heparin   Click here for help

GtoPdb Ligand ID: 4214

Synonyms: HepFlush®
Approved drug
heparin is an approved drug (FDA (1939))
Comment: Heparin is an endogenous secretory glycosaminoglycan (GAG) that is released predominantly from connective tissue mast cells. Isolated heparin is used clinically as an anti-coagulant. Structurally, heparins (generally known as unfractionated heparin) are a heterogeneous group of anionic, sulfated GAGs. Commercial preparations usually vary in size from 12-15 kDa, while a low molecular weight (fractionated) versions are also available. Database entries may specify the sodium salt forms.

SARS-CoV-2: There is strong experimental evidence which shows that heparin interacts directly with GAG-binding motifs on the Spike glycoprotein of SARS-CoV-2 [3], and that inhibiting this interaction can reduce SARS-CoV-2 infection of host cells [6,8]. These findings suggest that heparin may offer repurposing potential as a prophylactic COVID-19 therapeutic [2], in addition to its benefit as a treatment for COVID-19-related thrombotic complications.
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2D Structure
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Physico-chemical Properties
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Hydrogen bond acceptors 35
Hydrogen bond donors 14
Rotatable bonds 19
Topological polar surface area 588.61
Molecular weight 1039.04
XLogP -11.46
No. Lipinski's rules broken 3
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Canonical SMILES CC(=O)NC1C(OC2C(OC(C(C2O)O)OC2C(O)OC(C(C2CS(=O)(=O)O)OS(=O)(=O)O)OC2C(OC(C(C2O)OS(=O)(=O)O)O)C(=O)O)C(=O)O)OC(C(C1O)O)COS(=O)(=O)O
Isomeric SMILES CC(=O)N[C@H]1[C@@H](O[C@@H]2[C@H](O[C@H]([C@@H]([C@H]2O)O)O[C@@H]2[C@@H](O)O[C@@H]([C@@H]([C@H]2CS(=O)(=O)O)OS(=O)(=O)O)O[C@@H]2[C@@H](OC([C@@H]([C@H]2O)OS(=O)(=O)O)O)C(=O)O)C(=O)O)O[C@@H]([C@H]([C@@H]1O)O)COS(=O)(=O)O
InChI InChI=1S/C26H41NO34S4/c1-4(28)27-7-9(30)8(29)6(2-52-63(43,44)45)53-24(7)56-15-10(31)11(32)25(58-19(15)21(36)37)55-13-5(3-62(40,41)42)14(60-64(46,47)48)26(59-22(13)38)57-16-12(33)17(61-65(49,50)51)23(39)54-18(16)20(34)35/h5-19,22-26,29-33,38-39H,2-3H2,1H3,(H,27,28)(H,34,35)(H,36,37)(H,40,41,42)(H,43,44,45)(H,46,47,48)(H,49,50,51)/t5-,6+,7+,8+,9+,10+,11+,12-,13-,14+,15-,16-,17+,18+,19-,22-,23?,24+,25+,26-/m0/s1
Bioactivity Comments
Binding affinities to the Spike glycoproteins from SARS-CoV and MERS-CoV are lower than the affinity for SARS-CoV-2 Spike (500 nM, 1 nM and 0.073 nM respectively) [3].
Selectivity at enzymes
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Target Sp. Type Action Value Parameter Concentration range (M) Reference
serpin family C member 1 Primary target of this compound Hs Activator Activation 7.8 pKd - 1
pKd 7.8 (Kd 1.42x10-8 M) [1]
Description: Catalyses the inactivation of coagulation proteases by activatted antithrombin-III
Selectivity at other protein targets
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Target Sp. Type Action Value Parameter Concentration range (M) Reference
CoV Spike glycoprotein SARS-CoV-2 None Binding 10.1 pKd - 3
pKd 10.1 (Kd 7.3x10-11 M) [3]
Description: Binding affinity of trimeric SARS-CoV-2 spike protein to immobilized heparin.
CoV Spike glycoprotein MERS-CoV None Binding 9.0 pKd - 3
pKd 9.0 (Kd 1x10-9 M) [3]
CoV Spike glycoprotein SARS-CoV None Binding 6.3 pKd - 3
pKd 6.3 (Kd 5x10-7 M) [3]