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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View more information in the IUPHAR Pharmacology Education Project: fondaparinux

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
References
1. Paolucci F, Claviés MC, Donat F, Necciari J. (2002)
Fondaparinux sodium mechanism of action: identification of specific binding to purified and human plasma-derived proteins.
Clin Pharmacokinet, 41 Suppl 2: 11-8. [PMID:12383040]