ContaminantDB: Vancomycin

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References Targets (1)XML

Record Information

Version

1.0

Creation Date

2009-07-30 17:59:13 UTC

Update Date

2026-05-14 16:40:52 UTC

Accession Number

CHEM002536

Identification

Common Name

Vancomycin

Class

Small Molecule

Description

Vancomycin is only found in individuals that have used or taken this drug. It is an antibacterial obtained from Streptomyces orientalis. It is a glycopeptide related to ristocetin that inhibits bacterial cell wall assembly and is toxic to kidneys and the inner ear. [PubChem]The bactericidal action of vancomycin results primarily from inhibition of cell-wall biosynthesis. Specifically, vancomycin prevents incorporation of N-acetylmuramic acid (NAM)- and N-acetylglucosamine (NAG)-peptide subunits from being incorporated into the peptidoglycan matrix; which forms the major structural component of Gram-positive cell walls. The large hydrophilic molecule is able to form hydrogen bond interactions with the terminal D-alanyl-D-alanine moieties of the NAM/NAG-peptides. Normally this is a five-point interaction. This binding of vancomycin to the D-Ala-D-Ala prevents the incorporation of the NAM/NAG-peptide subunits into the peptidoglycan matrix. In addition, vancomycin alters bacterial-cell-membrane permeability and RNA synthesis. There is no cross-resistance between vancomycin and other antibiotics. Vancomycin is not active in vitro against gram-negative bacilli, mycobacteria, or fungi.

Contaminant Sources

HMDB Contaminants - Urine
STOFF IDENT Compounds
T3DB toxins

Contaminant Type

Amine
Anti-Bacterial Agent
Drug
Ether
Glycopeptide Antibacterial
Metabolite
Organic Compound
Organochloride
Synthetic Compound

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(1S,2R,18R,22S,25R,28R,40S)-22-(2-Amino-2-oxoethyl)-48-[2-O-(3-amino-2,3,6-trideoxy-3-methyl-alpha-L-lyxo-hexopyranosyl)-beta-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[26.14.2.2(3,6).2(14,17).1(8,12).1(29,33).0(10,25).0(34,39)]pentaconta-3,5,8(48),9,11,14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylic acid	ChEBI
(2.2Sp,3.5Sa,2.6Sp)-O(4.2),C(3.4):C(5.4),O(4.6):c(3.5),C(2.7)-tricyclo[N-methyl-D-leucyl-3-chloro-(R)-beta-hydroxy-D-tyrosyl-L-asparaginyl-D-2-(4-{[2-O-(3-amino-2,3,6-trideoxy-3-C-methyl-alpha-L-lyxo-hexopyranosyl)-beta-D-glucopyranosyl]oxy}phenyl)glycyl-D-2-(4-hydroxyphenyl)glycyl-3-chloro-(R)-beta-hydroxy-L-tyrosyl-L-2-(3,5-dihydroxyphenyl)glycine]	ChEBI
Vancocin	ChEBI
Vancomicin	ChEBI
Vancomicina	ChEBI
Vancomycine	ChEBI
Vancomycinum	ChEBI
(1S,2R,18R,22S,25R,28R,40S)-22-(2-Amino-2-oxoethyl)-48-[2-O-(3-amino-2,3,6-trideoxy-3-methyl-a-L-lyxo-hexopyranosyl)-b-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[26.14.2.2(3,6).2(14,17).1(8,12).1(29,33).0(10,25).0(34,39)]pentaconta-3,5,8(48),9,11,14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylate	Generator
(1S,2R,18R,22S,25R,28R,40S)-22-(2-Amino-2-oxoethyl)-48-[2-O-(3-amino-2,3,6-trideoxy-3-methyl-a-L-lyxo-hexopyranosyl)-b-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[26.14.2.2(3,6).2(14,17).1(8,12).1(29,33).0(10,25).0(34,39)]pentaconta-3,5,8(48),9,11,14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylic acid	Generator
(1S,2R,18R,22S,25R,28R,40S)-22-(2-Amino-2-oxoethyl)-48-[2-O-(3-amino-2,3,6-trideoxy-3-methyl-alpha-L-lyxo-hexopyranosyl)-beta-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[26.14.2.2(3,6).2(14,17).1(8,12).1(29,33).0(10,25).0(34,39)]pentaconta-3,5,8(48),9,11,14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylate	Generator
(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[26.14.2.2(3,6).2(14,17).1(8,12).1(29,33).0(10,25).0(34,39)]pentaconta-3,5,8(48),9,11,14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylate	Generator
(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[26.14.2.2(3,6).2(14,17).1(8,12).1(29,33).0(10,25).0(34,39)]pentaconta-3,5,8(48),9,11,14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylic acid	Generator
(2.2Sp,3.5Sa,2.6Sp)-O(4.2),C(3.4):C(5.4),O(4.6):c(3.5),C(2.7)-tricyclo[N-methyl-D-leucyl-3-chloro-(R)-b-hydroxy-D-tyrosyl-L-asparaginyl-D-2-(4-{[2-O-(3-amino-2,3,6-trideoxy-3-C-methyl-a-L-lyxo-hexopyranosyl)-b-D-glucopyranosyl]oxy}phenyl)glycyl-D-2-(4-hydroxyphenyl)glycyl-3-chloro-(R)-b-hydroxy-L-tyrosyl-L-2-(3,5-dihydroxyphenyl)glycine]	Generator
(2.2Sp,3.5Sa,2.6Sp)-O(4.2),C(3.4):C(5.4),O(4.6):c(3.5),C(2.7)-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]	Generator
Vancomycin HCL	HMDB
AB-vancomycin	HMDB
Azupharma brand OF vancomycin hydrochloride	HMDB
Combino brand OF vancomycin hydrochloride	HMDB
MIP brand OF vancomycin hydrochloride	HMDB
Norman brand OF vancomycin hydrochloride	HMDB
Vanco azupharma	HMDB
Vanco-saar	HMDB
Vancomicina chiesi	HMDB
Vancomycin lilly	HMDB
Vancomycin phosphate (1:2)	HMDB
Cell pharm brand OF vancomycin hydrochloride	HMDB
Chiesi brand OF vancomycin hydrochloride	HMDB
Vanco-cell	HMDB
Vancomicina abbott	HMDB
Vancomycin phosphate (1:2), decahydrate	HMDB
Vancomycin-ratiopharm	HMDB
Vancomycine dakota	HMDB
Abbott brand OF vancomycin hydrochloride	HMDB
Diatracin	HMDB
Hexal brand OF vancomycin hydrochloride	HMDB
Lilly brand OF vancomycin hydrochloride	HMDB
Sulfate, vancomycin	HMDB
Vancomicina norman	HMDB
Dakota brand OF vancomycin hydrochloride	HMDB
Dista brand OF vancomycin hydrochloride	HMDB
Eli lilly brand OF vancomycin hydrochloride	HMDB
Hydrochloride, vancomycin	HMDB
Vancocin HCL	HMDB
Vancocine	HMDB
Vancomicina combino phar	HMDB
Vancomycin hexal	HMDB
Vancomycin hydrochloride	HMDB
Vancomycin sulfate	HMDB
Curasan brand OF vancomycin hydrochloride	HMDB
Ratiopharm brand OF vancomycin hydrochloride	HMDB

