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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:50 UTC
Update Date2020-02-26 21:40:05 UTC
HMDB IDHMDB0014653
Secondary Accession Numbers
  • HMDB14653
Metabolite Identification
Common NameVancomycin
DescriptionVancomycin 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.
Structure
Data?1582753204
Synonyms
ValueSource
(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 acidChEBI
(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
VancocinChEBI
VancomicinChEBI
VancomicinaChEBI
VancomycineChEBI
VancomycinumChEBI
(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-carboxylateGenerator
(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 acidGenerator
(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-carboxylateGenerator
(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-carboxylateGenerator
(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 acidGenerator
(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 HCLHMDB
AB-vancomycinHMDB
Azupharma brand OF vancomycin hydrochlorideHMDB
Combino brand OF vancomycin hydrochlorideHMDB
MIP brand OF vancomycin hydrochlorideHMDB
Norman brand OF vancomycin hydrochlorideHMDB
Vanco azupharmaHMDB
Vanco-saarHMDB
Vancomicina chiesiHMDB
Vancomycin lillyHMDB
Vancomycin phosphate (1:2)HMDB
Cell pharm brand OF vancomycin hydrochlorideHMDB
Chiesi brand OF vancomycin hydrochlorideHMDB
Vanco-cellHMDB
Vancomicina abbottHMDB
Vancomycin phosphate (1:2), decahydrateHMDB
Vancomycin-ratiopharmHMDB
Vancomycine dakotaHMDB
Abbott brand OF vancomycin hydrochlorideHMDB
DiatracinHMDB
Hexal brand OF vancomycin hydrochlorideHMDB
Lilly brand OF vancomycin hydrochlorideHMDB
Sulfate, vancomycinHMDB
Vancomicina normanHMDB
Dakota brand OF vancomycin hydrochlorideHMDB
Dista brand OF vancomycin hydrochlorideHMDB
Eli lilly brand OF vancomycin hydrochlorideHMDB
Hydrochloride, vancomycinHMDB
Vancocin HCLHMDB
VancocineHMDB
Vancomicina combino pharHMDB
Vancomycin hexalHMDB
Vancomycin hydrochlorideHMDB
Vancomycin sulfateHMDB
Curasan brand OF vancomycin hydrochlorideHMDB
Ratiopharm brand OF vancomycin hydrochlorideHMDB
Chemical FormulaC66H75Cl2N9O24
Average Molecular Weight1449.254
Monoisotopic Molecular Weight1447.430199787
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[26.14.2.2³,⁶.2¹⁴,¹⁷.1⁸,¹².1²⁹,³³.0¹⁰,²⁵.0³⁴,³⁹]pentaconta-3,5,8,10,12(48),14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylic acid
Traditional Namevancomycin
CAS Registry Number1404-90-6
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 KeyMYPYJXKWCTUITO-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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentCyclic 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 FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

Disposition

Route of exposure:

