clarithromycin

CHEBI:3732 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

The 6-O-methyl ether of erythromycin A, clarithromycin is a macrolide antibiotic used in the treatment of respiratory-tract, skin and soft-tissue infections. It is also used to eradicate Helicobacter pylori in the treatment of peptic ulcer disease. It prevents bacteria from growing by interfering with their protein synthesis. — 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

macrolide antibioticARO:0000000

Strictly broader compounds or drug classes this molecule belongs to.

CHEBI:25105 CHEBI:25105
ARO:0000000 ARO:0000000

Chemical structure

Computed structure properties
Molecular formula	C38H69NO13
Charge	0
Average mass	747.964 Da
Monoisotopic mass	747.47689 Da
Source	ChEBI
InChIKey	AGOYDEPGAOXOCK-KCBOHYOISA-N

SMILES

[H][C@]1(O[C@H]2[C@H](C)[C@@H](O[C@]3([H])O[C@H](C)C[C@H](N(C)C)[C@H]3O)[C@](C)(OC)C[C@@H](C)C(=O)[C@H](C)[C@@H](O)[C@](C)(O)[C@@H](CC)OC(=O)[C@@H]2C)C[C@@](C)(OC)[C@@H](O)[C@H](C)O1

InChI

InChI=1S/C38H69NO13/c1-15-26-38(10,45)31(42)21(4)28(40)19(2)17-37(9,47-14)33(52-35-29(41)25(39(11)12)16-20(3)48-35)22(5)30(23(6)34(44)50-26)51-27-18-36(8,46-13)32(43)24(7)49-27/h19-27,29-33,35,41-43,45H,15-18H2,1-14H3/t19-,20-,21+,22+,23-,24+,25+,26-,27+,29-,30+,31-,32+,33-,35+,36-,37-,38-/m1/s1

Also called

clarithromycina (INN)— chebi
clarithromycine (INN)— chebi
clarithromycinum (INN)— chebi
O6-methylerythromycin (EXACT_SYNONYM)— chebi
6-O-methylerythromycin (EXACT_SYNONYM)— chebi
6-O-methylerythromycin A (EXACT_SYNONYM)— chebi
CLA (EXACT_SYNONYM)— chebi
CLARITHROMYCIN (EXACT_SYNONYM)— chebi
Clarithromycin (EXACT_SYNONYM)— chebi
Biaxin (EXACT_SYNONYM)— aro
CLR (EXACT_SYNONYM)— aro
Clambiotic (EXACT_SYNONYM)— aro
Clarith (EXACT_SYNONYM)— aro
Clathromycin (EXACT_SYNONYM)— aro
Klacid (EXACT_SYNONYM)— aro
Klaricid (EXACT_SYNONYM)— aro
Macladin (EXACT_SYNONYM)— aro
Naxy (EXACT_SYNONYM)— aro
Veclam (EXACT_SYNONYM)— aro

Cross-references

Equivalent identifiers for this same structure in other resources.

ARO:0000065
cas:81103-11-9
drugbank:DB01211
drugcentral:668
kegg.compound:C06912
kegg.drug:D00276
lincs.smallmolecule:LSM-5606
lipidmaps:LMPK04000014
patent:EP41355
patent:US4331803
pdb-ccd:CTY
reaxys:3581974
chembl:CHEMBL1741
pubchem.compound:84029

Activity roles

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

CHEBI:33281 CHEBI:33281
CHEBI:36047 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:0000065`	clarithromycin	`antibioticmech:aro-5c92a4ddc8`	2026-08-30
CHEBI	`CHEBI:3732`	clarithromycin	`antibioticmech:chebi-e63133b2eb`	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.

50S ribosomal subunit P-site RIBOSOMAL_SUBUNIT DIRECT_BINDING_TARGET

ARO:3000757

CARD/ARO database assertion; target organism, strain, and assay are not specified. The 50S P-site is asserted as the target site. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000757 (CARD/ARO asserts targeted_by_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)

Mechanism summary

Mode of action: PROTEIN_SYNTHESIS_INHIBITION microbial target — CURATOR: Confirmed as bacterial 50S macrolide-site inhibition after primary clarithromycin mechanism review. PMID:9425251; PMID:34935599.
Clinical status: APPROVED

