paromomycin

CHEBI:7934 ·resolve ·ANTIBACTERIAL ·EXACT REVIEWED

An amino cyclitol glycoside that is the 1-O-(2-amino-2-deoxy-α-D-glucopyranoside) and the 3-O-(2,6-diamino-2,6-dideoxy-β-L-idopyranosyl)-β-D-ribofuranoside of 4,6-diamino-2,3-dihydroxycyclohexane (the 1R,2R,3S,4R,6S diastereoisomer). It is obtained from various Streptomyces species. A broad-spectrum antibiotic, it is used (generally as the sulfate salt) for the treatment of acute and chronic intestinal protozoal infections, but is not effective for extraintestinal protozoal infections. It is also used as a therapeutic against visceral leishmaniasis. — ChEBI

Classification

aminoglycoside antibioticARO:0000016

Strictly broader compounds or drug classes this molecule belongs to.

Label unavailable CHEBI:22479
aminoglycoside antibiotic CHEBI:22507
aminoglycoside antibiotic ARO:0000016

Chemical structure

Computed structure properties
Molecular formula	C23H45N5O14
Charge	0
Average mass	615.634 Da
Monoisotopic mass	615.2963 Da
Source	ChEBI
InChIKey	UOZODPSAJZTQNH-LSWIJEOBSA-N

SMILES

NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@@H]3[C@@H](O)[C@H](N)C[C@H](N)[C@H]3O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N)O[C@@H]2CO)[C@H](N)[C@@H](O)[C@@H]1O

InChI

InChI=1S/C23H45N5O14/c24-2-7-13(32)15(34)10(27)21(37-7)41-19-9(4-30)39-23(17(19)36)42-20-12(31)5(25)1-6(26)18(20)40-22-11(28)16(35)14(33)8(3-29)38-22/h5-23,29-36H,1-4,24-28H2/t5-,6+,7+,8-,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1

Also called

paromomicina (INN)— chebi
paromomycine (INN)— chebi
paromomycinum (INN)— chebi
(1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-β-L-idopyranosyl)-β-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-α-D-glucopyranoside (EXACT_SYNONYM)— chebi
(1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside (EXACT_SYNONYM)— chebi
Aminosidin (EXACT_SYNONYM)— chebi
Catenulin (EXACT_SYNONYM)— chebi
Hydroxymycin (EXACT_SYNONYM)— chebi
Monomycin A (EXACT_SYNONYM)— chebi
Neomycin E (EXACT_SYNONYM)— chebi
PAROMOMYCIN (EXACT_SYNONYM)— chebi
Paromomycin (EXACT_SYNONYM)— chebi
Paromomycin I (EXACT_SYNONYM)— chebi
R 400 (EXACT_SYNONYM)— chebi
R-400 (EXACT_SYNONYM)— chebi
Zygomycin A1 (EXACT_SYNONYM)— chebi
aminosidine (EXACT_SYNONYM)— chebi
crestomycin (EXACT_SYNONYM)— chebi
estomycin (EXACT_SYNONYM)— chebi
hydroxymycin (EXACT_SYNONYM)— chebi
neomycin E (EXACT_SYNONYM)— chebi
paucimycin (EXACT_SYNONYM)— chebi
paucimycinum (EXACT_SYNONYM)— chebi
Gabbomycin (EXACT_SYNONYM)— aro
Humagel (EXACT_SYNONYM)— aro
Humatin (EXACT_SYNONYM)— aro
aminosidin (EXACT_SYNONYM)— aro
catenulin (EXACT_SYNONYM)— aro
monomycin A (EXACT_SYNONYM)— aro

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.

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.

Patents and articles

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

Activity roles

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

antimicrobial agent CHEBI:33281
antiprotozoal drug CHEBI:35820
antibacterial drug CHEBI:36047

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
ARO	`ARO:3000657`	paromomycin	`antibioticmech:aro-7aea35b214`	2026-08-30
CHEBI	`CHEBI:7934`	paromomycin	`antibioticmech:chebi-c0019b6d96`	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.

antibiotic sensitive 16S rRNA NUCLEIC_ACID DIRECT_BINDING_TARGET

ARO:3000755

CARD/ARO database assertion; target organism, strain, and assay are not specified. 16S rRNA is asserted as the target. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000755 (CARD/ARO asserts targeted_by_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)

16S-rRNA decoding A-site oligonucleotide NUCLEIC_ACID DIRECT_BINDING_TARGET

A 2.5-angstrom complex directly observed paromomycin bound to an RNA construct containing two E. coli decoding A sites, with extensive direct and water-mediated contacts; this was not a whole-ribosome structure. Evidence status: PRIMARY_EVIDENCE. Source: PRIMARY_LITERATURE 2001-08 (retrieved 2026-09-02).

Escherichia coli NCBITaxon:562

PMID:11587639 (Primary paromomycin-bound bacterial decoding-A-site RNA structure (DOI:10.1016/S0969-2126(01)00629-3).)

Mechanism summary

Mode of action: PROTEIN_SYNTHESIS_INHIBITION host shared target — CURATOR: PMID:11587639 resolved paromomycin at 2.5 angstrom with oligoribonucleotides containing the Escherichia coli 16S-rRNA decoding A site. Direct and water-mediated contacts stabilize bulged A1492/A1493; the construct models the decoding site and its crystal packing, not an intact ribosomal subunit.

Resistance mechanisms

16 source-backed resistance determinants or associations, with ARO grounding where reported. Grouped by reported mechanism type.

ANTIBIOTIC_INACTIVATION 15

ANTIBIOTIC_INACTIVATION
Determinant	ARO ID	Organism	Gene families	Evidence
AAC(3)-IIIa	ARO:3002536	not organism-specific	—	ARO:3002536 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
AAC(3)-IIIb	ARO:3002537	not organism-specific	—	ARO:3002537 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
AAC(3)-VIIa	ARO:3002541	not organism-specific	—	ARO:3002541 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-IIIa	ARO:3002647	not organism-specific	—	ARO:3002647 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-IIa	ARO:3002644	not organism-specific	—	ARO:3002644 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-IIb	ARO:3002645	not organism-specific	—	ARO:3002645 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-IIc	ARO:3002646	not organism-specific	—	ARO:3002646 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-IVa	ARO:3002648	not organism-specific	—	ARO:3002648 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-Ia	ARO:3002641	not organism-specific	—	ARO:3002641 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-Ib	ARO:3002642	not organism-specific	—	ARO:3002642 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-VIa	ARO:3002652	not organism-specific	—	ARO:3002652 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-VIb	ARO:3002653	not organism-specific	—	ARO:3002653 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-Va	ARO:3002649	not organism-specific	—	ARO:3002649 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-Vb	ARO:3002650	not organism-specific	—	ARO:3002650 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)
APH(3')-Vc	ARO:3002651	not organism-specific	—	ARO:3002651 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)

ANTIBIOTIC_TARGET_ALTERATION 1

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to paromomycin	ARO:3003403	not organism-specific	—	ARO:3003403 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000657 (paromomycin); database assertion, not a primary citation.)

Record-level evidence

PMID:11587639 (Primary exact-paromomycin bacterial decoding-A-site RNA cocrystal study.)

Curation history

SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Seeded from data/raw/ inventories (ARO, 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
RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
Re-seeded from updated data/raw/ inventories
REVIEWED 2026-09-03 · codex · LLM-assisted
Verified exact ChEBI/CARD identity, structure, antibiotic roles, class, FDA provenance, and retained CARD target/resistance assertions; added protein-synthesis inhibition and the directly bound decoding-site RNA model with its reduced-construct boundary.
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).

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