Biological location:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.22 g/LNot Available
LogP-3.1Not Available
Predicted Properties
PropertyValueSource
Water Solubility0.22 g/LALOGPS
logP1.11ALOGPS
logP-4.4ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)2.99ChemAxon
pKa (Strongest Basic)9.93ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count24ChemAxon
Hydrogen Donor Count19ChemAxon
Polar Surface Area530.49 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity346.61 m³·mol⁻¹ChemAxon
Polarizability138.7 ųChemAxon
Number of Rings10ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
LC-MS/MSLC-MS/MS Spectrum - DI-ESI-Ion Trap , Positivesplash10-00di-2901000023-e1b4c2a4d54a44d851b1Spectrum
LC-MS/MSLC-MS/MS Spectrum - DI-ESI-Hybrid FT , Positivesplash10-00di-2901000023-e1b4c2a4d54a44d851b1Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0f8c-1923700000-67a86ecb329876118249Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ufu-2921000000-029bb9d69d210833797cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-8920000000-971cf434a71ef3cbb223Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0h0d-2823900000-fe4b7f6b1b8574952eaaSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ox-3911100000-0b893eaecbca11b8af4eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-03dl-3900000000-03d8e77b98241f93c67dSpectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00512 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00512 details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00512
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00016052
Chemspider ID14253
KEGG Compound IDC06689
BioCyc IDCPD-12245
BiGG IDNot Available
Wikipedia LinkVancomycin
METLIN IDNot Available
PubChem Compound14969
PDB IDNot Available
ChEBI ID28001
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
References
Synthesis Reference# Boger DL. Vancomycin, teicoplanin, and ramoplanin: synthetic and mechanistic studies. Med Res Rev. 2001 Sep;21(5):356-81. 'Pubmed':http://www.ncbi.nlm.nih.gov/pubmed/11579438
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Small PM, Chambers HF: Vancomycin for Staphylococcus aureus endocarditis in intravenous drug users. Antimicrob Agents Chemother. 1990 Jun;34(6):1227-31. [PubMed:2393284 ]
  2. Cantu TG, Yamanaka-Yuen NA, Lietman PS: Serum vancomycin concentrations: reappraisal of their clinical value. Clin Infect Dis. 1994 Apr;18(4):533-43. [PubMed:8038306 ]
  3. Schafer M, Schneider TR, Sheldrick GM: Crystal structure of vancomycin. Structure. 1996 Dec 15;4(12):1509-15. [PubMed:8994975 ]
  4. Gonzalez C, Rubio M, Romero-Vivas J, Gonzalez M, Picazo JJ: Bacteremic pneumonia due to Staphylococcus aureus: A comparison of disease caused by methicillin-resistant and methicillin-susceptible organisms. Clin Infect Dis. 1999 Nov;29(5):1171-7. [PubMed:10524959 ]
  5. Sivagnanam S, Deleu D: Red man syndrome. Crit Care. 2003 Apr;7(2):119-20. Epub 2002 Dec 23. [PubMed:12720556 ]
  6. Levine DP: Vancomycin: a history. Clin Infect Dis. 2006 Jan 1;42 Suppl 1:S5-12. [PubMed:16323120 ]

Transporters

General function:
Involved in ion transmembrane transporter activity
Specific function:
Involved in the renal elimination of endogenous and exogenous organic anions. Functions as organic anion exchanger when the uptake of one molecule of organic anion is coupled with an efflux of one molecule of endogenous dicarboxylic acid (glutarate, ketoglutarate, etc). Mediates the sodium-independent uptake of 2,3-dimercapto-1-propanesulfonic acid (DMPS). Mediates the sodium-independent uptake of p- aminohippurate (PAH), ochratoxin (OTA), acyclovir (ACV), 3'-azido- 3-'deoxythymidine (AZT), cimetidine (CMD), 2,4-dichloro- phenoxyacetate (2,4-D), hippurate (HA), indoleacetate (IA), indoxyl sulfate (IS) and 3-carboxy-4-methyl-5-propyl-2- furanpropionate (CMPF), cidofovir, adefovir, 9-(2- phosphonylmethoxyethyl) guanine (PMEG), 9-(2- phosphonylmethoxyethyl) diaminopurine (PMEDAP) and edaravone sulfate. PAH uptake is inhibited by p- chloromercuribenzenesulphonate (PCMBS), diethyl pyrocarbonate (DEPC), sulindac, diclofenac, carprofen, glutarate and okadaic acid. PAH uptake is inhibited by benzothiazolylcysteine (BTC), S-chlorotrifluoroethylcysteine (CTFC), cysteine S-conjugates S-dichlorovinylcysteine (DCVC), furosemide, steviol, phorbol 12-myristate 13-acetate (PMA), calcium ionophore A23187, benzylpenicillin, furosemide, indomethacin, bumetamide, losartan, probenecid, phenol red, urate, and alpha-ketoglutarate
Gene Name:
SLC22A6
Uniprot ID:
Q4U2R8
Molecular weight:
61815.8
References
  1. Jariyawat S, Sekine T, Takeda M, Apiwattanakul N, Kanai Y, Sophasan S, Endou H: The interaction and transport of beta-lactam antibiotics with the cloned rat renal organic anion transporter 1. J Pharmacol Exp Ther. 1999 Aug;290(2):672-7. [PubMed:10411577 ]