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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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species

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View more information in the IUPHAR Pharmacology Education Project: fondaparinux

2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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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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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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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
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
serpin family C member 1 Primary target of this compound Hs Activator Activation 7.5 pKd - 1
⤷ pKd 7.5 (Kd 3.2x10-8 M) [1]
Description: Catalyses the inactivation of coagulation proteases by activated antithrombin-III