novobiocin

CHEBI:28368 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

A coumarin-derived antibiotic obtained from Streptomyces niveus. — ChEBI

Machine-generated and unreviewed. Identity, structure and cross-references come straight from ChEBI's and CARD's own data; no curator has signed off on this record yet.

Classification

aminocoumarin antibioticARO:3000103

Strictly broader compounds or drug classes this molecule belongs to.

CHEBI:23003 CHEBI:23003
CHEBI:25698 CHEBI:25698
CHEBI:29347 CHEBI:29347
CHEBI:33853 CHEBI:33853
CHEBI:35313 CHEBI:35313
CHEBI:37912 CHEBI:37912
CHEBI:63367 CHEBI:63367
ARO:3000103 ARO:3000103

Chemical structure

Computed structure properties
Molecular formula	C31H36N2O11
Charge	0
Average mass	612.632 Da
Monoisotopic mass	612.23191 Da
Source	ChEBI
InChIKey	YJQPYGGHQPGBLI-KGSXXDOSSA-N

SMILES

CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](Oc2ccc3c(O)c(NC(=O)c4ccc(O)c(CC=C(C)C)c4)c(=O)oc3c2C)OC1(C)C

InChI

InChI=1S/C31H36N2O11/c1-14(2)7-8-16-13-17(9-11-19(16)34)27(37)33-21-22(35)18-10-12-20(15(3)24(18)42-28(21)38)41-29-23(36)25(43-30(32)39)26(40-6)31(4,5)44-29/h7,9-13,23,25-26,29,34-36H,8H2,1-6H3,(H2,32,39)(H,33,37)/t23-,25+,26-,29-/m1/s1

Also called

novobiocina (INN)— chebi
novobiocine (INN)— chebi
novobiocinum (INN)— chebi
N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-β-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-chromen-3-yl}-4-hydroxy-3-(3-methylbut-2-en-1-yl)benzamide (EXACT_SYNONYM)— chebi
Novobiocin (EXACT_SYNONYM)— chebi
cathomycin (EXACT_SYNONYM)— aro
streptonivicin (EXACT_SYNONYM)— aro

Cross-references

Equivalent identifiers for this same structure in other resources.

ARO:3000111
cas:303-81-1
drugbank:DB01051
drugcentral:1974
hmdb:HMDB0015185
kegg.compound:C05080
knapsack:C00002487
lincs.smallmolecule:LSM-5910
patent:WO2012049521
patent:WO2012103487
pdb-ccd:NOV
reaxys:1445842
chembl:CHEMBL36506
pubchem.compound:54675769

Activity roles

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

CHEBI:33281 CHEBI:33281
CHEBI:33282 CHEBI:33282

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:3000111`	novobiocin	`antibioticmech:aro-de163f36e9`	2026-08-30
CHEBI	`CHEBI:28368`	novobiocin	`antibioticmech:chebi-e739e10a6f`	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.

aminocoumarin sensitive parE PROTEIN DIRECT_BINDING_TARGET

ARO:3000023

CARD/ARO database assertion; target organism, strain, and assay are not specified. Topoisomerase IV subunit asserted as the aminocoumarin-sensitive target. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000023 (CARD/ARO asserts targeted_by_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)

antibiotic sensitive DNA topoisomerase subunit gyrB PROTEIN DIRECT_BINDING_TARGET

ARO:3000734

CARD/ARO database assertion; target organism, strain, and assay are not specified. ARO explicitly describes ligand binding to gyrase subunit B. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000734 (CARD/ARO asserts targeted_by_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)

aminocoumarin sensitive parY PROTEIN DIRECT_BINDING_TARGET

ARO:3003253

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

ARO:3003253 (CARD/ARO asserts targeted_by_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)

aminocoumarin sensitive gyrB PROTEIN DIRECT_BINDING_TARGET

ARO:3003260

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

ARO:3003260 (CARD/ARO asserts targeted_by_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)

Mechanism summary

Mode of action: NUCLEIC_ACID_SYNTHESIS_INHIBITION host shared target — Assigned from ChEBI role CHEBI:50750 (EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor). ChEBI asserts the role on the compound. The target it names is one the host has too, so the mechanism is true but is not evidence of selectivity — see mode_of_action_target_scope. Not a curator's mechanistic review.

Resistance mechanisms

14 known routes by which microbes resist this compound, grounded in ARO where CARD models them. Grouped by mechanism type — expand a group to see its determinants.

