vancomycin

CHEBI:28001 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. — 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

glycopeptide antibioticARO:3000081

Strictly broader compounds or drug classes this molecule belongs to.

Label unavailable CHEBI:24396
glycopeptide antibiotic ARO:3000081

Chemical structure

Computed structure properties
Molecular formula	C66H75Cl2N9O24
Charge	0
Average mass	1449.271 Da
Monoisotopic mass	1447.4302 Da
Source	ChEBI
InChIKey	MYPYJXKWCTUITO-LYRMYLQWSA-N

SMILES

CN[C@H](CC(C)C)C(=O)N[C@H]1C(=O)N[C@@H](CC(N)=O)C(=O)N[C@H]2C(=O)N[C@H]3C(=O)N[C@H](C(=O)N[C@H](C(=O)O)c4cc(O)cc(O)c4-c4cc3ccc4O)[C@H](O)c3ccc(c(Cl)c3)Oc3cc2cc(c3O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O[C@H]2C[C@](C)(N)[C@H](O)[C@H](C)O2)Oc2ccc(cc2Cl)[C@H]1O

InChI

InChI=1S/C66H75Cl2N9O24/c1-23(2)12-34(71-5)58(88)76-49-51(83)26-7-10-38(32(67)14-26)97-40-16-28-17-41(55(40)101-65-56(54(86)53(85)42(22-78)99-65)100-44-21-66(4,70)57(87)24(3)96-44)98-39-11-8-27(15-33(39)68)52(84)50-63(93)75-48(64(94)95)31-18-29(79)19-37(81)45(31)30-13-25(6-9-36(30)80)46(60(90)77-50)74-61(91)47(28)73-59(89)35(20-43(69)82)72-62(49)92/h6-11,13-19,23-24,34-35,42,44,46-54,56-57,65,71,78-81,83-87H,12,20-22,70H2,1-5H3,(H2,69,82)(H,72,92)(H,73,89)(H,74,91)(H,75,93)(H,76,88)(H,77,90)(H,94,95)/t24-,34+,35-,42+,44-,46+,47+,48-,49+,50-,51+,52+,53+,54-,56+,57+,65-,66-/m0/s1

Also called

Vancocin (BRAND_NAME)— chebi
vancomicina (INN)— chebi
vancomycine (INN)— chebi
vancomycinum (INN)— chebi
(3S,6R,7R,11R,23S,26S,30aS,36R,38aR)-44-[2-O-(3-amino-2,3,6-trideoxy-3-C-methyl-α-L-lyxo-hexopyranosyl)-β-D-glucopyranosyloxy]-3-(carbamoylmethyl)-10,19-dichloro-2,3,4,5,6,7,23,25,26,36,37,38,38a-tetradecahydro-7,22,28,30,32-pentahydroxy-6-(N-methyl-D-leucyl)-2,5,24,38,39-pentaoxo-1H,22H-23,36-(epiminomethano)-8,11:18,21-dietheno-13,16:31,35-di(metheno)[1,6,9]oxadiazacyclohexadecino[4,5-m][10,2,16]benzoxadiazacyclotetracosine-26-carboxylic acid (EXACT_SYNONYM)— chebi
(1S,2R,18R,22S,25R,28R,40S)-22-(2-amino-2-oxoethyl)-48-[2-O-(3-amino-2,3,6-trideoxy-3-methyl-α-L-lyxo-hexopyranosyl)-β-D-glucopyranosyloxy]-5,15-dichloro-2,18,32,35,37-pentahydroxy-19-[(N-methyl-D-leucyl)amino]-20,23,26,42,44-pentaoxo-7,13-dioxa-21,24,27,41,43-pentaazaoctacyclo[26.14.2.23,6.214,17.18,12.129,33.010,25.034,39]pentaconta-3,5,8(48),9,11,14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylic acid (EXACT_SYNONYM)— chebi
(2.2Sp,3.5Sa,2.6Sp)-O4.2,C3.4:C5.4,O4.6:C3.5,C2.7-tricyclo[N-methyl-D-leucyl-3-chloro-(R)-β-hydroxy-D-tyrosyl-L-asparaginyl-D-2-(4-{[2-O-(3-amino-2,3,6-trideoxy-3-C-methyl-α-L-lyxo-hexopyranosyl)-β-D-glucopyranosyl]oxy}phenyl)glycyl-D-2-(4-hydroxyphenyl)glycyl-3-chloro-(R)-β-hydroxy-L-tyrosyl-L-2-(3,5-dihydroxyphenyl)glycine] (EXACT_SYNONYM)— chebi
VANCOMYCIN (EXACT_SYNONYM)— chebi
Vancomycin (EXACT_SYNONYM)— chebi
vancomicin (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.

