Heparin Pentasaccharide
(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-(sulfooxymethyl)oxan-3-yl]oxy-5-sulfooxyoxan-3-yl]oxy-5-(sulfoamino)-4-sulfooxy-2-(sulfooxymethyl)oxan-3-yl]oxy-3-[(2R,3R,4R,5S,6R)-4,5-dihydroxy-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-4,5-dihydroxyoxane-2-carboxylic acid
Molecular Identity
Heparin Pentasaccharide
(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-(sulfooxymethyl)oxan-3-yl]oxy-5-sulfooxyoxan-3-yl]oxy-5-(sulfoamino)-4-sulfooxy-2-(sulfooxymethyl)oxan-3-yl]oxy-3-[(2R,3R,4R,5S,6R)-4,5-dihydroxy-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-4,5-dihydroxyoxane-2-carboxylic acid
PubChem CID: 5282448
Fondaparinux is 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. It has a role as an anticoagulant. It is an amino sugar, an oligosaccharide sulfate and a pentasaccharide derivative. It is functionally related to a normethylfondaparinux. It is a conjugate acid of a fondaparinux(10-).
2D Structure
Properties
C31H53N3O49S8
Molecular Formula
1508.30
Molecular Weight
g/mol
1506.9513
Exact Mass
Da
-14.7
XLogP
Drug-like (Lipinski: < 5)
873
TPSA
May have limited oral absorption
19
H-Bond Donors
52
H-Bond Acceptors
3450
Complexity
SMILES
Canonical SMILES
SMILES: COC1C(C(C(C(O1)COS(=O)(=O)O)OC2C(C(C(C(O2)C(=O)O)OC3C(C(C(C(O3)COS(=O)(=O)O)OC4C(C(C(C(O4)C(=O)O)OC5C(C(C(C(O5)COS(=O)(=O)O)O)O)NS(=O)(=O)O)O)O)OS(=O)(=O)O)NS(=O)(=O)O)O)OS(=O)(=O)O)O)NS(=O)(=O)OIsomeric SMILES
SMILES: CO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)COS(=O)(=O)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](O2)C(=O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)COS(=O)(=O)O)O[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)C(=O)O)O[C@@H]5[C@@H]([C@H]([C@@H]([C@H](O5)COS(=O)(=O)O)O)O)NS(=O)(=O)O)O)O)OS(=O)(=O)O)NS(=O)(=O)O)O)OS(=O)(=O)O)O)NS(=O)(=O)OSynonyms(20)
Fondaparinux104993-28-4Heparin pentasaccharideNatural heparin pentasaccharideORG31540 free acidORG-31540 free acidJ177FOW5JLCHEBI:61033SR 901107ASR-901107ADTXSID10146903methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranosyl-(1->4)-beta-D-glucopyranuronosyl-(1->4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranosyl-(1->4)-2-O-sulfo-alpha-L-idopyranuronosyl-(1->4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranosideIC 85158RefChem:55228DTXCID9069394
Data from PubChem (NCBI)
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