ANTIBIOTIC_EFFLUX 7

ANTIBIOTIC_EFFLUX
Determinant	ARO ID	Organism	Gene families	Evidence
LptD	ARO:3005059	not organism-specific	—	ARO:3005059 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
MdtABC-TolC	ARO:3000787	not organism-specific	—	ARO:3000787 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
MexAB-OprM	ARO:3000386	not organism-specific	—	ARO:3000386 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
MexCD-OprJ	ARO:3000797	not organism-specific	—	ARO:3000797 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
MuxABC-OpmB	ARO:3004076	not organism-specific	—	ARO:3004076 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
abeS	ARO:3000768	not organism-specific	—	ARO:3000768 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
novA	ARO:3002522	not organism-specific	—	ARO:3002522 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)

ANTIBIOTIC_TARGET_ALTERATION 7

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
Bartonella bacilliformis gyrB conferring resistance to aminocoumarin	ARO:3003302	not organism-specific	—	ARO:3003302 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
Escherichia coli gyrB conferring resistance to aminocoumarin	ARO:3003303	not organism-specific	—	ARO:3003303 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
Staphylococcus aureus gyrB conferring resistance to aminocoumarin	ARO:3003301	not organism-specific	—	ARO:3003301 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
Staphylococcus aureus parE conferring resistance to aminocoumarin	ARO:3003314	not organism-specific	—	ARO:3003314 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
Streptomyces rishiriensis parY mutant conferring resistance to aminocoumarin	ARO:3003318	not organism-specific	—	ARO:3003318 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
aminocoumarin-resistant alaS	ARO:3003830	not organism-specific	—	ARO:3003830 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)
aminocoumarin-resistant cysB	ARO:3003840	not organism-specific	—	ARO:3003840 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:3000111 (novobiocin); database assertion, not a primary citation.)

Causal graphs

Evidence-backed mechanism graphs: how the compound reaches its target, what the target does, and how the effect propagates to growth inhibition or death.

Novobiocin inhibits GyrB ATPase-dependent DNA supercoiling MECHANISTIC

Novobiocin binds the amino-terminal coumarin-binding region of bacterial DNA gyrase subunit GyrB, competitively inhibits its ATPase activity, and blocks ATP-dependent DNA supercoiling by gyrase.

Nodes — novobiocin_gyrb_atpase_inhibition
Node	Label	Type	Grounding
`novobiocin`	novobiocin	COMPOUND	`CHEBI:28368`
`gyrb`	bacterial DNA gyrase subunit GyrB	GENE_OR_PROTEIN	`ARO:3000734`
`gyrb_coumarin_binding_domain`	GyrB amino-terminal coumarin-binding domain	STATE	REVIEWED_LABEL_ONLY
`gyrb_atpase_activity`	GyrB ATPase activity	MOLECULAR_FUNCTION	REVIEWED_LABEL_ONLY
`dna_supercoiling`	ATP-dependent DNA supercoiling	BIOLOGICAL_PROCESS	REVIEWED_LABEL_ONLY
`dna_topology_control`	bacterial DNA topology control	BIOLOGICAL_PROCESS	REVIEWED_LABEL_ONLY

Edges — novobiocin_gyrb_atpase_inhibition
Subject	Predicate	Object	Evidence
`novobiocin`	binds	`gyrb_coumarin_binding_domain`	PMID:8065258 (Gilbert and Maxwell mapped coumarin-drug binding to a 24 kDa N-terminal GyrB subdomain.)
`gyrb`	contains	`gyrb_coumarin_binding_domain`	PMID:8065258 (The GyrB 24 kDa amino-terminal fragment retained coumarin-drug binding.)
`gyrb`	enables	`gyrb_atpase_activity`	PMID:6269086 (Purified GyrB carried the ATPase activity inhibited competitively by novobiocin and related coumarins.)
`novobiocin`	inhibits	`gyrb_atpase_activity`	PMID:6269086 (The affinity-purified GyrB study characterized novobiocin as a competitive inhibitor of GyrB ATPase activity.)
`gyrb_atpase_activity`	supports	`dna_supercoiling`	PMID:794878 (Gellert and colleagues showed novobiocin inhibits ATP-dependent DNA supercoiling catalyzed by purified DNA gyrase.)
`dna_supercoiling`	supports	`dna_topology_control`	PMID:794878 (The purified gyrase assays connect GyrB ATPase inhibition to loss of DNA supercoiling.)

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
CURATED_CAUSAL_GRAPH 2026-09-04 · codex · LLM-assisted
Added a PMID-supported causal graph for novobiocin inhibition of GyrB ATPase-dependent DNA supercoiling.

Provenance

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