Fondaparinux

Summary

Fondaparinux (CHEMBL1201202) is an approved oligosaccharide anticoagulant (ATC B01AX05) targeting SERPINC1; indicated across 13 conditions including thrombotic disease and venous thromboembolism.

At a glance

• Status: Approved (max clinical phase 4)
• Modality: Oligosaccharide
• ATC class: B01AX05
• Targets: 1 (SERPINC1)
• Indications: 13 conditions
• Clinical trials: 38
• Chemistry: 1508.3 Da · C31H53N3O49S8

Identifiers

Drug identity and classification

Field	Value
ChEMBL ID	CHEMBL1201202
Name	Fondaparinux
Type	Oligosaccharide
Max phase	4
FDA approved	yes
PubChem CID	5282448
ChEBI	CHEBI:61033
ATC	B01AX05
Molecular formula	C31H53N3O49S8
Molecular weight	1508.3
InChIKey	KANJSNBRCNMZMV-ABRZTLGGSA-N

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)O

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-(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

ChEBI definition: 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.

Pharmacological roles (ChEBI): anticoagulant.

Also known as: Fondaparinux, ORG-31540 FREE ACID, ORG31540 FREE ACID, SR 901107A, SR-901107A, FONDAPARINUX

Parent form; salt/anhydrous children: CHEMBL1200644

Patent coverage: 63 distinct patent families (140 SureChEMBL compound mentions), from 1 matched compound structure(s). Mentions count patents naming the compound (not distinct inventions), so promiscuous / reference molecules inflate the mention figure — families are the dedup metric.

Targets

Targets

Primary targets (GtoPdb curated mechanism): the Cancer dependency column is the DepMap CRISPR fitness signal (% of screened cell lines dependent on the target).

Gene	Target	Action	pAffinity	Cancer dependency	UniProt
SERPINC1	serpin family C member 1	Activation	7.49	0%	P01008

Broader ChEMBL bioactivity targets: 1 (assay-derived). Sample: Coagulation factor X.

Bioactivity

ChEMBL activities: 1 potent at pChembl ≥ 5 of 1 total. Top 30 by potency (10 = 0.1 nM, 6 = 1 µM):

Target	pChembl	Type	Value	Unit	Activity ID
F10	7.96	IC50	11	nM	CHEMBL_ACT_19011076

Target pathways

Aggregated over 1 target gene(s): SERPINC1.

Top Reactome pathways

12 total, by targets touching each:

Pathway	Targets	Genes
Hemostasis	1	SERPINC1
R-HSA-140837	1	SERPINC1
R-HSA-140875	1	SERPINC1
R-HSA-140877	1	SERPINC1
Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)	1	SERPINC1
Metabolism of proteins	1	SERPINC1
Post-translational protein modification	1	SERPINC1
Post-translational protein phosphorylation	1	SERPINC1
Fibrin formation	1	SERPINC1
Initiation of coagulation cascade	1	SERPINC1
Regulation of clotting cascade	1	SERPINC1
Amplification and propagation of coagulation cascade	1	SERPINC1

Dominant GO biological processes

GO term	Targets
blood coagulation	1
regulation of blood coagulation	1
hemostasis	1

Indications & clinical

Indications

13 indications (1 at ChEMBL trial phase 4). Phase below is the highest clinical-trial phase recorded for this drug against each disease — not the molecule’s overall approval status (that is in the Summary).

Indication	Trial phase	MONDO	EFO
thrombotic disease	4	MONDO:0000831	HP:0004419
venous thromboembolism	3	MONDO:0005399	EFO:0004286
acute coronary syndrome	3	MONDO:0005542	EFO:0005672
atrial fibrillation	2	MONDO:0004981	EFO:0000275
viral pneumonia	2	MONDO:0006012	EFO:0007541
respiratory failure	2	MONDO:0021113	EFO:0009686
thrombocytopenia	2	MONDO:0002049	HP:0001873
severe acute respiratory syndrome	2	MONDO:0005091	MONDO:0100096
morbid obesity	1	MONDO:0005139	EFO:0001074
ovarian carcinoma	1	MONDO:0005140	EFO:0001075
kidney failure	1	MONDO:0001106	HP:0000083

2 further indication records had no mapped disease name (EFO/MeSH-only) or were duplicates, and are omitted.

Clinical trials

Total trials: 38.

