MiMeDB: Showing metabocard for N(4)-bis(aminopropyl)spermidine (MMDBc0056184)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:18:56 UTC

Update Date

2025-10-07 16:09:38 UTC

Metabolite ID

MMDBc0056184

Metabolite Identification

Common Name

N(4)-bis(aminopropyl)spermidine

Description

N(4)-bis(aminopropyl)spermidine is a polyamine compound belonging to the class of aliphatic amines. There is limited literature available on this metabolite, indicating that further research may be needed to fully understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222182D          

 18 17  0  0  0  0            999 V2000
   -1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3480    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3184    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5855    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0329    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9980    2.5559    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.0164    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -2.9684    0.4125    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.7474    0.4125    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.1105    0.4125    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  6  1  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  1  0  0  0  0
 10  2  1  0  0  0  0
 11  3  1  0  0  0  0
 12  4  1  0  0  0  0
 13  5  1  0  0  0  0
 14  6  1  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17  9  1  0  0  0  0
 18 10  1  0  0  0  0
 18 11  1  0  0  0  0
 18 12  1  0  0  0  0
 18 13  1  0  0  0  0
M  CHG  5  14   1  15   1  16   1  17   1  18   1
M  END
> <DATABASE_ID>
MMDBc0056184

> <DATABASE_NAME>
MIME

> <SMILES>
[NH3+]CCCC[N+](CCC[NH3+])(CCC[NH3+])CCC[NH3+]

> <INCHI_IDENTIFIER>
InChI=1S/C13H34N5/c14-6-1-2-10-18(11-3-7-15,12-4-8-16)13-5-9-17/h1-17H2/q+1/p+4

> <INCHI_KEY>
FMTAVYOBEGHWPT-UHFFFAOYSA-R

> <FORMULA>
C13H38N5

> <MOLECULAR_WEIGHT>
264.479

> <EXACT_MASS>
264.309978344

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
34.73071931837968

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4-azaniumylbutyl)tris(3-azaniumylpropyl)azanium

> <JCHEM_LOGP>
-6.402900758471746

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA_STRONGEST_BASIC>
10.670513363496848

> <JCHEM_POLAR_SURFACE_AREA>
110.56

> <JCHEM_REFRACTIVITY>
136.9783

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4-ammoniobutyl)tris(3-ammoniopropyl)azanium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.516   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.874   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.461   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.826   3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.874  -1.897   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.207   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.795   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.976   2.104   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.540   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.127   1.540   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -5.596   4.771   0.000  0.00  0.00           N+1
HETATM   15  N   UNK     0       4.414  -1.897   0.000  0.00  0.00           N+1
HETATM   16  N   UNK     0      -5.541   0.770   0.000  0.00  0.00           N+1
HETATM   17  N   UNK     0       5.128   0.770   0.000  0.00  0.00           N+1
HETATM   18  N   UNK     0      -0.206   0.770   0.000  0.00  0.00           N+1
CONECT    1    2    6                                                       
CONECT    2    1   10                                                       
CONECT    3    7   11                                                       
CONECT    4    8   12                                                       
CONECT    5    9   13                                                       
CONECT    6    1   14                                                       
CONECT    7    3   15                                                       
CONECT    8    4   16                                                       
CONECT    9    5   17                                                       
CONECT   10    2   18                                                       
CONECT   11    3   18                                                       
CONECT   12    4   18                                                       
CONECT   13    5   18                                                       
CONECT   14    6                                                            
CONECT   15    7                                                            
CONECT   16    8                                                            
CONECT   17    9                                                            
CONECT   18   10   11   12   13                                             
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

Synonyms

Value	Source
N(4)-Bis(aminopropyl)spermidine	ChEBI

Molecular Formula

C₁₃H₃₈N₅

Average Mass

264.479

Monoisotopic Mass

264.309978344

IUPAC Name

(4-azaniumylbutyl)tris(3-azaniumylpropyl)azanium

Traditional Name

(4-ammoniobutyl)tris(3-ammoniopropyl)azanium

CAS Registry Number

Not Available

SMILES

[NH3+]CCCC[N+](CCC[NH3+])(CCC[NH3+])CCC[NH3+]

InChI Identifier

InChI=1S/C13H34N5/c14-6-1-2-10-18(11-3-7-15,12-4-8-16)13-5-9-17/h1-17H2/q+1/p+4

InChI Key

FMTAVYOBEGHWPT-UHFFFAOYSA-R

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetraalkylammonium salts. These are organonitrogen compounds containing a quaternary ammonium substituted with four alkyl chains.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Quaternary ammonium salts

Direct Parent

Tetraalkylammonium salts

Alternative Parents

Substituents

Tetraalkylammonium salt
Organopnictogen compound
Hydrocarbon derivative
Organic salt
Primary amine
Primary aliphatic amine
Amine
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

quaternary ammonium ion (CHEBI:82771 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-6.4	ChemAxon
pKa (Strongest Basic)	10.67	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	110.56 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	136.98 m³·mol⁻¹	ChemAxon
Polarizability	34.73 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	592.5
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	519.8
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	67.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	288.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	232.2
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	201.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	291.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	1253.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	273.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	168.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	783.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	180.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	113.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	347.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	1255.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	60.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	237.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	751.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	549.1

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Archaea/Archaea	Euryarchaeota	2
Bacteria/Eubacteria	Deinococcus-thermus	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

34448600

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

86289948

PDB ID

Not Available

ChEBI ID

82771

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for N(4)-bis(aminopropyl)spermidine (MMDBc0056184)

MOL for #<Metabolite:0x00007f9ac000c4b0>

3D MOL for #<Metabolite:0x00007f9ac000c4b0>

3D SDF for #<Metabolite:0x00007f9ac000c4b0>

3D-SDF for #<Metabolite:0x00007f9ac000c4b0>

PDB for #<Metabolite:0x00007f9ac000c4b0>

3D PDB for #<Metabolite:0x00007f9ac000c4b0>

SMILES for #<Metabolite:0x00007f9ac000c4b0>

INCHI for #<Metabolite:0x00007f9ac000c4b0>

Structure for #<Metabolite:0x00007f9ac000c4b0>

3D Structure for #<Metabolite:0x00007f9ac000c4b0>