Hmdb loader

Showing metabocard for Norspermidine (HMDB0011634)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (20) Show 20 proteinsXML
enzymes (20) Show 20 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-01-30 15:03:41 UTC
Update Date2023-02-21 17:17:31 UTC
HMDB IDHMDB0011634
Secondary Accession Numbers
  • HMDB11634
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
Data?1676999851
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011634 (Norspermidine)


  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
Download

3D MOL for HMDB0011634 (Norspermidine)

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 HMDB0011634 (Norspermidine)


  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>
HMDB0011634

> <DATABASE_NAME>
hmdb

> <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

$$$$
Download

3D-SDF for HMDB0011634 (Norspermidine)

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

PDB for HMDB0011634 (Norspermidine)

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
Download

3D PDB for HMDB0011634 (Norspermidine)

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
Download

SMILES for HMDB0011634 (Norspermidine)

NCCCNCCCN
Download

INCHI for HMDB0011634 (Norspermidine)

InChI=1S/C6H17N3/c7-3-1-5-9-6-2-4-8/h9H,1-8H2
Download
View in JSmolView NMR AssignmentsView Stereo Labels
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
Chemical FormulaC6H17N3
Average Molecular Weight131.2193
Monoisotopic Molecular Weight131.142247559
IUPAC Namebis(3-aminopropyl)amine
Traditional Namenorspermidine
CAS Registry Number56-18-8
SMILES
NCCCNCCCN
InChI Identifier
InChI=1S/C6H17N3/c7-3-1-5-9-6-2-4-8/h9H,1-8H2
InChI KeyOTBHHUPVCYLGQO-UHFFFAOYSA-N
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentDialkylamines
Alternative Parents
Substituents
  • Secondary aliphatic amine
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary aliphatic amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-14 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available127.8http://allccs.zhulab.cn/database/detail?ID=AllCCS00002047
Predicted Molecular Properties
PropertyValueSource
Water Solubility120 g/LALOGPS
logP-1.1ALOGPS
logP-1.7ChemAxon
logS-0.04ALOGPS
pKa (Strongest Basic)10.4ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area64.07 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity40.32 m³·mol⁻¹ChemAxon
Polarizability16.71 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+128.2131661259
DarkChem[M-H]-123.75731661259
DeepCCS[M+H]+132.24530932474
DeepCCS[M-H]-129.98530932474
DeepCCS[M-2H]-165.86230932474
DeepCCS[M+Na]+140.82430932474
AllCCS[M+H]+129.832859911
AllCCS[M+H-H2O]+125.932859911
AllCCS[M+NH4]+133.532859911
AllCCS[M+Na]+134.532859911
AllCCS[M-H]-131.132859911
AllCCS[M+Na-2H]-133.932859911
AllCCS[M+HCOO]-137.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.08 minutes32390414
Predicted by Siyang on May 30, 20227.4638 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20228.21 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid471.2 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid282.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid256.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid49.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid181.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid62.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid268.8 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid218.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)1171.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid487.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid37.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid457.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid185.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid264.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate1073.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA782.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water338.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
NorspermidineNCCCNCCCN1958.2Standard polar33892256
NorspermidineNCCCNCCCN1313.5Standard non polar33892256
NorspermidineNCCCNCCCN1203.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Norspermidine,1TMS,isomer #1C[Si](C)(C)NCCCNCCCN1518.8Semi standard non polar33892256
Norspermidine,1TMS,isomer #1C[Si](C)(C)NCCCNCCCN1545.4Standard non polar33892256
Norspermidine,1TMS,isomer #1C[Si](C)(C)NCCCNCCCN2443.1Standard polar33892256
Norspermidine,1TMS,isomer #2C[Si](C)(C)N(CCCN)CCCN1446.3Semi standard non polar33892256
Norspermidine,1TMS,isomer #2C[Si](C)(C)N(CCCN)CCCN1490.3Standard non polar33892256
Norspermidine,1TMS,isomer #2C[Si](C)(C)N(CCCN)CCCN2777.8Standard polar33892256
