CodeSPM
NameSpermine
Synonyms4,9-diazadodecane-1,12-diamine
Identifier
FormulaC10 H26 N4
Molecular Weight202.34
SMILES
PubChem1103
Formal Charge0
Total Atoms40
Total Chiral Atoms0
Total Bonds39
Total Aromatic Bonds0
Networks5
 missing image

This ligand is also present in the following 5 networks:
Show PDB Class SubFamily Type SubType Species Orthosteric Ligand Other Ligand(s) Protein Partners Resolution Date DOI
8SZF C Ion Calcium Sensing CaS Homo Sapiens - Ca; Ca; Tryptophan; Cinacalcet; PO4; Spermine - 2.8 2024-02-07 doi.org/10.1038/s41586-024-07055-2

A 2D representation of the interactions of SPM in 8SZF
colored according to ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  

(Click to enlarge 🔍)
Node1 Node2 LinkStrength Comm IsNode1Hub? IsNode2Hub? Node1Cons Node2Cons Node1Shell Node2Shell
H:H:?9 S:S:V258 4.01 0 No Yes 0 4 2 1
R:R:E228 X:X:?5 11.44 3 No Yes 3 0 1 0
S:S:D238 X:X:?5 11.72 3 Yes Yes 8 0 1 0
S:S:F239 X:X:?5 5.84 3 Yes Yes 6 0 1 0
S:S:S240 X:X:?5 5.76 3 No Yes 4 0 1 0
S:S:E241 X:X:?5 2.54 3 Yes Yes 5 0 1 0
S:S:V258 X:X:?5 2.86 3 Yes Yes 4 0 1 0
S:S:S262 X:X:?5 4.32 3 Yes Yes 7 0 1 0
X:X:?5 X:X:?6 114.73 3 Yes Yes 0 0 0 1
R:R:E228 R:R:K225 5.4 3 No Yes 3 3 1 2
R:R:E228 X:X:?6 11.44 3 No Yes 3 0 1 1
S:S:D238 S:S:W208 16.75 3 Yes Yes 8 9 1 2
S:S:F239 S:S:G210 9.03 3 Yes No 6 8 1 2
S:S:D238 S:S:F239 3.58 3 Yes Yes 8 6 1 1
S:S:D238 S:S:S262 5.89 3 Yes Yes 8 7 1 1
S:S:D238 X:X:?6 11.72 3 Yes Yes 8 0 1 1
S:S:F239 S:S:V258 3.93 3 Yes Yes 6 4 1 1
S:S:F239 S:S:I259 2.51 3 Yes No 6 6 1 2
S:S:F239 S:S:S262 5.28 3 Yes Yes 6 7 1 1
S:S:F239 S:S:I267 2.51 3 Yes Yes 6 7 1 2
S:S:F239 X:X:?6 5.84 3 Yes Yes 6 0 1 1
S:S:S240 X:X:?6 5.76 3 No Yes 4 0 1 1
S:S:E241 S:S:V255 5.7 3 Yes No 5 5 1 2
S:S:E241 S:S:V258 9.98 3 Yes Yes 5 4 1 1
S:S:E241 X:X:?6 2.54 3 Yes Yes 5 0 1 1
S:S:H254 S:S:V258 4.15 0 No Yes 3 4 2 1
S:S:V258 X:X:?6 2.86 3 Yes Yes 4 0 1 1
S:S:S262 X:X:?6 4.32 3 Yes Yes 7 0 1 1
StatisticsValue
Average Number Of Links8.00
Average Number Of Links With An Hub6.00
Average Interaction Strength19.90
Average Nodes In Shell17.00
Average Hubs In Shell10.00
Average Links In Shell28.00
Average Links Mediated by Hubs In Shell28.00
Physico-chemical properties of the nodes interacting with this ligand (click to enlarge 🔍)
Location of the nodes interacting with this ligand (click to enlarge 🔍)

A 2D representation of the interactions of SPM in 8SZF
colored according to ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  