Phase distribution

Phase	Trials
Not specified	13
PHASE4	8
PHASE3	8
PHASE1	4
PHASE2	3
PHASE2/PHASE3	1
EARLY_PHASE1	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT00377091	PHASE4	WITHDRAWN	Is Using Fondaparinux (Blood Thinner) to Treat Lung Clot Cheaper Than Traditional Therapy
NCT00555438	PHASE4	COMPLETED	Prospective, Multicentre, Open-label Study Evaluating 1.5 mg/Day of Fondaparinux.
NCT00603824	PHASE4	WITHDRAWN	Fondaparinux in Patients With Acute Heparin-Induced Thrombocytopenia (HIT)
NCT00909064	PHASE4	COMPLETED	The Effects of Arixtra on Wound Drainage Following Total Joint Arthroplasty
NCT00927602	PHASE4	TERMINATED	Fondaparinux 1,5 mg for the Prevention of Venous Thromboembolism (VTE) in Medical Patients With Renal Insufficiency
NCT01467583	PHASE4	COMPLETED	Fondaparinux in Critically Ill Patients With Renal Failure
NCT01727401	PHASE4	TERMINATED	Thromboprophylaxis of Venous Thromboembolism in Acutely-ill Medical Inpatients With Thrombocytopenia
NCT04447378	PHASE4	COMPLETED	Safety of Fondaparinux as Post Partum Thromboprophylaxis
NCT07228663	PHASE3	NOT_YET_RECRUITING	Hip Fracture Surgery Arterial and Venous Thrombotic Events Prevention
NCT00139815	PHASE3	COMPLETED	Michelangelo - Oasis 5
NCT00320398	PHASE3	COMPLETED	Total Hip Replacement Study Of GSK576428 (Fondaparinux Sodium)
NCT00320424	PHASE3	COMPLETED	Hip Fracture Study of GSK576428 (Fondaparinux Sodium)
NCT00474591	PHASE3	UNKNOWN	Fondaparinux to Prevent Thrombotic Complications and Graft Failure in Patients Undergoing Coronary Artery Bypass Graft Surgery: The Fonda CABG Study
NCT00493896	PHASE3	TERMINATED	Safety of Fondaparinux as Routine VTE Prophylaxis in Medical ICU Patients
NCT00881088	PHASE2/PHASE3	UNKNOWN	Prophylaxis of Thromboembolic Complications Trial: Thromboprophylaxis Needed in Below Knee Plaster Cast Immobilization for Ankle and Foot Fractures
NCT01499953	PHASE3	COMPLETED	Superficial Vein Thrombosis (SVT) Treated With Rivaroxaban Versus Fondaparinux
NCT01857583	PHASE3	COMPLETED	Safety and Pharmacokinetics Study of DU-176b Administered to Patients With Severe Renal Impairment Undergoing Orthopedic Surgery of The Lower Limbs
NCT00673439	PHASE2	TERMINATED	Fondaparinux for the Treatment of Heparin-Induced Thrombocytopenia (HIT)
NCT00911300	PHASE2	COMPLETED	Evaluation of Fondaparinux in Patients With a Heart Rhythm Disturbance Who Undergo Restoration of Normal Heart Rhythm
NCT04368377	PHASE2	COMPLETED	Enhanced Platelet Inhibition in Critically Ill Patients With COVID-19
NCT00346879	PHASE1	WITHDRAWN	Study to Determine Effective Dosing of Fondaparinux in Obese Persons
NCT00412464	PHASE1	COMPLETED	Pilot Dose Finding and Pharmacokinetic Study of Fondaparinux in Children With Thrombosis
NCT00659399	PHASE1	WITHDRAWN	Feasibility Study of Short Term Fondaparinux (Arixtra) in Chemotherapy-Pretreated Ovarian Carcinoma Patients at High Risk of Progression
NCT01121770	PHASE1	COMPLETED	Pharmacokinetic Study of Fondaparinux in Inpatients With Renal Dysfunction
NCT00894283	EARLY_PHASE1	COMPLETED	Comparing Enoxaparin to Fondaparinux to Prevent Venous Thromboembolism (VTE) in Bariatric Surgical Patients
NCT00378027	Not specified	WITHDRAWN	Arixtra PE Study- Outpatient Management of Stable Acute Pulmonary Embolism: Once Daily Subcutaneous Fondaparinux
NCT00413504	Not specified	COMPLETED	Fondaparinux as Monotherapy for DVT and/or Pulmonary Embolism
NCT00483600	Not specified	WITHDRAWN	Pharmacokinetic Study of Fondaparinux in Outpatients With Renal Dysfunction
NCT00789399	Not specified	TERMINATED	A Study of the Efficacy of Preventive Dosing of Fondaparinux Sodium Versus Placebo for the Prevention of Venous Thromboembolism (VTE) in Patients Undergoing Coronary Bypass Surgery Receiving Routine Mechanical Prophylaxis
NCT01004939	Not specified	COMPLETED	Retrospective Study of Patients Who Were Treated With Fondaparinux Pre-, Peri- and/or Postpartum for Prophylaxis or Treatment of Venous Thromboembolism
NCT01029743	Not specified	COMPLETED	Xarelto Regulatory Post-Marketing Surveillance
NCT01267305	Not specified	COMPLETED	The Impact of Different Anticoagulant Therapy on Hemorrhage and Coagulation After Thoracic Surgery
NCT01304238	Not specified	COMPLETED	Retrospective Registry of Patients With Acute Heparin-induced Thrombocytopenia Type II
NCT01406301	Not specified	COMPLETED	Fondaparinux EU-RMP (Adherence)
NCT01444612	Not specified	COMPLETED	Comparative Analysis of Injectable Anticoagulants for Thromboprophylaxis Post Cancer-related Surgery
NCT01691495	Not specified	COMPLETED	ARIXTRA® Adherence in SVT Patients.
NCT01727427	Not specified	COMPLETED	Prospective Study on the Treatment of Unsuspected Pulmonary Embolism in Cancer Patients
NCT02744092	Not specified	COMPLETED	Direct Oral Anticoagulants (DOACs) Versus LMWH +/- Warfarin for VTE in Cancer

Clinical evidence (CIViC)

No CIViC predictive evidence (expected for non-precision-medicine drugs).

Pharmacology

Pharmacogenomics

No PharmGKB pharmacogenomic data curated for this drug.

Related molecules

Related molecules

Molecules sharing ≥1 of this drug’s curated primary targets, merged from two biobtree sources and ranked by shared-target count, then clinical phase: ChEMBL clinical-stage candidates (development phase ≥2) and PubChem drug-class bioactivity (approved / known drugs acting on the target). Deduplicated by drug name; the drug’s own salt forms are excluded. Note: for a drug with few primary targets a shared-target match can reflect off-target / promiscuous binding rather than the same therapeutic mechanism — the phase ordering surfaces bona-fide therapeutics first.

1 molecules share ≥1 primary target. Top 1 by shared-target count:

Molecule	Source	Status	Shared targets
IDRAPARINUX	ChEMBL	Phase 3	SERPINC1