clindamycin

CHEBI:3745 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

A carbohydrate-containing antibiotic that is the semisynthetic derivative of lincomycin, a natural antibiotic. — 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

lincosamide antibioticARO:0000017

Strictly broader compounds or drug classes this molecule belongs to.

carbohydrate-containing antibiotic CHEBI:23007
Label unavailable CHEBI:35275
Label unavailable CHEBI:36683
Label unavailable CHEBI:46770
Label unavailable CHEBI:72588
lincosamide antibiotic ARO:0000017

Chemical structure

Computed structure properties
Charge
Source	ChEBI
InChIKey	KDLRVYVGXIQJDK-AWPVFWJPSA-N

SMILES

[H][C@]1([C@H](NC(=O)[C@@H]2C[C@@H](CCC)CN2C)[C@H](C)Cl)O[C@H](SC)[C@H](O)[C@@H](O)[C@H]1O

InChI

InChI=1S/C18H33ClN2O5S/c1-5-6-10-7-11(21(3)8-10)17(25)20-12(9(2)19)16-14(23)13(22)15(24)18(26-16)27-4/h9-16,18,22-24H,5-8H2,1-4H3,(H,20,25)/t9-,10+,11-,12+,13-,14+,15+,16+,18+/m0/s1

Also called

methyl 7-chloro-6,7,8-trideoxy-6-{[(4R)-1-methyl-4-propyl-L-prolyl]amino}-1-thio-L-threo-α-D-galacto-octopyranoside (EXACT_SYNONYM)— chebi
7(S)-chloro-7-deoxylincomycin (EXACT_SYNONYM)— chebi
7-CDL (EXACT_SYNONYM)— chebi
7-deoxy-7(S)-chlorolincomycin (EXACT_SYNONYM)— chebi
Cleocin (TN) (EXACT_SYNONYM)— chebi
Clindamycin (EXACT_SYNONYM)— chebi
Methyl 7-chloro-6,7,8-trideoxy-6-(1-methyl-trans-4-propyl-L-2-pyrrolidinecarboxamido)-1-thio-L-threo-alpha-D-galacto-octopyranoside (EXACT_SYNONYM)— chebi
CLI (EXACT_SYNONYM)— aro
Chlolincocin (EXACT_SYNONYM)— aro
Chlorlincocin (EXACT_SYNONYM)— aro
Cleocin (EXACT_SYNONYM)— aro
Clindamicina (EXACT_SYNONYM)— aro
Clindamycine (EXACT_SYNONYM)— aro
Clindamycinum (EXACT_SYNONYM)— aro
Clinimycin (EXACT_SYNONYM)— aro
Sobelin (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.

wikipedia.en:Clindamycin

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
ARO	`ARO:0000066`	clindamycin	`antibioticmech:aro-11403b4da5`	2026-08-30
CHEBI	`CHEBI:3745`	clindamycin	`antibioticmech:chebi-9aa5cc907d`	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 peptidyl transferase (23S rRNA) NUCLEIC_ACID DIRECT_BINDING_TARGET

ARO:3000754

CARD/ARO database assertion; target organism, strain, and assay are not specified. 23S rRNA peptidyl-transferase center is asserted as the target. Evidence status: PRIMARY_EVIDENCE_NEEDED. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000754 (CARD/ARO asserts targeted_by_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)

Activity spectrum

Measured or curated activity against specific taxa. A number without a method is not an observation — every row here carries an assay.

3 observations · Browse all observations · Complete record (JSON.gz)

Activity observations
Organism	Activity	MIC	Disk diffusion	Assay	Strain	Sample/genome	Evidence
Staphylococcus aureus NCBITaxon:1280	—	0.5 mg/L	—	Broth microdilution clindamycin MIC; modal MIC reported; interpreted using CLSI 2025 M100 S35.	0701	BioSample SAMN11953851	Evidence Page data (JSON.gz)
Staphylococcus haemolyticus NCBITaxon:1283	—	2.0 mg/L	—	Broth microdilution clindamycin MIC; modal MIC reported; interpreted using CLSI 2025 M100 S35.	0729	BioSample SAMN11953879	Evidence Page data (JSON.gz)
Staphylococcus haemolyticus NCBITaxon:1283	—	2.0 mg/L	—	Broth microdilution clindamycin MIC; modal MIC reported; interpreted using CLSI 2025 M100 S35.	0730	BioSample SAMN11953880	Evidence Page data (JSON.gz)