(Click to enlarge 🔍)
Node1 Node2 LinkStrength Comm IsNode1Hub? IsNode2Hub? Node1Cons Node2Cons Node1Shell Node2Shell
H:H:?9 S:S:V258 4.01 0 No Yes 0 4 2 1
R:R:E228 X:X:?5 11.44 3 No Yes 3 0 1 1
S:S:D238 X:X:?5 11.72 3 Yes Yes 8 0 1 1
S:S:F239 X:X:?5 5.84 3 Yes Yes 6 0 1 1
S:S:S240 X:X:?5 5.76 3 No Yes 4 0 1 1
S:S:E241 X:X:?5 2.54 3 Yes Yes 5 0 1 1
S:S:V258 X:X:?5 2.86 3 Yes Yes 4 0 1 1
S:S:S262 X:X:?5 4.32 3 Yes Yes 7 0 1 1
X:X:?5 X:X:?6 114.73 3 Yes Yes 0 0 1 0
R:R:E228 R:R:K225 5.4 3 No Yes 3 3 1 2
R:R:E228 X:X:?6 11.44 3 No Yes 3 0 1 0
S:S:D238 S:S:W208 16.75 3 Yes Yes 8 9 1 2
S:S:F239 S:S:G210 9.03 3 Yes No 6 8 1 2
S:S:D238 S:S:F239 3.58 3 Yes Yes 8 6 1 1
S:S:D238 S:S:S262 5.89 3 Yes Yes 8 7 1 1
S:S:D238 X:X:?6 11.72 3 Yes Yes 8 0 1 0
S:S:F239 S:S:V258 3.93 3 Yes Yes 6 4 1 1
S:S:F239 S:S:I259 2.51 3 Yes No 6 6 1 2
S:S:F239 S:S:S262 5.28 3 Yes Yes 6 7 1 1
S:S:F239 S:S:I267 2.51 3 Yes Yes 6 7 1 2
S:S:F239 X:X:?6 5.84 3 Yes Yes 6 0 1 0
S:S:S240 X:X:?6 5.76 3 No Yes 4 0 1 0
S:S:E241 S:S:V255 5.7 3 Yes No 5 5 1 2
S:S:E241 S:S:V258 9.98 3 Yes Yes 5 4 1 1
S:S:E241 X:X:?6 2.54 3 Yes Yes 5 0 1 0
S:S:H254 S:S:V258 4.15 0 No Yes 3 4 2 1
S:S:V258 X:X:?6 2.86 3 Yes Yes 4 0 1 0
S:S:S262 X:X:?6 4.32 3 Yes Yes 7 0 1 0
StatisticsValue
Average Number Of Links8.00
Average Number Of Links With An Hub6.00
Average Interaction Strength19.90
Average Nodes In Shell17.00
Average Hubs In Shell10.00
Average Links In Shell28.00
Average Links Mediated by Hubs In Shell28.00
Physico-chemical properties of the nodes interacting with this ligand (click to enlarge 🔍)
Location of the nodes interacting with this ligand (click to enlarge 🔍)
Show PDB Class SubFamily Type SubType Species Orthosteric Ligand Other Ligand(s) Protein Partners Resolution Date DOI
8SZG C Ion Calcium Sensing CaS Homo Sapiens - Ca; Ca; Tryptophan; Cinacalcet; PO4; Spermine chim(NtGi1-Gq)/Beta1/Gamma2 3.6 2024-02-07 doi.org/10.1038/s41586-024-07055-2

A 2D representation of the interactions of SPM in 8SZG
colored according to ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  

(Click to enlarge 🔍)
Node1 Node2 LinkStrength Comm IsNode1Hub? IsNode2Hub? Node1Cons Node2Cons Node1Shell Node2Shell
R:R:E757 R:R:L756 5.3 11 Yes No 4 5 2 2
R:R:F762 R:R:L756 8.53 11 Yes No 7 5 2 2
R:R:L756 R:R:Y829 17.58 11 No Yes 5 6 2 1
R:R:E757 R:R:Y829 7.86 11 Yes Yes 4 6 2 1
R:R:E757 W:W:?8 21.62 11 Yes Yes 4 0 2 1
R:R:F762 R:R:Y829 3.09 11 Yes Yes 7 6 2 1
R:R:S827 R:R:T828 4.8 11 No No 8 8 2 1
R:R:T828 S:S:Y829 3.75 11 No No 8 6 1 1
R:R:T828 X:X:?4 2.83 11 No Yes 8 0 1 0
R:R:Y829 X:X:?4 12.38 11 Yes Yes 6 0 1 0
R:R:Y829 W:W:?8 3.38 11 Yes Yes 6 0 1 1
R:R:F832 R:R:K831 4.96 0 No No 5 9 1 2
R:R:F832 S:S:S827 5.28 0 No No 5 8 1 2
R:R:F832 X:X:?4 8.18 0 No Yes 5 0 1 0
S:S:E757 S:S:I760 5.47 11 No Yes 4 5 2 2
S:S:E757 W:W:?8 33.06 11 No Yes 4 0 2 1
S:S:I760 W:W:?8 4.11 11 Yes Yes 5 0 2 1
S:S:Y829 X:X:?4 14.63 11 No Yes 6 0 1 0
W:W:?8 X:X:?4 7.65 11 Yes Yes 0 0 1 0
R:R:G830 R:R:Y829 1.45 0 No Yes 8 6 2 1
StatisticsValue
Average Number Of Links5.00
Average Number Of Links With An Hub2.00
Average Interaction Strength9.13
Average Nodes In Shell15.00
Average Hubs In Shell6.00
Average Links In Shell20.00
Average Links Mediated by Hubs In Shell16.00
Physico-chemical properties of the nodes interacting with this ligand (click to enlarge 🔍)
Location of the nodes interacting with this ligand (click to enlarge 🔍)
Show PDB Class SubFamily Type SubType Species Orthosteric Ligand Other Ligand(s) Protein Partners Resolution Date DOI
8SZH C Ion Calcium Sensing CaS Homo Sapiens - Ca; Ca; Tryptophan; Cinacalcet; PO4; Spermine Gi1/Beta1/Gamma2 3.1 2024-02-07 doi.org/10.1038/s41586-024-07055-2
StatisticsValue
Average Number Of Links6.50
Average Number Of Links With An Hub4.00
Average Interaction Strength14.52
Average Nodes In Shell16.00
Average Hubs In Shell8.00
Average Links In Shell24.00
Average Links Mediated by Hubs In Shell22.00

missing image


Physico-chemical properties of the nodes interacting with this ligand

(Click to enlarge 🔍)

missing image


Location of the nodes interacting with this ligand

(Click to enlarge 🔍)