Vancomycin

Athanor · official

C₆₆H₇₅Cl₂N₉O₂₄ · 1449.2 g/mol

IUPAC name: (1S,2R,18R,19R,22S,25R,28R,40S)-48-[(2S,3R,4S,5S,6R)-3-[(2S,4S,5S,6S)-4-amino-5-hydroxy-4,6-dimethyloxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-22-(2-amino-2-oxoethyl)-5,15-dichloro-2,18,32,35,37-pentahydroxy-19-[[(2R)-4-methyl-2-(methylamino)pentanoyl]amino]-20,23,26,42,44-pentaoxo-7,13-dioxa-21,24,27,41,43-pentazaoctacyclo[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(39),35,37,46,49-pentadecaene-40-carboxylic acid

Also called Vancocin, glycopeptide antibiotic, MRSA, cell wall inhibitor

Drugs

Open in Athanor

Drawn from its SMILES with RDKit

DangerMay cause allergy or asthma symptoms or breathing difficulties if inhaled

Names and identifiers

IUPAC name: (1S,2R,18R,19R,22S,25R,28R,40S)-48-[(2S,3R,4S,5S,6R)-3-[(2S,4S,5S,6S)-4-amino-5-hydroxy-4,6-dimethyloxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-22-(2-amino-2-oxoethyl)-5,15-dichloro-2,18,32,35,37-pentahydroxy-19-[[(2R)-4-methyl-2-(methylamino)pentanoyl]amino]-20,23,26,42,44-pentaoxo-7,13-dioxa-21,24,27,41,43-pentazaoctacyclo[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(39),35,37,46,49-pentadecaene-40-carboxylic acid
Synonyms: Vancocin, glycopeptide antibiotic, MRSA
+ 39 more
cell wall inhibitor, Vancomicina, Vancomycine, Vancomycinum, 6Q205EH1VU, DTXSID0042664, CHEBI:28001, Vancocin HCL, Vancomycin Lilly, Sulfate, Vancomycin, RefChem:6345, A07AA09, J01XA01, S01AA28, DTXCID401031367, 215-772-6, (1S,2R,18R,19R,22S,25R,28R,40S)-48-(((2S,3R,4S,5S,6R)-3-(((2S,4S,5S,6S)-4-amino-5-hydroxy-4,6-dimethyloxan-2-yl)oxy)-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy)-22-(carbamoylmethyl)-5,47-dichloro-2,18,32,35,37-pentahydroxy-19-((2R)-4-methyl-2-(methylamino)pentanamido)-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-3,5,8,10,12(48),14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylic acid, (1S,2R,18R,19R,22S,25R,28R,40S)-48-((2S,3R,4S,5S,6R)-3-((2S,4S,5S,6S)-4-amino-5-hydroxy-4,6-dimethyloxan-2-yl)oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy-22-(2-amino-2-oxoethyl)-5,15-dichloro-2,18,32,35,37-pentahydroxy-19-(((2R)-4-methyl-2-(methylamino)pentanoyl)amino)-20,23,26,42,44-pentaoxo-7,13-dioxa-21,24,27,41,43-pentazaoctacyclo(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(39),35,37,46,49-pentadecaene-40-carboxylic acid, Vancocine, Vancomycin EP Impurity I, CHEMBL262777, MFCD05664587, C66H75Cl2N9O24, Vancomycin ( >85%), Vancomycin (USP), Vancomycine [INN-French], Vancomycinum [INN-Latin], Vancomicina [INN-Spanish], HSDB 3262, EINECS 215-772-6, vancomicin, vanomycin, UNII-6Q205EH1VU, Vancomycin [USP:INN:BAN], Vancomycin hydrochloride from Streptomyces orientalis, Viomycin derivative, [(2S,3R,4S,5S,6R)-3-[(2S,4S,5S,6S)-4-amino-5-hydroxy-4,6-dimethyl-tetrahydropyran-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-(2-amino-2-oxo-ethyl)-dichloro-pentahydroxy-[[(2R)-4-methyl-2-(methylamino)pentanoyl]amino]-pentaoxo-[?]carboxylic acid, Vancomycin Impurity M, Vancomycin (Standard)
Molecular formula: C₆₆H₇₅Cl₂N₉O₂₄
Empirical formula: C₆₆H₇₅Cl₂N₉O₂₄
Molecular weight: 1449.2 g/mol
Exact mass: 1447.43020
CAS number: 1404-90-6
PubChem CID: 14969
Canonical SMILES: CC1C(C(CC(O1)OC2C(C(C(OC2OC3=C4C=C5C=C3OC6=C(C=C(C=C6)C(C(C(=O)NC(C(=O)NC5C(=O)NC7C8=CC(=C(C=C8)O)C9=C(C=C(C=C9O)O)C(NC(=O)C(C(C1=CC(=C(O4)C=C1)Cl)O)NC7=O)C(=O)O)CC(=O)N)NC(=O)C(CC(C)C)NC)O)Cl)CO)O)O)(C)N)O
Isomeric SMILES: C[C@H]1[C@H]([C@@](C[C@@H](O1)O[C@@H]2[C@H]([C@@H]([C@H](O[C@H]2OC3=C4C=C5C=C3OC6=C(C=C(C=C6)[C@H]([C@H](C(=O)N[C@H](C(=O)N[C@H]5C(=O)N[C@@H]7C8=CC(=C(C=C8)O)C9=C(C=C(C=C9O)O)[C@H](NC(=O)[C@H]([C@@H](C1=CC(=C(O4)C=C1)Cl)O)NC7=O)C(=O)O)CC(=O)N)NC(=O)[C@@H](CC(C)C)NC)O)Cl)CO)O)O)(C)N)O
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
InChIKey: MYPYJXKWCTUITO-LYRMYLQWSA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Physical properties

