CodeSPD
NameSpermidine
SynonymsN-(3-Aminopropyl)-1,4-butane-diamine
IdentifierN-(3-aminopropyl)butane-1,4-diamine
FormulaC7 H19 N3
Molecular Weight145.246
SMILESC(CCNCCCN)CN
PubChem1102
Formal Charge0
Total Atoms29
Total Chiral Atoms0
Total Bonds28
Total Aromatic Bonds0
Networks2
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This ligand is also present in the following 2 networks:
Show PDB Class SubFamily Type SubType Species Orthosteric Ligand Other Ligand(s) Protein Partners Resolution Date DOI
8IW4 A Orphan A orphans TAAR9 Mus Musculus Spermidine - chim(NtGi1-Gs)/Beta1/Gamma2 3.49 2023-05-31 10.1038/s41586-023-06106-4

A 2D representation of the interactions of SPD in 8IW4
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:S89 R:R:V85 3.23 2 Yes Yes 6 7 2 2
R:R:D112 R:R:V85 4.38 2 Yes Yes 6 7 1 2
R:R:V85 R:R:Y301 5.05 2 Yes Yes 7 8 2 1
R:R:M86 R:R:W298 3.49 2 Yes Yes 7 5 2 2
R:R:M86 R:R:Y301 4.79 2 Yes Yes 7 8 2 1
R:R:S89 R:R:W298 3.71 2 Yes Yes 6 5 2 2
R:R:S89 R:R:Y301 8.9 2 Yes Yes 6 8 2 1
R:R:F168 R:R:T109 5.19 2 Yes No 5 5 1 2
R:R:D112 R:R:T113 4.34 2 Yes Yes 6 4 1 1
R:R:D112 R:R:Y301 12.64 2 Yes Yes 6 8 1 1
L:L:?1 R:R:D112 11.83 2 Yes Yes 0 6 0 1
R:R:T113 R:R:Y163 4.99 2 Yes Yes 4 5 1 2
R:R:S164 R:R:T113 3.2 0 No Yes 7 4 2 1
R:R:F168 R:R:T113 10.38 2 Yes Yes 5 4 1 1
L:L:?1 R:R:T113 9 2 Yes Yes 0 4 0 1
R:R:C116 R:R:W271 2.61 0 No Yes 7 8 1 2
L:L:?1 R:R:C116 2.77 2 Yes No 0 7 0 1
R:R:I167 R:R:Y163 6.04 2 Yes Yes 5 5 2 2
R:R:F168 R:R:I167 3.77 2 Yes Yes 5 5 1 2
R:R:F168 R:R:N173 7.25 2 Yes Yes 5 4 1 2
R:R:A192 R:R:F168 2.77 2 No Yes 4 5 1 1
R:R:F168 R:R:L194 4.87 2 Yes Yes 5 4 1 2
L:L:?1 R:R:F168 7.43 2 Yes Yes 0 5 0 1
R:R:L194 R:R:N173 4.12 2 Yes Yes 4 4 2 2
L:L:?1 R:R:A192 2.75 2 Yes No 0 4 0 1
R:R:I275 R:R:W271 4.7 2 Yes Yes 7 8 2 2
R:R:V300 R:R:W271 9.81 2 No Yes 7 8 1 2
R:R:I275 R:R:Y274 3.63 2 Yes Yes 7 6 2 1
R:R:A278 R:R:Y274 4 0 No Yes 5 6 2 1
R:R:V300 R:R:Y274 3.79 2 No Yes 7 6 1 1
L:L:?1 R:R:Y274 14.31 2 Yes Yes 0 6 0 1
R:R:V297 R:R:Y293 5.05 2 No No 6 4 1 2
R:R:V297 R:R:Y301 8.83 2 No Yes 6 8 1 1
L:L:?1 R:R:V297 9.09 2 Yes No 0 6 0 1
R:R:W298 R:R:Y301 8.68 2 Yes Yes 5 8 2 1
L:L:?1 R:R:V300 6.49 2 Yes No 0 7 0 1
L:L:?1 R:R:Y301 5.11 2 Yes Yes 0 8 0 1
R:R:C110 R:R:F168 1.4 0 No Yes 6 5 2 1
StatisticsValue
Average Number Of Links9.00
Average Number Of Links With An Hub5.00
Average Interaction Strength7.64
Average Nodes In Shell25.00
Average Hubs In Shell16.00
Average Links In Shell38.00
Average Links Mediated by Hubs In Shell37.00
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
8IWE A Orphan A orphans TAAR9 Mus Musculus Spermidine - - 3.4 2023-05-31 10.1038/s41586-023-06106-4