Chemical Formula

C₆₆H₇₅Cl₂N₉O₂₄

Average Molecular Mass

1449.254 g/mol

Monoisotopic Mass

1447.430 g/mol

CAS Registry Number

1404-90-6

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-(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[26.14.2.2^{3,6}.2^{14,17}.1^{8,12}.1^{29,33}.0^{10,25}.0^{34,39}]pentaconta-3,5,8,10,12(48),14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylic acid

Traditional Name

vancomycin

SMILES

CN[C@H](CC(C)C)C(=O)N[C@@H]1[C@H](O)C2=CC=C(OC3=C(O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O[C@H]4C[C@](C)(N)[C@H](O)[C@H](C)O4)C4=CC(=C3)[C@@H](NC(=O)[C@H](CC(N)=O)NC1=O)C(=O)N[C@@H]1C3=CC(=C(O)C=C3)C3=C(O)C=C(O)C=C3[C@H](NC(=O)[C@@H](NC1=O)[C@H](O)C1=CC(Cl)=C(O4)C=C1)C(O)=O)C(Cl)=C2

InChI Identifier

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

InChI Key

MYPYJXKWCTUITO-LYRMYLQWSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Cyclic peptides

Alternative Parents

Substituents

Aminoglycoside core
Cyclic alpha peptide
Phenolic glycoside
O-glycosyl compound
Glycosyl compound
Disaccharide
Diaryl ether
Alpha-amino acid or derivatives
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Amino saccharide
Oxane
Benzenoid
Aryl chloride
Aryl halide
Cyclic carboximidic acid
Secondary alcohol
Amino acid
1,2-aminoalcohol
Amino acid or derivatives
Acetal
Oxacycle
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid
Azacycle
Secondary aliphatic amine
Organoheterocyclic compound
Organic 1,3-dipolar compound
Ether
Propargyl-type 1,3-dipolar organic compound
Monocarboxylic acid or derivatives
Secondary amine
Polyol
Organic oxide
Organopnictogen compound
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Primary aliphatic amine
Alcohol
Organic oxygen compound
Organohalogen compound
Organochloride
Organonitrogen compound
Organooxygen compound
Primary amine
Amine
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

glycopeptide (CHEBI:28001 )

Biological Properties

Status

Detected and Not Quantified

Origin

Exogenous

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Applications

Biological Roles

Chemical Roles

Not Available

Physical Properties

State

Liquid

Appearance

Clear solution.

