nogalamycin

CHEBI:44504 ·resolve ·ANTIMICROBIAL_UNSPECIFIED ·EXACT REVIEWED

An anthracycline antibiotic isolated from Streptomyces nogalater. It is a DNA intercalator and exhibits anticancer properties. — ChEBI

Classification

Strictly broader compounds or drug classes this molecule belongs to.

Label unavailable CHEBI:25248
Label unavailable CHEBI:26188
Label unavailable CHEBI:33573
anthracycline antibiotic CHEBI:49322
Label unavailable CHEBI:50996
Label unavailable CHEBI:51914
Label unavailable CHEBI:63367

Chemical structure

Computed structure properties
Molecular formula	C39H49NO16
Charge	0
Average mass	787.812 Da
Monoisotopic mass	787.30513 Da
Source	ChEBI
InChIKey	KGTDRFCXGRULNK-JYOBTZKQSA-N

SMILES

[H][C@@]12Oc3c(cc(O)c4c3C(=O)c3cc5c(c(O)c3C4=O)[C@@H](O[C@@H]3O[C@@H](C)[C@H](OC)[C@@](C)(OC)[C@H]3OC)C[C@](C)(O)[C@@H]5C(=O)OC)[C@@](C)(O1)[C@H](O)[C@@H](N(C)C)[C@@H]2O

InChI

InChI=1S/C39H49NO16/c1-14-32(49-7)39(4,52-10)33(50-8)36(53-14)54-19-13-37(2,48)24(34(47)51-9)15-11-16-21(27(43)20(15)19)28(44)22-18(41)12-17-30(23(22)26(16)42)55-35-29(45)25(40(5)6)31(46)38(17,3)56-35/h11-12,14,19,24-25,29,31-33,35-36,41,43,45-46,48H,13H2,1-10H3/t14-,19-,24-,25-,29-,31+,32-,33-,35+,36-,37-,38+,39+/m0/s1

Also called

nogalamicina (INN)— chebi
nogalamycine (INN)— chebi
nogalamycinum (INN)— chebi
methyl (2R,3S,4R,5R,6R,11S,13S,14R)-11-[(6-deoxy-3-C-methyl-2,3,4-tri-O-methyl-α-L-mannopyranosyl)oxy]-4-(dimethylamino)-3,5,8,10,13-pentahydroxy-6,13-dimethyl-9,16-dioxo-3,4,5,6,9,11,12,13,14,16-decahydro-2H-2,6-epoxytetraceno[1,2-b]oxocine-14-carboxylate (EXACT_SYNONYM)— chebi
U 15167 (EXACT_SYNONYM)— chebi
U-15167 (EXACT_SYNONYM)— chebi
antibiotic 205t3 (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.

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.

kegg.drug:D05198

Patents and articles

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

wikipedia.en:Nogalamycin

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:44504`	nogalamycin	`antibioticmech:chebi-61422a1afb`	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.

double-stranded DNA NUCLEIC_ACID DIRECT_BINDING_TARGET

An X-ray structure of nogalamycin with a self-complementary DNA hexamer showed terminal-CpG intercalation, two-strand/two-groove contacts, and large departures from B-DNA geometry. Evidence status: PRIMARY_EVIDENCE. Source: PRIMARY_LITERATURE 1991-02 (retrieved 2026-09-02).

PMID:1991116 (Primary nogalamycin-DNA cocrystal study (DOI:10.1021/bi00219a029).)

Mechanism summary

Mode of action: NUCLEIC_ACID_SYNTHESIS_INHIBITION host shared target — CURATOR: PMID:1991116 resolved nogalamycin intercalated at terminal CpG steps of a DNA hexamer. The drug contacts both strands in both grooves and causes substantial base-pair and backbone distortions; the observed hydrogen bonds did not establish sequence-specific binding.

Record-level evidence

PMID:1991116 (Primary exact-nogalamycin DNA intercalation structure.)

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 nucleic-acid synthesis inhibition and directly observed, non-sequence-specific DNA intercalation.
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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