ChemFOnt: Showing chemical card for Vancomycin (CFc000009010)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 18:56:01 UTC

Chemfont ID

CFc000009010

Molecule Identification

Common Name

Vancomycin

Definition

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.

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 Weight

1449.254

Monoisotopic Molecular Weight

1447.430199787

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 Name

vancomycin

CAS Registry Number

1404-90-6

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 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 )

Functional Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Source

Exogenous

Exogenous (HMDB: HMDB0014653)

Process

Not Available

Role

Industrial application

Pharmaceutical industry

Antimicrobial agent

Antibiotic (HMDB: HMDB0014653)

Antibacterial drug (HMDB: HMDB0014653)

Physical Properties

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	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0014653

DrugBank ID

DB00512

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Vancomycin

METLIN ID

Not Available

PubChem Compound

14969

PDB ID

Not Available

ChEBI ID

28001

Food Biomarker Ontology

Not Available

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

Showing chemical card for Vancomycin (CFc000009010)

MOL for CFc000009010 (Vancomycin)

3D MOL for CFc000009010 (Vancomycin)

3D SDF for CFc000009010 (Vancomycin)

3D-SDF for CFc000009010 (Vancomycin)

PDB for CFc000009010 (Vancomycin)

3D PDB for CFc000009010 (Vancomycin)

SMILES for CFc000009010 (Vancomycin)

INCHI for CFc000009010 (Vancomycin)

Structure for CFc000009010 (Vancomycin)

3D Structure for CFc000009010 (Vancomycin)