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	2.25e-01 g/L

Predicted Properties

Property	Value	Source
Water Solubility	0.22 g/L	ALOGPS
logP	1.11	ALOGPS
logP	-4.4	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	2.99	ChemAxon
pKa (Strongest Basic)	9.93	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	24	ChemAxon
Hydrogen Donor Count	19	ChemAxon
Polar Surface Area	530.49 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	346.61 m³·mol⁻¹	ChemAxon
Polarizability	138.7 Å³	ChemAxon
Number of Rings	10	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
LC-MS/MS	LC-MS/MS Spectrum - DI-ESI-Ion Trap , Positive	splash10-00di-2901000023-e1b4c2a4d54a44d851b1	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - DI-ESI-Hybrid FT , Positive	splash10-00di-2901000023-e1b4c2a4d54a44d851b1	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0f8c-1923700000-67a86ecb329876118249	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ufu-2921000000-029bb9d69d210833797c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-8920000000-971cf434a71ef3cbb223	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0h0d-2823900000-fe4b7f6b1b8574952eaa	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01ox-3911100000-0b893eaecbca11b8af4e	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-03dl-3900000000-03d8e77b98241f93c67d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0211900000-f24779f1d821404377b6	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udu-2978300000-a0525e253b6b74e02fe2	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-03dl-9400000001-6c5351c29770dd239a4b	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0561-0514900000-39f639f12190a86270f2	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dr-2017900000-0c61b2f71bf19d9c7d4f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-015c-9314000000-bf2ff9546716a688f6d5	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum

Toxicity Profile

Route of Exposure

Poorly absorbed from gastrointestinal tract, however systemic absorption may occur following IV administration.

Mechanism of Toxicity

The bactericidal action of vancomycin results primarily from inhibition of cell-wall biosynthesis. Specifically, vancomycin prevents incorporation of N-acetylmuramic acid (NAM)- and N-acetylglucosamine (NAG)-peptide subunits from being incorporated into the peptidoglycan matrix; which forms the major structural component of Gram-positive cell walls. The large hydrophilic molecule is able to form hydrogen bond interactions with the terminal D-alanyl-D-alanine moieties of the NAM/NAG-peptides. Normally this is a five-point interaction. This binding of vancomycin to the D-Ala-D-Ala prevents the incorporation of the NAM/NAG-peptide subunits into the peptidoglycan matrix. In addition, vancomycin alters bacterial-cell-membrane permeability and RNA synthesis. There is no cross-resistance between vancomycin and other antibiotics. Vancomycin is not active in vitro against gram-negative bacilli, mycobacteria, or fungi.

Metabolism

Free toxin may be removed by opsonization via the reticuloendothelial system (primarily the liver and kidneys) or it may be degraded through cellular internalization via the lysosomes. Lysosomes are membrane-enclosed organelles that contain an array of digestive enzymes, including several proteases. Route of Elimination: In the first 24 hours, about 75% of an administered dose of vancomycin is excreted in urine by glomerular filtration. Half Life: Half-life in normal renal patients is approximately 6 hours (range 4 to 11 hours). In the first 24 hours, about 75% of an administered dose of vancomycin is excreted in urine by glomerular filtration. In anephric patients, the average half-life of elimination is 7.5 days.

Toxicity Values

LD50: 5000 mg/kg (Oral, Mouse) (1) LD50: 319 mg/kg (Intravenous, Rat) (1) LD50: 400 mg/kg (Intravenous, Mouse) (1)

Lethal Dose

Not Available

Carcinogenicity (IARC Classification)

No indication of carcinogenicity to humans (not listed by IARC).

Uses/Sources

Vancomycin is indicated for the treatment of serious or severe infections caused by susceptible strains of methicillin-resistant (beta-lactam-resistant) staphylococci.

Minimum Risk Level

Not Available

Health Effects

Renal failure, principally manifested by increased serum creatinine or BUN concentrations, especially in patients administered large doses of vancomycin, has been reported rarely. A few dozen cases of hearing loss associated with vancomycin have been reported. Reversible neutropenia, usually starting 1 week or more after onset of therapy with vancomycin or after a total dosage of more than 25 g, has been reported for several dozen patients.

Symptoms

Inflammation at the injection site has been reported. During or soon after rapid infusion of vancomycin, patients may develop anaphylactoid reactions, including hypotension, wheezing, dyspnea, urticaria, or pruritus. Rapid infusion may also cause flushing of the upper body ("red neck") or pain and muscle spasm of the chest and back. These reactions usually resolve within 20 minutes but may persist for several hours. Such events are infrequent if vancomycin is given by a slow infusion over 60 minutes. In studies of normal volunteers, infusion-related events did not occur when vancomycin was administered at a rate of 10 mg/min or less.

Treatment

Supportive care is advised, with maintenance of glomerular filtration. Vancomycin is poorly removed by dialysis. (8)

Concentrations

Not Available

External Links

DrugBank ID

DB00512

HMDB ID

HMDB0014653

FooDB ID

Not Available

Phenol Explorer ID