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.

CHEBI:23007 CHEBI:23007
CHEBI:35275 CHEBI:35275
CHEBI:36683 CHEBI:36683
CHEBI:46770 CHEBI:46770
CHEBI:72588 CHEBI:72588
ARO:0000017 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

Equivalent identifiers for this same structure in other resources.

ARO:0000066
cas:18323-44-9
drugbank:DB01190
drugcentral:678
hmdb:HMDB0015321
kegg.compound:C06914
kegg.drug:D00277
pdb-ccd:CLY
reaxys:5624049
wikipedia.en:Clindamycin
chembl:CHEMBL1753
pubchem.compound:446598

Activity roles

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

CHEBI:33281 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.)

Resistance mechanisms

62 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 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

Provenance

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