Patents and articles

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

Activity roles

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

antimicrobial agent CHEBI:33281
antibacterial drug 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:0000028`	vancomycin	`antibioticmech:aro-aab2a8f06b`	2026-08-30
CHEBI	`CHEBI:28001`	vancomycin	`antibioticmech:chebi-b6a7496b60`	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.

acyl-D-alanyl-D-alanine CELL_WALL_COMPONENT ATTACKED_COMPONENT

ARO:3000720

CARD/ARO database assertion; target organism, strain, and assay are not specified. The D-Ala-D-Ala chemical group is bound as a cell-wall precursor component. Evidence status: DATABASE_ASSERTION_ONLY. Source: CARD_ARO 2026-08-30 (retrieved 2026-08-30).

ARO:3000720 (CARD/ARO asserts targeted_by_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)

Mechanism summary

Clinical status: APPROVED

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
Enterococcus faecalis NCBITaxon:1351	—	>64.0 mg/L	—	Broth microdilution vancomycin MIC; modal MIC reported; interpreted using CLSI 2025 M100 S35.	0781	BioSample SAMN15040080	Evidence Page data (JSON.gz)
Enterococcus faecalis NCBITaxon:1351	—	32.0 mg/L	—	Broth microdilution vancomycin MIC; modal MIC reported; interpreted using CLSI 2025 M100 S35.	0782	BioSample SAMN15040081	Evidence Page data (JSON.gz)
Enterococcus faecium NCBITaxon:1352	—	64.0 mg/L	—	Broth microdilution vancomycin MIC; modal MIC reported; interpreted using CLSI 2025 M100 S35.	0783	BioSample SAMN15040082	Evidence Page data (JSON.gz)