Resistance mechanisms

44 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_TARGET_ALTERATION 35

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
Erm(33)	ARO:3000599	not organism-specific	—	ARO:3000599 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Erm(34)	ARO:3000600	not organism-specific	—	ARO:3000600 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Erm(35)	ARO:3000604	not organism-specific	—	ARO:3000604 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Erm(36)	ARO:3000605	not organism-specific	—	ARO:3000605 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Erm(37)	ARO:3000392	not organism-specific	—	ARO:3000392 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Erm(38)	ARO:3000601	not organism-specific	—	ARO:3000601 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Erm(39)	ARO:3000602	not organism-specific	—	ARO:3000602 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Erm(41)	ARO:3000603	not organism-specific	—	ARO:3000603 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Erm(50)	ARO:3007032	not organism-specific	—	ARO:3007032 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Erm(51)	ARO:3007033	not organism-specific	—	ARO:3007033 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmA	ARO:3000347	not organism-specific	—	ARO:3000347 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmB	ARO:3000375	not organism-specific	—	ARO:3000375 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmC	ARO:3000250	not organism-specific	—	ARO:3000250 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmD	ARO:3000495	not organism-specific	—	ARO:3000495 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmE	ARO:3000326	not organism-specific	—	ARO:3000326 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmF	ARO:3000498	not organism-specific	—	ARO:3000498 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmG	ARO:3000522	not organism-specific	—	ARO:3000522 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmN	ARO:3000592	not organism-specific	—	ARO:3000592 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmQ	ARO:3000593	not organism-specific	—	ARO:3000593 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmR	ARO:3000594	not organism-specific	—	ARO:3000594 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmT	ARO:3000595	not organism-specific	—	ARO:3000595 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
ErmX	ARO:3000596	not organism-specific	—	ARO:3000596 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Escherichia coli 23S rRNA with mutation conferring resistance to clarithromycin	ARO:3004160	not organism-specific	—	ARO:3004160 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin	ARO:3004134	not organism-specific	—	ARO:3004134 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Mycobacterium avium 23S rRNA with mutation conferring resistance to clarithromycin	ARO:3004164	not organism-specific	—	ARO:3004164 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Mycobacterium intracellulare 23S rRNA with mutation conferring resistance to clarithromycin	ARO:3004166	not organism-specific	—	ARO:3004166 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Mycobacterium kansasii 23S rRNA with mutation conferring resistance to clarithromycin	ARO:3004168	not organism-specific	—	ARO:3004168 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Mycobacteroides abscessus 23S rRNA with mutation conferring resistance to clarithromycin	ARO:3004163	not organism-specific	—	ARO:3004163 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Mycobacteroides chelonae 23S rRNA with mutation conferring resistance to clarithromycin	ARO:3004165	not organism-specific	—	ARO:3004165 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Mycolicibacterium smegmatis 23S rRNA with mutation conferring resistance to clarithromycin	ARO:3004169	not organism-specific	—	ARO:3004169 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Mycoplasma hominis 23S rRNA with mutation conferring resistance to macrolide antibiotics	ARO:3004176	not organism-specific	—	ARO:3004176 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
Mycoplasmopsis fermentans 23S rRNA with mutation conferring resistance to macrolide antibiotics	ARO:3004177	not organism-specific	—	ARO:3004177 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
erm(40)	ARO:3004606	not organism-specific	—	ARO:3004606 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
erm(46)	ARO:3004596	not organism-specific	—	ARO:3004596 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
erm(55)	ARO:3009647	not organism-specific	—	ARO:3009647 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)

ANTIBIOTIC_INACTIVATION 8

ANTIBIOTIC_INACTIVATION
Determinant	ARO ID	Organism	Gene families	Evidence
EreA	ARO:3000361	not organism-specific	—	ARO:3000361 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
EreB	ARO:3000363	not organism-specific	—	ARO:3000363 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
mphA	ARO:3000316	not organism-specific	—	ARO:3000316 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
mphB	ARO:3000318	not organism-specific	—	ARO:3000318 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
mphC	ARO:3000319	not organism-specific	—	ARO:3000319 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
mphF	ARO:3003071	not organism-specific	—	ARO:3003071 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
mphG	ARO:3003742	not organism-specific	—	ARO:3003742 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)
mphL	ARO:3003072	not organism-specific	—	ARO:3003072 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); database assertion, not a primary citation.)

ANTIBIOTIC_EFFLUX 1

ANTIBIOTIC_EFFLUX
Determinant	ARO ID	Organism	Gene families	Evidence
lmrP	ARO:3003969	not organism-specific	—	ARO:3003969 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000065 (clarithromycin); 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.

Clarithromycin blocks the bacterial 50S exit tunnel MECHANISTIC

Clarithromycin binds the macrolide site in the bacterial 50S nascent-peptide exit tunnel, restricting translation elongation and reducing protein synthesis.

Nodes — clarithromycin_50s_exit_tunnel_inhibition
Node	Label	Type	Grounding
`clarithromycin`	clarithromycin	COMPOUND	`CHEBI:3732`
`ribosomal_50s_macrolide_site`	bacterial 50S nascent-peptide exit tunnel macrolide site	RNA	REVIEWED_LABEL_ONLY
`clarithromycin_bound_50s`	clarithromycin-bound 50S exit tunnel	STATE	REVIEWED_LABEL_ONLY
`translation_elongation`	bacterial translation elongation	BIOLOGICAL_PROCESS	REVIEWED_LABEL_ONLY
`protein_synthesis`	bacterial protein synthesis	BIOLOGICAL_PROCESS	REVIEWED_LABEL_ONLY

Edges — clarithromycin_50s_exit_tunnel_inhibition
Subject	Predicate	Object	Evidence
`clarithromycin`	binds	`clarithromycin_bound_50s`	PMID:34935599 (Zhang and colleagues resolved Mycobacterium tuberculosis 50S subunits with bound clarithromycin and observed drug interactions in the 50S tunnel.)
`ribosomal_50s_macrolide_site`	participates in	`clarithromycin_bound_50s`	PMID:34935599 (The clarithromycin-bound 50S cryo-EM structure localizes the drug in the mycobacterial large-subunit exit tunnel.)
`clarithromycin_bound_50s`	decreases	`translation_elongation`	PMID:9425251 (Champney and Burdine measured clarithromycin-dependent inhibition of translation in Staphylococcus aureus cells.)
`translation_elongation`	supports	`protein_synthesis`	PMID:9425251 (The cellular clarithromycin study measured translation inhibition as a protein-synthesis endpoint.)

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
RESEEDED_FROM_SOURCES 2026-08-31 · 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 clarithromycin binding to the bacterial 50S macrolide site.

Provenance

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