Resistance mechanisms

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

ANTIBIOTIC_TARGET_ALTERATION 42

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
Clostridioides difficile 23S rRNA with mutation conferring resistance to erythromycin and clindamycin	ARO:3004654	not organism-specific	—	ARO:3004654 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(33)	ARO:3000599	not organism-specific	—	ARO:3000599 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(34)	ARO:3000600	not organism-specific	—	ARO:3000600 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(35)	ARO:3000604	not organism-specific	—	ARO:3000604 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(36)	ARO:3000605	not organism-specific	—	ARO:3000605 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(37)	ARO:3000392	not organism-specific	—	ARO:3000392 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(38)	ARO:3000601	not organism-specific	—	ARO:3000601 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(39)	ARO:3000602	not organism-specific	—	ARO:3000602 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(41)	ARO:3000603	not organism-specific	—	ARO:3000603 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(42)	ARO:3003106	not organism-specific	—	ARO:3003106 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(43)	ARO:3003205	not organism-specific	—	ARO:3003205 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(44)v	ARO:3003971	not organism-specific	—	ARO:3003971 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(47)	ARO:3003908	not organism-specific	—	ARO:3003908 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(48)	ARO:3004094	not organism-specific	—	ARO:3004094 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(49)	ARO:3004626	not organism-specific	—	ARO:3004626 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(50)	ARO:3007032	not organism-specific	—	ARO:3007032 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(51)	ARO:3007033	not organism-specific	—	ARO:3007033 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Erm(52)	ARO:3007041	not organism-specific	—	ARO:3007041 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmA	ARO:3000347	not organism-specific	—	ARO:3000347 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmB	ARO:3000375	not organism-specific	—	ARO:3000375 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmC	ARO:3000250	not organism-specific	—	ARO:3000250 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmD	ARO:3000495	not organism-specific	—	ARO:3000495 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmE	ARO:3000326	not organism-specific	—	ARO:3000326 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmF	ARO:3000498	not organism-specific	—	ARO:3000498 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmG	ARO:3000522	not organism-specific	—	ARO:3000522 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmN	ARO:3000592	not organism-specific	—	ARO:3000592 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmQ	ARO:3000593	not organism-specific	—	ARO:3000593 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmR	ARO:3000594	not organism-specific	—	ARO:3000594 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmT	ARO:3000595	not organism-specific	—	ARO:3000595 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
ErmX	ARO:3000596	not organism-specific	—	ARO:3000596 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Escherichia coli 23S rRNA with mutation conferring resistance to clindamycin	ARO:3004149	not organism-specific	—	ARO:3004149 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
LlmA 23S ribosomal RNA methyltransferase	ARO:3003982	not organism-specific	—	ARO:3003982 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
cfr(B)	ARO:3004649	not organism-specific	—	ARO:3004649 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
cfrA	ARO:3003441	not organism-specific	—	ARO:3003441 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
cipA	ARO:3003907	not organism-specific	—	ARO:3003907 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
clbA	ARO:3002814	not organism-specific	—	ARO:3002814 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
clbB	ARO:3002815	not organism-specific	—	ARO:3002815 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
clbC	ARO:3002816	not organism-specific	—	ARO:3002816 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
clcD	ARO:3004599	not organism-specific	—	ARO:3004599 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
erm(40)	ARO:3004606	not organism-specific	—	ARO:3004606 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
erm(45)	ARO:3004595	not organism-specific	—	ARO:3004595 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
erm(56)	ARO:3007654	not organism-specific	—	ARO:3007654 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)

ANTIBIOTIC_TARGET_PROTECTION 16

ANTIBIOTIC_TARGET_PROTECTION
Determinant	ARO ID	Organism	Gene families	Evidence
Clostridioides difficile cplR	ARO:3007637	not organism-specific	—	ARO:3007637 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Clostridium perfringes cplR	ARO:3007644	not organism-specific	—	ARO:3007644 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
Clostridium sporogenes cplR	ARO:3007645	not organism-specific	—	ARO:3007645 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
lmrC	ARO:3002881	not organism-specific	—	ARO:3002881 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
lsaA	ARO:3000300	not organism-specific	—	ARO:3000300 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
lsaB	ARO:3003111	not organism-specific	—	ARO:3003111 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
lsaC	ARO:3003112	not organism-specific	—	ARO:3003112 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
lsaD	ARO:3005121	not organism-specific	—	ARO:3005121 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
salA	ARO:3003749	not organism-specific	—	ARO:3003749 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
salB	ARO:3007026	not organism-specific	—	ARO:3007026 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
salC	ARO:3007027	not organism-specific	—	ARO:3007027 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
vga(E) Staphylococcus cohnii	ARO:3004715	not organism-specific	—	ARO:3004715 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
vgaA	ARO:3002829	not organism-specific	—	ARO:3002829 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
vgaALC	ARO:3002830	not organism-specific	—	ARO:3002830 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
vgaC	ARO:3002831	not organism-specific	—	ARO:3002831 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
vgaE	ARO:3002833	not organism-specific	—	ARO:3002833 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)

ANTIBIOTIC_INACTIVATION 4

ANTIBIOTIC_INACTIVATION
Determinant	ARO ID	Organism	Gene families	Evidence
LnuH	ARO:3004600	not organism-specific	—	ARO:3004600 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
lnuB	ARO:3002836	not organism-specific	—	ARO:3002836 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
lnuD	ARO:3002838	not organism-specific	—	ARO:3002838 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)
lnuF	ARO:3002839	not organism-specific	—	ARO:3002839 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000066 (clindamycin); database assertion, not a primary citation.)

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 2026-09-10 · seed_from_sources
Re-seeded from updated data/raw/ inventories
CURATED_RESISTANT_TAXA 2026-09-13 · codex · LLM-assisted
Added three stable-URL CDC/FDA AR Isolate Bank Panel 1125 clindamycin-resistant Staphylococcus activity observations for AR-0701, AR-0729, and AR-0730.
STRUCTURED_ACTIVITY_BIOSAMPLE_ACCESSIONS 2026-09-26 · codex · LLM-assisted
Structured BioSample accessions on 3 activity_spectrum observation(s) where evidence notes already named exactly one accession.

Provenance

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

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