Resistance mechanisms

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

ANTIBIOTIC_TARGET_ALTERATION 23

ANTIBIOTIC_TARGET_ALTERATION
Determinant	ARO ID	Organism	Gene families	Evidence
Clostridioides difficile murG with mutation conferring resistance to vancomycin	ARO:3004561	not organism-specific	—	ARO:3004561 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
Clostridioides difficile rpoC with mutation conferring resistance to vancomycin	ARO:3004681	not organism-specific	—	ARO:3004681 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
D-Ala-D-Ala ligase	ARO:3003970	not organism-specific	—	ARO:3003970 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
DSY3690-associated vancomycin resistance in native Desulfitobacterium hafniense Y51 Native resistance and separate recombinant-ligase biochemistry support the proposed target-alteration route, not isolated DSY3690 necessity or sufficiency. UniProtKB:Q24R63 is locus-matched reference context only; DSY1579/UniProtKB:Q24X74 is the distinct biochemical comparator. No exact experimental protein, allele or genome is assigned. AP008230.1 and its sample are reference context, not an assay-genome assignment.	—	Desulfitobacterium hafniense `NCBITaxon:49338` strain Y51 `NCBITaxon:138119` DSY3690	VanA-like ligase	PMID:19414574 (Publisher native susceptibility Results, locus identification and separate biochemical Results/Table 2; qualitative finding only.) Disk diffusion and Etest
VanM-cluster-associated vancomycin resistance in native Efm-HS0661 Native-isolate phenotype and precursor analysis support a cluster-associated target-alteration route, not isolated VanM sufficiency. UniProtKB:B8XGS3 and FJ349556.1 are source-bound ligase references only; CP039730.1 belongs to a different isolate. No exact experimental protein, allele or genome is assigned. Laboratory-recipient findings are not assigned here.	ARO:3000256	Enterococcus faecium `NCBITaxon:1352` strain Efm-HS0661	vanM	PMID:20733041 (Publisher Table 1, native-isolate Results, precursor analysis and accession statement; qualitative finding only.) Etest
cfr(D)	ARO:3005021	not organism-specific	—	ARO:3005021 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanA	ARO:3000236	not organism-specific	—	ARO:3000236 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanB	ARO:3000238	not organism-specific	—	ARO:3000238 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanC	ARO:3000246	not organism-specific	—	ARO:3000246 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanD	ARO:3000253	not organism-specific	—	ARO:3000253 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanE	ARO:3000259	not organism-specific	—	ARO:3000259 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanF	ARO:3000255	not organism-specific	—	ARO:3000255 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanG	ARO:3000257	not organism-specific	—	ARO:3000257 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanI	ARO:3003722	not organism-specific	—	ARO:3003722 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanL	ARO:3000260	not organism-specific	—	ARO:3000260 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanM	ARO:3000256	not organism-specific	—	ARO:3000256 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanN	ARO:3002917	not organism-specific	—	ARO:3002917 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster VanO	ARO:3002918	not organism-specific	—	ARO:3002918 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
glycopeptide resistance gene cluster vanP	ARO:3007187	not organism-specific	—	ARO:3007187 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
murG transferase	ARO:3004560	not organism-specific	—	ARO:3004560 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
vanD cluster-associated vancomycin resistance in 10/96A Native phenotype and precursor evidence support a cluster-associated route, not isolated VanD sufficiency. UniProtKB:Q9EZQ9/AY082011 is source-bound reference context. Other native strains and laboratory-host findings are not merged with 10/96A. No exact experimental protein, allele or genome is assigned.	—	Enterococcus faecium `NCBITaxon:1352` strain 10/96A	vanD	PMID:12499162 (Native Table 2, Results and AY082011 accession statement; Table 2 assay footnote. Qualitative finding only.) MIC determination (Steers et al. method)
vanE cluster-associated vancomycin resistance in BM4405 Native precursor evidence supports a cluster-associated route, not isolated ligase sufficiency. UniProtKB:Q9S4K1 is a fragment reference, not a complete experimental protein. No exact experimental protein, allele or genome is assigned.	—	Enterococcus faecalis `NCBITaxon:1351` strain BM4405	vanE	PMID:10471558 (Native Results and precursor Table 2; susceptibility assay and accession statement. Qualitative finding only.) Agar dilution
vanN cluster-associated vancomycin resistance in UCN71 Native precursor evidence supports a cluster-associated route, not isolated ligase sufficiency. Further characterization used UCN71 only; it is not assigned to UCN72. UniProtKB:G4XFK8/JF802084 is reference context; its AB701345 link belongs to isolate 121.1, not UCN71. Laboratory recipients remain separate. No exact experimental protein, allele or genome is assigned.	—	Enterococcus faecium `NCBITaxon:1352` strain UCN71	vanN	PMID:21807981 (Native Results, precursor Table 4 and accession statement; susceptibility assay. Qualitative finding only.) Broth microdilution

ANTIBIOTIC_EFFLUX 2

ANTIBIOTIC_EFFLUX
Determinant	ARO ID	Organism	Gene families	Evidence
VRA-F	ARO:3007843	not organism-specific	—	ARO:3007843 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)
mlaFEDB	ARO:3005058	not organism-specific	—	ARO:3005058 (CARD/ARO asserts confers_resistance_to_antibiotic ARO:0000028 (vancomycin); database assertion, not a primary citation.)

