agrocin 84

CHEBI:82809 ·resolve ·ANTIMICROBIAL_UNSPECIFIED ·EXACT REVIEWED

A nucleotide conjugate that is produced by Agrobacterium radiobacter strain K-84. A 'Trojan horse' antibiotic used to control crown gall. — ChEBI

Classification

Strictly broader compounds or drug classes this molecule belongs to.

Label unavailable CHEBI:27577
Label unavailable CHEBI:47784
Label unavailable CHEBI:63367

Chemical structure

Computed structure properties
Molecular formula	C22H36N6O17P2
Charge	0
Average mass	718.503 Da
Monoisotopic mass	718.16122 Da
Source	ChEBI
InChIKey	YNCRAYSPLQSJIP-JHNPATRKSA-N

SMILES

[H][C@@]1([C@H](O)CO)OC(OP(=O)(O)Nc2ncnc3c2ncn3[C@@H]2O[C@H](COP(=O)(O)NC(=O)[C@@H](O)[C@H](O)C(C)C)[C@@H](O)[C@H]2O)[C@H](O)[C@H]1O

InChI

InChI=1S/C22H36N6O17P2/c1-7(2)11(31)14(34)20(37)27-46(38,39)42-4-9-12(32)15(35)21(43-9)28-6-25-10-18(23-5-24-19(10)28)26-47(40,41)45-22-16(36)13(33)17(44-22)8(30)3-29/h5-9,11-17,21-22,29-36H,3-4H2,1-2H3,(H2,27,37,38,39)(H2,23,24,26,40,41)/t8-,9-,11-,12-,13-,14+,15-,16-,17+,21-,22?/m1/s1

Also called

Agrocin (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.

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.

Upstream concepts merged into this record
Source	Native ID	Label	Minted CURIE	Version
CHEBI	`CHEBI:82809`	agrocin 84	`antibioticmech:chebi-64c2c445fa`	2026-08-30

Molecular targets

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

leucyl-tRNA synthetase–tRNA(Leu) complex PROTEIN_COMPLEX DOWNSTREAM_AFFECTED_PROCESS

Agrocin 84 is an imported precursor that is processed intracellularly to TM84. Crystal, thermodynamic, and kinetic analyses showed that TM84—not the intact precursor—binds tightly to the LeuRS-tRNA(Leu) complex. Evidence status: PRIMARY_EVIDENCE. Source: PRIMARY_LITERATURE 2013-01 (retrieved 2026-09-02).

PMID:23361008 (Primary agrocin-84 activation and TM84-bound LeuRS-tRNA structural/mechanistic study (DOI:10.1038/ncomms2421).)

Mechanism summary

Mode of action: PROTEIN_SYNTHESIS_INHIBITION host shared target — CURATOR: PMID:23361008 showed that agrocin 84 is processed inside susceptible Agrobacterium into the toxic moiety TM84. TM84 requires tRNA(Leu) for tight binding to the leucyl-tRNA synthetase synthetic active site and traps an aminoacylation-like enzyme-tRNA complex. The direct structural target claim therefore applies to the active metabolite, not to unprocessed agrocin 84.

Record-level evidence

PMID:23361008 (Primary agrocin-84 Trojan-horse activation and translation-target study.)

Curation history

SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Seeded from data/raw/ inventories (CHEBI)
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
REVIEWED 2026-09-02 · codex · LLM-assisted
Verified exact ChEBI identity, structure, antibiotic role, and unspecified filing class; added protein-synthesis inhibition and explicitly separated agrocin 84 from the directly LeuRS-bound active metabolite TM84.

Provenance

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

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