pKa: pka1 = 2.6[1]
6 values
Only one source reports it.
Value As written Source
–shown pka1 = 2.6 [1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
– pKa2 = 7.2 [1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
– pKa3 = 8.6 [1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
– pKa4 = 9.6 [1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
– pKa5 = 10.5 [1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
– pKa6 = 11.7 [1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)

Value	As written	Source
–shown	pka1 = 2.6	[1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
–	pKa2 = 7.2	[1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
–	pKa3 = 8.6	[1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
–	pKa4 = 9.6	[1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
–	pKa5 = 10.5	[1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)
–	pKa6 = 11.7	[1] Hazardous Substances Data Bank (HSDB)cites PMID:16570623 Dodd MC et al; Environ Sci Technol 40: 1969-77 (2006)

Each value as its source reports it, with the source's number after it (listed under References). Where several sources report a property, the row shows the value most of them agree on, the rule the app uses; open the values to see every one.

Calculated

Heavy atoms: 101
Rings: 12
Aromatic rings: 5
Fraction sp³ carbons (Fsp3): 0.42
H-bond donors: 19
H-bond acceptors: 25 computed here · PubChem 26
Rotatable bonds: 13
TPSA (Å²): 530.5 computed here · PubChem 530
Formal charge: 0
XLogP3: -2.6 PubChem
Complexity: 2960 PubChem
Stereocenters: 18 definedCIP: C3: R · C11: S · C12: R · C32: R · C34: S · C38: R · C42: R · C46: S · C69: S · C78: S · C80: R · C83: S
Double-bond geometry: None specified
Point group: C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

C54.70%
H5.22%
Cl4.89%
N8.70%
O26.49%

Isotope pattern

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P: 0.11 Crippen (Wildman and Crippen 1999)
log S (water solubility): -8.25 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 8.21 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 1449.27
log P ≤ 5 (Crippen): 0.11
H-bond donors ≤ 5: 19
H-bond acceptors ≤ 10: 25

Breaks 3 of the four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

Danger

Most widely reported: 72 company reports to ECHA. Source [2].

Health hazard

H334May cause allergy or asthma symptoms or breathing difficulties if inhaled (95.8% of reports)

Precautionary statements: P233, P260, P271, P284, P304+P340, P342+P316, P403, P501

Storage

Store in a tight, light-resistant container as defined in the usp-nf. This material should be handled and stored per label instructions to ensure product integrity. Store in a freezer. (vancomycin hydrochloride)[1]
Commercially available vancomycin hydrochloride capsules and powder for IV administration should be stored at 15 - 30 °C.[1]

Safety data sheets on the supplier’s page: Accela ChemBio Inc., Angene Chemical, DC Chemicals.

Always read the supplier’s safety data sheet before working with it.

Spectra

Experimental spectra held by these sources; each link opens the source's own record.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

[1]Hazardous Substances Data Bank (HSDB) · Public domain (US NLM) · via PubChem · retrieved 2026-10-14
[2]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
[3]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
[4]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
[5]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
·Literature on PubChem

Data last updated 2026-10-14.