UNKNOWN 2

UNKNOWN
Determinant	ARO ID	Organism	Gene families	Evidence
vanE co-occurrence with source-reported vancomycin resistance in N00-410 Same-isolate co-occurrence is retained without transferring BM4405 precursor findings. ENA replaces AF430807 with FJ872411, supporting reference context for UniProtKB:Q93A46. Source N00-410 and reference N00-0410 labels are preserved separately; archive succession does not prove allele equality. No exact experimental protein, allele or genome is assigned.	—	Enterococcus faecalis `NCBITaxon:1351` strain N00-410	vanE	PMID:12019119 (Native susceptibility and locus findings; accession statement; induction data not shown. Qualitative finding only.) Etest
vanL co-occurrence with source-reported vancomycin resistance in N06-0364 The source reports low-level resistance with vanL but explicitly leaves functionality unproven. This is co-occurrence, not a demonstrated biochemical route or a new clinical category. UniProtKB:A9LN35 is reference context only. No exact experimental protein, allele or genome is assigned.	—	Enterococcus faecalis `NCBITaxon:1351` strain N06-0364	vanL	PMID:18458129 (Native susceptibility, locus findings and final functionality caveat; induction data not shown. Qualitative finding only.) Broth microdilution and Etest

Producer organisms

Organisms that biosynthesize this compound. Cluster link evidence is how the upstream source graded the gene cluster, so it is populated only for a source that grades it. An empty cell is not weaker support: a curator-authored producer carries its support in Evidence instead. Where the source entry named several compounds, the evidence is marked inherited, meaning it covers this compound together with the cluster's other products rather than singling it out. Those products need not be related to each other: a cluster can list an intermediate, a precursor and a finished antibiotic side by side.

Producer organisms
Organism	BGC	Cluster link evidence	Source	Quality	Note	Evidence
Amycolatopsis orientalis NCBITaxon:1156913 strain HCCB10007 (ATCC43491)	BGC0000455	Knock-out studies compound specific	MIBIG 4.0.1 (entry 6); reviewed	questionable	MIBiG active entry; compound 'vancomycin' joined by exact Standard InChIKey.	DOI:10.1021/ja00361a029 (MIBiG attaches this reference to the compound, as support for its STRUCTURE: every compound-level method in the release is structure elucidation (NMR, mass spectrometry, X-ray, total synthesis). It establishes what the molecule is. It is NOT evidence that this organism produces it; MIBiG attaches no reference to the producer link at all.)

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
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RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
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RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
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RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
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RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
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RESEEDED_FROM_SOURCES 2026-09-03 · seed_from_sources
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RESEEDED_FROM_SOURCES 2026-09-08 · seed_from_sources
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RESEEDED_FROM_SOURCES 2026-09-08 · seed_from_sources
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RESEEDED_FROM_SOURCES 2026-09-08 · seed_from_sources
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RESEEDED_FROM_SOURCES 2026-09-10 · seed_from_sources
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CURATED_RESISTANT_TAXA 2026-09-12 · codex · LLM-assisted
Added three stable-URL CDC/FDA AR Isolate Bank vancomycin-resistant Enterococcus faecalis/faecium isolate MIC observations.
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.
CURATED_RESISTANCE_EVIDENCE 2026-10-10 · codex · LLM-assisted
Added two primary-supported native vancomycin resistance claims with species/strain taxonomy and explicitly reference-only UniProt context. Kept VanM cluster evidence, Y51 native phenotype, recombinant biochemistry and comparator identity distinct. Preserved prior assertions and all other fields; whole-record review remains open.
CURATED_RESISTANCE_EVIDENCE 2026-10-10 · codex · LLM-assisted
Added five qualitative native vancomycin findings with species taxonomy and reference-only UniProt context. Distinguished three precursor-supported cluster routes from two gene/phenotype co-occurrences; preserved explicit functional uncertainty and archive succession without exact allele assignments. Preserved all previous claims, observations and other fields; whole-record review remains open.

Provenance

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

Explore across X-Mech: MediaIngredientMech (vancomycin) · CultureMech · NaturalProductMech · PathwayMech · TraitMech · TaxonMech (Amycolatopsis orientalis)