saxitoxin   Click here for help

GtoPdb Ligand ID: 2625

PDB Ligand
Compound class: Natural product
Comment: Saxitoxin is a potent paralytic neurotoxin saxitoxin that is produced by water-dwelling prokaryotic cyanobacteria and eukaryotic dinoflagellates [3]. Mechanistically it is a voltage-gated sodium (NaV) ion channel blocker.
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2D Structure
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Physico-chemical Properties
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Hydrogen bond acceptors 11
Hydrogen bond donors 6
Rotatable bonds 3
Topological polar surface area 184.81
Molecular weight 299.13
XLogP -2.59
No. Lipinski's rules broken 2

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

SMILES / InChI / InChIKey
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Canonical SMILES NC(=O)OCC1N=C(N)N2C3(C1NC(=N3)N)C(O)(O)CC2
Isomeric SMILES NC(=O)OC[C@@H]1N=C(N)N2[C@@]3([C@H]1NC(=N3)N)C(O)(O)CC2
InChI InChI=1S/C10H17N7O4/c11-6-15-5-4(3-21-8(13)18)14-7(12)17-2-1-9(19,20)10(5,17)16-6/h4-5,19-20H,1-3H2,(H2,12,14)(H2,13,18)(H3,11,15,16)/t4-,5-,10-/m0/s1
InChI Key RPQXVSUAYFXFJA-HGRQIUPRSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

Selectivity at ion channels
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Target Sp. Type Action Value Parameter Concentration range (M) Reference
Nav1.5 Rn Channel blocker Pore blocker 7.4 pKd - 2,6
pKd 7.4 [2,6]
Voltage: -80.0 mV
Nav1.2 Rn Channel blocker Pore blocker 8.8 pIC50 - 1
pIC50 8.8 (IC50 1.7x10-9 M) [1]
Voltage: -120.0 mV
Nav1.4 Rn Channel blocker Pore blocker 8.4 pIC50 - 4
pIC50 8.4 (IC50 4.1x10-9 M) [4]
Voltage: -100.0 mV
Nav1.7 Hs Channel blocker Pore blocker 6.2 pIC50 - 5
pIC50 6.2 (IC50 7.02x10-7 M) [5]
Nav1.1 Hs Channel blocker Pore blocker - - -
Nav1.3 Hs Channel blocker Pore blocker - - -
Nav1.6 Hs Channel blocker Pore blocker - - -