CodeSPD
NameSpermidine
Synonyms4-azaoctane-1,8-diamine
Identifier
FormulaC7 H19 N3
Molecular Weight145.246
SMILES
PubChem1102
Formal Charge0
Total Atoms29
Total Chiral Atoms0
Total Bonds28
Total Aromatic Bonds0
Networks3
 missing image

This ligand is also present in the following 3 networks:
Show PDB Class SubFamily Type SubType Species Orthosteric Ligand Other Ligand(s) Protein Partners Resolution Date DOI
8IW4 A Orphan Orphan TA9 Mus Musculus Spermidine - chim(NtGi1-Gs)/Beta1/Gamma2 3.49 2023-05-31 doi.org/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 11.98 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 9.11 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 2.8 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 7.52 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 2.78 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 14.48 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 9.2 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 6.57 2 Yes No 0 7 0 1
L:L:?1 R:R:Y301 5.17 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 Strength7.73
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 Orphan TA9 Mus Musculus Spermidine - - 3.4 2023-05-31 doi.org/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
L:L:?1 R:R:D112 11.98 1 Yes Yes 0 6 0 1
L:L:?1 R:R:T113 9.11 1 Yes Yes 0 4 0 1
L:L:?1 R:R:C116 2.8 1 Yes No 0 7 0 1
L:L:?1 R:R:F168 7.52 1 Yes Yes 0 5 0 1
L:L:?1 R:R:A192 2.78 1 Yes No 0 4 0 1
L:L:?1 R:R:Y274 14.48 1 Yes Yes 0 6 0 1
L:L:?1 R:R:V297 9.2 1 Yes No 0 6 0 1
L:L:?1 R:R:V300 6.57 1 Yes No 0 7 0 1
L:L:?1 R:R:Y301 5.17 1 Yes Yes 0 8 0 1
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: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
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
R:R:C116 R:R:W271 2.61 0 No Yes 7 8 1 2
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 No 5 4 1 2
R:R:A192 R:R:F168 2.77 1 No Yes 4 5 1 1
R:R:A192 R:R:P193 1.87 1 No Yes 4 3 1 2
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
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
R:R:W298 R:R:Y301 8.68 1 Yes Yes 5 8 2 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 Strength7.73
Average Nodes In Shell24.00
Average Hubs In Shell15.00
Average Links In Shell36.00
Average Links Mediated by Hubs In Shell36.00
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 Strength7.73
Average Nodes In Shell25.00
Average Hubs In Shell16.33
Average Links In Shell38.00
Average Links Mediated by Hubs In Shell37.67

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 🔍)