Showing metabocard for Norspermidine (MMDBc0028705)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-05-15 18:27:17 UTC
Update Date2024-10-09 15:03:52 UTC
Metabolite IDMMDBc0028705
Metabolite Identification
Common NameNorspermidine
DescriptionNorspermidine, also known as caldine or dipropylentriamin, belongs to the class of organic compounds known as dialkylamines. These are organic compounds containing a dialkylamine group, characterized by two alkyl groups bonded to the amino nitrogen. While norspermidine has been found to occur naturally in some species of plants, bacteria, and algae, it is not known to exist in humans. Norspermidine is a very strong basic compound (based on its pKa). Norspermidine exists in all living organisms, ranging from bacteria to humans. Outside of the human body, Norspermidine is found, on average, in the highest concentration within white wines and red wines. Norspermidine has also been detected, but not quantified in, several different foods, such as japanese pumpkins, black cabbages, natal plums, cabbages, and jackfruits. This could make norspermidine a potential biomarker for the consumption of these foods. Norspermidine is being researched for use as a cancer medication. Norspermidine is a polyamine of similar structure to the more common spermidine.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000559d03777b58>


  Mrv1652305271900242D          

  9  8  0  0  0  0            999 V2000
    5.7685  -11.3671    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4830  -10.9546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1975  -11.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9119  -10.9546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6264  -11.3671    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.3409  -10.9546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0554  -11.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7699  -10.9546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4844  -11.3671    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000559d03777b58>

HMDB0011634
     RDKit          3D
Norspermidine
 26 25  0  0  0  0  0  0  0  0999 V2000
    3.9032    0.6951   -0.7093 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9758    0.2366    0.3016 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9407   -0.6384   -0.3924 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9443   -1.1767    0.6062 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2264   -0.1804    1.3091 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7498    0.5608    0.6240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9947   -0.2370    0.2754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9594    0.6479   -0.4565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1826   -0.0505   -0.8193 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4934    1.5033   -1.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8216    0.9753   -0.2791 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5222    1.0697    0.8797 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5494   -0.3842    1.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4789   -1.5022   -0.8226 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4735   -0.0878   -1.2261 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2386   -1.8150    0.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5152   -1.8147    1.3159 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1247   -0.2965    2.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2906    0.9601   -0.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0146    1.4579    1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4574   -0.6874    1.1473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6904   -1.0711   -0.4029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1814    1.5285    0.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5098    0.9571   -1.4383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0196    0.4155   -0.3982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1578   -1.0658   -0.6747 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
M  END
Download

3D SDF for #<Metabolite:0x0000559d03777b58>


  Mrv1652305271900242D          

  9  8  0  0  0  0            999 V2000
    5.7685  -11.3671    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4830  -10.9546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1975  -11.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9119  -10.9546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6264  -11.3671    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.3409  -10.9546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0554  -11.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7699  -10.9546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4844  -11.3671    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0028705

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCNCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C6H17N3/c7-3-1-5-9-6-2-4-8/h9H,1-8H2

> <INCHI_KEY>
OTBHHUPVCYLGQO-UHFFFAOYSA-N

> <FORMULA>
C6H17N3

> <MOLECULAR_WEIGHT>
131.2193

> <EXACT_MASS>
131.142247559

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
16.711363715959948

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
bis(3-aminopropyl)amine

> <ALOGPS_LOGP>
-1.11

> <JCHEM_LOGP>
-1.666926611

> <ALOGPS_LOGS>
-0.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA_STRONGEST_BASIC>
10.401722635685779

> <JCHEM_POLAR_SURFACE_AREA>
64.07

> <JCHEM_REFRACTIVITY>
40.3238

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
norspermidine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000559d03777b58>

HMDB0011634
     RDKit          3D
Norspermidine
 26 25  0  0  0  0  0  0  0  0999 V2000
    3.9032    0.6951   -0.7093 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9758    0.2366    0.3016 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9407   -0.6384   -0.3924 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9443   -1.1767    0.6062 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2264   -0.1804    1.3091 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7498    0.5608    0.6240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9947   -0.2370    0.2754 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9594    0.6479   -0.4565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1826   -0.0505   -0.8193 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4934    1.5033   -1.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8216    0.9753   -0.2791 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5222    1.0697    0.8797 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5494   -0.3842    1.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4789   -1.5022   -0.8226 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4735   -0.0878   -1.2261 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2386   -1.8150    0.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5152   -1.8147    1.3159 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1247   -0.2965    2.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2906    0.9601   -0.3147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0146    1.4579    1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4574   -0.6874    1.1473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6904   -1.0711   -0.4029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1814    1.5285    0.1408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5098    0.9571   -1.4383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0196    0.4155   -0.3982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1578   -1.0658   -0.6747 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
M  END
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PDB for #<Metabolite:0x0000559d03777b58>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  N   UNK     0      10.768 -21.219   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      12.102 -20.449   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.435 -21.219   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.769 -20.449   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      16.103 -21.219   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      17.436 -20.449   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.770 -21.219   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      20.104 -20.449   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      21.438 -21.219   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x0000559d03777b58>

