiers for this same structure in other resources. An accession that lands on two different structures in this corpus is withheld from both rather than shown here, since it names at most one of them.

• cas:7229-50-7
• pdb-ccd:STD
• reaxys:9977901

Drug registries

Identifiers that name a drug rather than a structure. One of these can cover a parent compound, its salts and its stereoisomers, which this corpus keeps as separate records, so it is not an equivalence of structure.

• drugbank:DB04785

Patents and articles

Documents about this compound. A patent covers a class and an article covers a topic; neither identifies a structure.

• wikipedia.en:Streptolydigin

Activity roles

Every antimicrobial role a source asserts for this compound — the unreduced evidence behind its antimicrobial_class.

• antimicrobial agent CHEBI:33281

Source concepts

Every upstream concept that resolved to this record. The merge is the product: this is what shows ChEBI and CARD are describing the same structure.

Molecular targets

The molecular entity or process this compound acts on. Each target carries evidence — this is a mechanistic claim, not a classification.

bacterial DNA-directed RNA polymerase bridge-helix/trigger-loop site PROTEIN_COMPLEX DIRECT_BINDING_TARGET

Independent 2.4-angstrom RNAP-streptolydigin structures and biochemical experiments localized binding adjacent to the active center and defined conformational inhibition. Evidence status: PRIMARY_EVIDENCE. Source: PRIMARY_LITERATURE 2005-08; 2005-09 (retrieved 2026-09-02).

Thermus thermophilus NCBITaxon:274

• PMID:16122422 (Primary bacterial RNAP-streptolydigin structural mechanism study (DOI:10.1016/j.cell.2005.07.017).)
• PMID:16167380 (Independent bacterial RNAP-streptolydigin cocrystal and biochemical study (DOI:10.1016/j.molcel.2005.07.020).)

Mechanism summary

Mode of action

NUCLEIC_ACID_SYNTHESIS_INHIBITION microbial target — CURATOR: PMIDs 16122422 and 16167380 resolved streptolydigin bound to bacterial RNA polymerase beside the active center, contacting the bridge helix and trigger loop. The inhibitor stabilizes a catalytically inactive preinsertion conformation rather than preventing nucleotide binding, DNA translocation, or phosphodiester-bond formation.

Producer organisms

Organisms that biosynthesize this compound. Cluster link evidence is how the upstream source graded the gene cluster, so it is populated only for a source that grades it. An empty cell is not weaker support: a curator-authored producer carries its support in Evidence instead. Where the source entry named several compounds, the evidence is marked inherited, meaning it covers this compound together with the cluster's other products rather than singling it out. Those products need not be related to each other: a cluster can list an intermediate, a precursor and a finished antibiotic side by side.

Record-level evidence

• PMID:16122422 (Primary bacterial RNAP-streptolydigin structural mechanism study.)
• PMID:16167380 (Independent bacterial RNAP-streptolydigin structural mechanism study.)

Curation history

1. SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources

   Seeded from data/raw/ inventories (CHEBI)

2. RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources

   Re-seeded from updated data/raw/ inventories

3. RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources

   Re-seeded from updated data/raw/ inventories

4. REVIEWED 2026-09-02 · codex · LLM-assisted

   Verified exact ChEBI identity, structure, antibiotic role, and unspecified filing class; curator-confirmed transcription inhibition, corrected scope to the specifically studied bacterial target, and added the directly bound RNA-polymerase complex.

5. RESEEDED_FROM_SOURCES 2026-09-08 · seed_from_sources

   Re-seeded from updated data/raw/ inventories

6. RESEEDED_FROM_SOURCES 2026-09-08 · seed_from_sources

   Re-seeded from updated data/raw/ inventories

7. RESEEDED_FROM_SOURCES 2026-09-10 · seed_from_sources

   Re-seeded from updated data/raw/ inventories

Provenance

Seeded by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record (YAML).

Explore across X-Mech: MediaIngredientMech (streptolydigin) · CultureMech · NaturalProductMech · PathwayMech · TraitMech · TaxonMech (Streptomyces lydicus)