ContaminantDB: Fondaparinux sodium

Identification Taxonomy Biological Properties Physical Properties Toxicity Profile Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-05-25 18:21:21 UTC

Update Date

2016-11-09 01:17:26 UTC

Accession Number

CHEM022138

Identification

Common Name

Fondaparinux sodium

Class

Small Molecule

Description

A synthetic pentasaccharide which, apart from the O-methyl group at the reducing end of the molecule, consists of monomeric sugar units which are identical to a sequence of five monomeric sugar units that can be isolated after either chemical or enzymatic cleavage of the polymeric glycosaminoglycans heparin and heparan sulfate.

Contaminant Sources

HMDB Contaminants - Urine

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Natural heparin pentasaccharide	ChEBI
Arixtra	HMDB
Quixidar	HMDB
Fondaparinux sodium	MeSH
Fondaparinux	MeSH

Chemical Formula

C₃₁H₄₅N₃Na₁₀O₄₉S₈

Average Molecular Mass

1730.097 g/mol

Monoisotopic Mass

1728.786 g/mol

CAS Registry Number

114870-03-0

IUPAC Name

(2S,3S,4R,5R,6R)-6-{[(2R,3R,4R,5R,6R)-6-{[(2R,3S,4S,5R,6R)-2-carboxy-4-hydroxy-6-{[(2R,3S,4R,5R,6S)-4-hydroxy-6-methoxy-5-(sulfoamino)-2-[(sulfooxy)methyl]oxan-3-yl]oxy}-5-(sulfooxy)oxan-3-yl]oxy}-5-(sulfoamino)-4-(sulfooxy)-2-[(sulfooxy)methyl]oxan-3-yl]oxy}-3-{[(2R,3R,4R,5S,6R)-4,5-dihydroxy-3-(sulfoamino)-6-[(sulfooxy)methyl]oxan-2-yl]oxy}-4,5-dihydroxyoxane-2-carboxylic acid

Traditional Name

SMILES

[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].[Na+].CO[C@H]1O[C@H](COS([O-])(=O)=O)[C@@H](O[C@@H]2O[C@H]([C@@H](O[C@H]3O[C@H](COS([O-])(=O)=O)[C@@H](O[C@@H]4O[C@@H]([C@@H](O[C@H]5O[C@H](COS([O-])(=O)=O)[C@@H](O)[C@H](O)[C@H]5NS([O-])(=O)=O)[C@H](O)[C@H]4O)C(O)=O)[C@H](OS([O-])(=O)=O)[C@H]3NS([O-])(=O)=O)[C@H](O)[C@H]2OS([O-])(=O)=O)C(O)=O)[C@H](O)[C@H]1NS([O-])(=O)=O

InChI Identifier

InChI=1S/C31H53N3O49S8.10Na/c1-69-27-9(33-85(48,49)50)13(37)17(6(74-27)3-71-88(57,58)59)76-31-22(83-91(66,67)68)16(40)21(24(81-31)26(43)44)79-29-10(34-86(51,52)53)19(82-90(63,64)65)18(7(75-29)4-72-89(60,61)62)77-30-15(39)14(38)20(23(80-30)25(41)42)78-28-8(32-84(45,46)47)12(36)11(35)5(73-28)2-70-87(54,55)56;;;;;;;;;;/h5-24,27-40H,2-4H2,1H3,(H,41,42)(H,43,44)(H,45,46,47)(H,48,49,50)(H,51,52,53)(H,54,55,56)(H,57,58,59)(H,60,61,62)(H,63,64,65)(H,66,67,68);;;;;;;;;;/q;10*+1/p-8/t5-,6-,7-,8-,9-,10-,11-,12-,13-,14-,15-,16+,17-,18-,19-,20+,21+,22-,23+,24-,27+,28-,29-,30-,31-;;;;;;;;;;/m1........../s1

InChI Key

XEKSTYNIJLDDAZ-JASSWCPGSA-F

Chemical Taxonomy

Description

belongs to the class of organic compounds known as glutamic acid and derivatives. Glutamic acid and derivatives are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Glutamic acid and derivatives

Alternative Parents

Substituents

Glutamic acid or derivatives
Hippuric acid or derivatives
Hippuric acid
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Aminobenzamide
Aminobenzoic acid or derivatives
Pteridine
Benzamide
Benzoic acid or derivatives
Benzoyl
Aniline or substituted anilines
Tertiary aliphatic/aromatic amine
Dialkylarylamine
Aminopyrimidine
Aralkylamine
Benzenoid
Pyrimidine
Pyrazine
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Heteroaromatic compound
Tertiary amine
Secondary carboxylic acid amide
Carboxamide group
Amino acid
Carboxylic acid
Organoheterocyclic compound
Azacycle
Organic oxygen compound
Primary amine
Carbonyl group
Amine
Organic oxide
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

monocarboxylic acid amide (CHEBI:44185 )
dicarboxylic acid (CHEBI:44185 )
pteridines (CHEBI:44185 )

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	7.91 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-10	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	-3	ChemAxon
Physiological Charge	-10	ChemAxon
Hydrogen Acceptor Count	44	ChemAxon
Hydrogen Donor Count	19	ChemAxon
Polar Surface Area	805.48 Å²	ChemAxon
Rotatable Bond Count	27	ChemAxon
Refractivity	255.85 m³·mol⁻¹	ChemAxon
Polarizability	122.99 Å³	ChemAxon
Number of Rings	5	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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4r-0114900001-9323a38b77102e548f67	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0kci-1117910004-0f7cdb0213b585bc23db	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0ufr-1439300002-2c4abfd1ec89116a6c22	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2547926000-889b28d41cea5344a8d1	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ufs-4529705300-3d451621459930d5825d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0udj-8409300002-3757a2d013ff9afff4ef	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-052r-2001940021-7140eb6c962761a73fab	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-053s-3009710020-535b247611c82a9229f2	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0f76-1292520010-00739c9719c0df91a821	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0000190000-4a6302ca85bfea56626b	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06r2-4500970000-9f6a040b4861e4cda438	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001j-9602212003-79334b82e961eb0610f1	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
1D NMR	13C NMR Spectrum	Not Available	Spectrum