A 2D representation of the interactions of SPD in 8IWE
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:S89 R:R:V85 3.23 1 Yes Yes 6 7 2 2
R:R:D112 R:R:V85 4.38 1 Yes Yes 6 7 1 2
R:R:V85 R:R:Y301 5.05 1 Yes Yes 7 8 2 1
R:R:M86 R:R:W298 3.49 1 Yes Yes 7 5 2 2
R:R:M86 R:R:Y301 4.79 1 Yes Yes 7 8 2 1
R:R:S89 R:R:W298 3.71 1 Yes Yes 6 5 2 2
R:R:S89 R:R:Y301 8.9 1 Yes Yes 6 8 2 1
R:R:F168 R:R:T109 5.19 1 Yes No 5 5 1 2
R:R:D112 R:R:T113 4.34 1 Yes Yes 6 4 1 1
R:R:D112 R:R:Y301 12.64 1 Yes Yes 6 8 1 1
L:L:?1 R:R:D112 11.83 1 Yes Yes 0 6 0 1
R:R:T113 R:R:Y163 4.99 1 Yes Yes 4 5 1 2
R:R:S164 R:R:T113 3.2 0 No Yes 7 4 2 1
R:R:F168 R:R:T113 10.38 1 Yes Yes 5 4 1 1
L:L:?1 R:R:T113 9 1 Yes Yes 0 4 0 1
R:R:C116 R:R:W271 2.61 0 No Yes 7 8 1 2
L:L:?1 R:R:C116 2.77 1 Yes No 0 7 0 1
R:R:I167 R:R:Y163 6.04 1 Yes Yes 5 5 2 2
R:R:F168 R:R:I167 3.77 1 Yes Yes 5 5 1 2
R:R:F168 R:R:N173 7.25 1 Yes Yes 5 4 1 2
R:R:A192 R:R:F168 2.77 1 No Yes 4 5 1 1
R:R:F168 R:R:L194 4.87 1 Yes Yes 5 4 1 2
L:L:?1 R:R:F168 7.43 1 Yes Yes 0 5 0 1
R:R:L194 R:R:N173 4.12 1 Yes Yes 4 4 2 2
R:R:A192 R:R:P193 1.87 1 No Yes 4 3 1 2
L:L:?1 R:R:A192 2.75 1 Yes No 0 4 0 1
R:R:I275 R:R:W271 4.7 1 Yes Yes 7 8 2 2
R:R:V300 R:R:W271 9.81 1 No Yes 7 8 1 2
R:R:I275 R:R:Y274 3.63 1 Yes Yes 7 6 2 1
R:R:A278 R:R:Y274 4 0 No Yes 5 6 2 1
R:R:Y274 R:R:Y293 1.99 1 Yes Yes 6 4 1 2
R:R:V300 R:R:Y274 3.79 1 No Yes 7 6 1 1
L:L:?1 R:R:Y274 14.31 1 Yes Yes 0 6 0 1
R:R:V297 R:R:Y293 5.05 1 No Yes 6 4 1 2
R:R:V297 R:R:Y301 8.83 1 No Yes 6 8 1 1
L:L:?1 R:R:V297 9.09 1 Yes No 0 6 0 1
R:R:W298 R:R:Y301 8.68 1 Yes Yes 5 8 2 1
L:L:?1 R:R:V300 6.49 1 Yes No 0 7 0 1
L:L:?1 R:R:Y301 5.11 1 Yes Yes 0 8 0 1
R:R:C110 R:R:F168 1.4 0 No Yes 6 5 2 1
StatisticsValue
Average Number Of Links9.00
Average Number Of Links With An Hub5.00
Average Interaction Strength7.64
Average Nodes In Shell26.00
Average Hubs In Shell18.00
Average Links In Shell40.00
Average Links Mediated by Hubs In Shell40.00
Physico-chemical properties of the nodes interacting with this ligand (click to enlarge 🔍)
Location of the nodes interacting with this ligand (click to enlarge 🔍)
StatisticsValue
Average Number Of Links9.00
Average Number Of Links With An Hub5.00
Average Interaction Strength7.64
Average Nodes In Shell25.50
Average Hubs In Shell17.00
Average Links In Shell39.00
Average Links Mediated by Hubs In Shell38.50

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 🔍)