fondaparinux   Click here for help

GtoPdb Ligand ID: 6819

Synonyms: Arixtra®
Approved drug PDB Ligand
fondaparinux is an approved drug (FDA (2001), EMA (2002))
Compound class: Synthetic organic
Comment: Synthetic pentasaccharide Factor Xa inhibitor (via ATIII binding). The ChEMBL and PubChem links given here are without the sodium ions contained in the INN structure of this compound. Database entries include the sodium salt (e.g. PubChem CID 636380).
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2D Structure
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Physico-chemical Properties
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Hydrogen bond acceptors 52
Hydrogen bond donors 19
Rotatable bonds 30
Topological polar surface area 872.52
Molecular weight 1506.95
XLogP -18.67
No. Lipinski's rules broken 3
SMILES / InChI / InChIKey
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Canonical SMILES COC1OC(COS(=O)(=O)O)C(C(C1NS(=O)(=O)O)O)OC1OC(C(=O)O)C(C(C1OS(=O)(=O)O)O)OC1OC(COS(=O)(=O)O)C(C(C1NS(=O)(=O)O)OS(=O)(=O)O)OC1OC(C(=O)O)C(C(C1O)O)OC1OC(COS(=O)(=O)O)C(C(C1NS(=O)(=O)O)O)O
Isomeric SMILES CO[C@H]1O[C@H](COS(=O)(=O)O)[C@H]([C@@H]([C@H]1NS(=O)(=O)O)O)O[C@@H]1O[C@@H](C(=O)O)[C@H]([C@@H]([C@H]1OS(=O)(=O)O)O)O[C@H]1O[C@H](COS(=O)(=O)O)[C@H]([C@@H]([C@H]1NS(=O)(=O)O)OS(=O)(=O)O)O[C@@H]1O[C@H](C(=O)O)[C@H]([C@@H]([C@H]1O)O)O[C@H]1O[C@H](COS(=O)(=O)O)[C@H]([C@@H]([C@H]1NS(=O)(=O)O)O)O
InChI InChI=1S/C31H53N3O49S8/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)/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 KANJSNBRCNMZMV-ABRZTLGGSA-N
Classification Click here for help
Compound class Synthetic organic
Approved drug? Yes (FDA (2001), EMA (2002))
IUPAC Name Click here for help
(2R,3S,4S,5R,6R)-3-{[(2R,3R,4R,5R,6R)-5-{[(2R,3R,4R,5S,6S)-6-carboxy-5-{[(2R,3R,4R,5S,6R)-4,5-dihydroxy-3-(sulfoamino)-6-[(sulfooxy)methyl]oxan-2-yl]oxy}-3,4-dihydroxyoxan-2-yl]oxy}-3-(sulfoamino)-4-(sulfooxy)-6-[(sulfooxy)methyl]oxan-2-yl]oxy}-4-hydroxy-6-{[(2R,3S,4R,5R,6S)-4-hydroxy-6-methoxy-5-(sulfoamino)-2-[(sulfooxy)methyl]oxan-3-yl]oxy}-5-(sulfooxy)oxane-2-carboxylic acid
International Nonproprietary Names Click here for help
INN number INN
7653 fondaparinux sodium
Synonyms Click here for help
Arixtra®
Database Links Click here for help
Specialist databases
Reactome Drug Reactome logo R-ALL-9693054
Reactome Reaction Reactome logo R-HSA-140791, R-HSA-140806, R-HSA-140870, R-HSA-140872
Other databases
CAS Registry No. 114870-03-0
ChEMBL Ligand CHEMBL1201202
DrugBank Ligand DB00569
DrugCentral Ligand 1236
GtoPdb PubChem SID 178103425
PubChem CID 5282448
RCSB PDB Ligand NTO
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Search PubMed clinical trials fondaparinux sodium
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Search UniChem for chemical match using the InChIKey KANJSNBRCNMZMV-ABRZTLGGSA-N
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Wikipedia Fondaparinux