spermine   Click here for help

GtoPdb Ligand ID: 710

PDB Ligand
Compound class: Metabolite or derivative
Click here for help

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.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

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.

✖
Hydrogen bond acceptors 4
Hydrogen bond donors 4
Rotatable bonds 11
Topological polar surface area 76.1
Molecular weight 202.22
XLogP -0.68
No. Lipinski's rules broken 1
SMILES / InChI / InChIKey
Click here for help

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.

✖
Canonical SMILES NCCCNCCCCNCCCN
Isomeric SMILES NCCCNCCCCNCCCN
InChI InChI=1S/C10H26N4/c11-5-3-9-13-7-1-2-8-14-10-4-6-12/h13-14H,1-12H2
InChI Key PFNFFQXMRSDOHW-UHFFFAOYSA-N
Natural/Endogenous Targets
Target
CaS receptor
Transporters Moving this Compound Across a Lipid Membrane
Transporter EC number Reaction Reference
Cation-chloride cotransporter 9
Vesicular polyamine transporter 2
Selectivity at GPCRs
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
CaS receptor Ligand is endogenous in the given species Hs Agonist Full agonist 3.5 pKd - 10
⤷ pKd 3.5 [10]
Selectivity at ion channels
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
Kir2.3 Ligand is endogenous in the given species Hs Channel blocker Antagonist - - 5x10-5 - 1x10-3 6
⤷ Conc range: 5x10-5 - 1x10-3 M [6]
Voltage: -80.0 – 80.0 mV
Kir2.1 Ligand is endogenous in the given species Mm Channel blocker Antagonist 9.1 pKd - 4,12
⤷ pKd 9.1 [4,12]
Voltage: 40.0 mV
TRPM7 Rn Channel blocker Inhibition 5.6 pKi - 5
⤷ pKi 5.6 (Ki 2.3x10-6 M) Reversible, voltage dependent inhibition in RBL2H3 rats [5]
Voltage: -110.0 – 80.0 mV
TRPM4 Mm Channel blocker Antagonist 4.5 pIC50 - 11
⤷ pIC50 4.5 [11]
Voltage: 100.0 mV
TRPM5 Hs Channel blocker (intracellular spermine) - 4.4 pIC50 -
⤷ pIC50 4.4 (IC50 3.7x10-5 M)
TRPM4 Hs Channel blocker Antagonist 4.2 pIC50 - 8
⤷ pIC50 4.2 (IC50 6.1x10-5 M) [8]
Voltage: 100.0 mV
Additional information and targets (data relate to human unless otherwise stated)
Description Data Reference
Polyamine rank order of potency at CaS receptor spermine > spermidine > putrescine 10
Endogenous activators at PLCδ1 Transglutaminase II, p122-RhoGAP, spermine, Gβγ 1,3,7,9
Ligand mentioned in the following text fields
Mitochondrial amino acid transporter subfamily comments