COMPND    HMDB0011634
HETATM    1  N1  UNL     1       3.903   0.695  -0.709  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.976   0.237   0.302  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.941  -0.638  -0.392  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.944  -1.177   0.606  1.00  0.00           C  
HETATM    5  N2  UNL     1       0.226  -0.180   1.309  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.750   0.561   0.624  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.995  -0.237   0.275  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.959   0.648  -0.457  1.00  0.00           C  
HETATM    9  N3  UNL     1      -4.183  -0.050  -0.819  1.00  0.00           N  
HETATM   10  H1  UNL     1       3.493   1.503  -1.264  1.00  0.00           H  
HETATM   11  H2  UNL     1       4.822   0.975  -0.279  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.522   1.070   0.880  1.00  0.00           H  
HETATM   13  H4  UNL     1       3.549  -0.384   1.017  1.00  0.00           H  
HETATM   14  H5  UNL     1       2.479  -1.502  -0.823  1.00  0.00           H  
HETATM   15  H6  UNL     1       1.474  -0.088  -1.226  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.239  -1.815   0.016  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.515  -1.815   1.316  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.125  -0.297   2.312  1.00  0.00           H  
HETATM   19  H10 UNL     1      -0.291   0.960  -0.315  1.00  0.00           H  
HETATM   20  H11 UNL     1      -1.015   1.458   1.249  1.00  0.00           H  
HETATM   21  H12 UNL     1      -2.457  -0.687   1.147  1.00  0.00           H  
HETATM   22  H13 UNL     1      -1.690  -1.071  -0.403  1.00  0.00           H  
HETATM   23  H14 UNL     1      -3.181   1.528   0.141  1.00  0.00           H  
HETATM   24  H15 UNL     1      -2.510   0.957  -1.438  1.00  0.00           H  
HETATM   25  H16 UNL     1      -5.020   0.416  -0.398  1.00  0.00           H  
HETATM   26  H17 UNL     1      -4.158  -1.066  -0.675  1.00  0.00           H  
CONECT    1    2   10   11
CONECT    2    3   12   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8    9   23   24
CONECT    9   25   26
END
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SMILES for #<Metabolite:0x0000559d03777b58>

NCCCNCCCN
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INCHI for #<Metabolite:0x0000559d03777b58>

InChI=1S/C6H17N3/c7-3-1-5-9-6-2-4-8/h9H,1-8H2
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Synonyms
ValueSource
1,7-Diamino-4-azaheptaneChEBI
3,3'-Iminobis(propylamine)ChEBI
3,3'-IminobispropylamineChEBI
3,3'-Iminodi(propylamine)ChEBI
3,3-DiaminodipropylamineChEBI
4-Azaheptane-1,7-diamineChEBI
DipropylenetriamineChEBI
N-(3-Aminopropyl)-1,3-propanediamineChEBI
N-(3-Aminopropyl)propane-1,3-diamineChEBI
N-3-Aminopropyl-1,3-diaminopropaneChEBI
Bis(3-aminopropyl)amineKegg
-1,3-PropanediamineHMDB
3, 3'-DiaminodipropylamineHMDB
3, {3'-iminobis[propylamine]}HMDB
3,3'-Diamino-dipropylamineHMDB
3,3'-DiaminodipropylamineHMDB
3,3'-Iminobis-1-propanamineHMDB
3,3'-Iminobis-propylamineHMDB
3,3'-IminopropylamineHMDB
4-AzaheptamethylenediamineHMDB
Aminobis(propylamine)HMDB
CaldineHMDB
Dipropylene triamineHMDB
DipropylentriaminHMDB
Imino-bis(3-propylamine)HMDB
Iminobis(propylamine)HMDB
Initiating explosive iminobispropylamineHMDB
Initiating explosive iminobispropylamine (dot)HMDB
N-(3-Aminopropyl)-1, 3-propanediamineHMDB
N-3-AminopropylHMDB
Bis(3,3'-aminopropyl)amineHMDB
3,3'-DiaminopropylamineHMDB
NorspermidineChEBI
Molecular FormulaC6H17N3
Average Mass131.2193
Monoisotopic Mass131.142247559
IUPAC Namebis(3-aminopropyl)amine
Traditional Namenorspermidine
CAS Registry NumberNot Available
SMILES
NCCCNCCCN
InChI Identifier
InChI=1S/C6H17N3/c7-3-1-5-9-6-2-4-8/h9H,1-8H2
InChI KeyOTBHHUPVCYLGQO-UHFFFAOYSA-N