Norspermidine,2TMS,isomer #1C[Si](C)(C)NCCCNCCCN[Si](C)(C)C1686.1Semi standard non polar33892256
Norspermidine,2TMS,isomer #1C[Si](C)(C)NCCCNCCCN[Si](C)(C)C1827.4Standard non polar33892256
Norspermidine,2TMS,isomer #1C[Si](C)(C)NCCCNCCCN[Si](C)(C)C1957.4Standard polar33892256
Norspermidine,2TMS,isomer #2C[Si](C)(C)N(CCCNCCCN)[Si](C)(C)C1721.6Semi standard non polar33892256
Norspermidine,2TMS,isomer #2C[Si](C)(C)N(CCCNCCCN)[Si](C)(C)C1770.1Standard non polar33892256
Norspermidine,2TMS,isomer #2C[Si](C)(C)N(CCCNCCCN)[Si](C)(C)C2376.2Standard polar33892256
Norspermidine,2TMS,isomer #3C[Si](C)(C)NCCCN(CCCN)[Si](C)(C)C1614.4Semi standard non polar33892256
Norspermidine,2TMS,isomer #3C[Si](C)(C)NCCCN(CCCN)[Si](C)(C)C1714.4Standard non polar33892256
Norspermidine,2TMS,isomer #3C[Si](C)(C)NCCCN(CCCN)[Si](C)(C)C2267.9Standard polar33892256
Norspermidine,3TMS,isomer #1C[Si](C)(C)NCCCNCCCN([Si](C)(C)C)[Si](C)(C)C1858.4Semi standard non polar33892256
Norspermidine,3TMS,isomer #1C[Si](C)(C)NCCCNCCCN([Si](C)(C)C)[Si](C)(C)C1981.6Standard non polar33892256
Norspermidine,3TMS,isomer #1C[Si](C)(C)NCCCNCCCN([Si](C)(C)C)[Si](C)(C)C1870.4Standard polar33892256
Norspermidine,3TMS,isomer #2C[Si](C)(C)NCCCN(CCCN[Si](C)(C)C)[Si](C)(C)C1733.4Semi standard non polar33892256
Norspermidine,3TMS,isomer #2C[Si](C)(C)NCCCN(CCCN[Si](C)(C)C)[Si](C)(C)C1942.1Standard non polar33892256
Norspermidine,3TMS,isomer #2C[Si](C)(C)NCCCN(CCCN[Si](C)(C)C)[Si](C)(C)C1877.7Standard polar33892256
Norspermidine,3TMS,isomer #3C[Si](C)(C)N(CCCN)CCCN([Si](C)(C)C)[Si](C)(C)C1847.7Semi standard non polar33892256
Norspermidine,3TMS,isomer #3C[Si](C)(C)N(CCCN)CCCN([Si](C)(C)C)[Si](C)(C)C1932.4Standard non polar33892256
Norspermidine,3TMS,isomer #3C[Si](C)(C)N(CCCN)CCCN([Si](C)(C)C)[Si](C)(C)C2176.4Standard polar33892256
Norspermidine,4TMS,isomer #1C[Si](C)(C)N(CCCNCCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C2083.0Semi standard non polar33892256
Norspermidine,4TMS,isomer #1C[Si](C)(C)N(CCCNCCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C2129.7Standard non polar33892256
Norspermidine,4TMS,isomer #1C[Si](C)(C)N(CCCNCCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C1832.1Standard polar33892256
Norspermidine,4TMS,isomer #2C[Si](C)(C)NCCCN(CCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C1953.1Semi standard non polar33892256
Norspermidine,4TMS,isomer #2C[Si](C)(C)NCCCN(CCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C2104.5Standard non polar33892256
Norspermidine,4TMS,isomer #2C[Si](C)(C)NCCCN(CCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C1862.8Standard polar33892256
Norspermidine,5TMS,isomer #1C[Si](C)(C)N(CCCN([Si](C)(C)C)[Si](C)(C)C)CCCN([Si](C)(C)C)[Si](C)(C)C2204.7Semi standard non polar33892256
Norspermidine,5TMS,isomer #1C[Si](C)(C)N(CCCN([Si](C)(C)C)[Si](C)(C)C)CCCN([Si](C)(C)C)[Si](C)(C)C2254.4Standard non polar33892256
Norspermidine,5TMS,isomer #1C[Si](C)(C)N(CCCN([Si](C)(C)C)[Si](C)(C)C)CCCN([Si](C)(C)C)[Si](C)(C)C1834.4Standard polar33892256
Norspermidine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCNCCCN1730.4Semi standard non polar33892256
Norspermidine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCNCCCN1742.2Standard non polar33892256
Norspermidine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCNCCCN2505.5Standard polar33892256
Norspermidine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N(CCCN)CCCN1685.5Semi standard non polar33892256
Norspermidine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N(CCCN)CCCN1688.2Standard non polar33892256
Norspermidine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N(CCCN)CCCN2850.3Standard polar33892256
Norspermidine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCNCCCN[Si](C)(C)C(C)(C)C2148.3Semi standard non polar33892256
Norspermidine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCNCCCN[Si](C)(C)C(C)(C)C2174.9Standard non polar33892256
Norspermidine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCNCCCN[Si](C)(C)C(C)(C)C2083.3Standard polar33892256
Norspermidine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)N(CCCNCCCN)[Si](C)(C)C(C)(C)C2143.3Semi standard non polar33892256
Norspermidine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)N(CCCNCCCN)[Si](C)(C)C(C)(C)C2149.4Standard non polar33892256
Norspermidine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)N(CCCNCCCN)[Si](C)(C)C(C)(C)C2339.5Standard polar33892256
Norspermidine,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)NCCCN(CCCN)[Si](C)(C)C(C)(C)C2099.9Semi standard non polar33892256
Norspermidine,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)NCCCN(CCCN)[Si](C)(C)C(C)(C)C2121.9Standard non polar33892256
Norspermidine,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)NCCCN(CCCN)[Si](C)(C)C(C)(C)C2301.8Standard polar33892256
Norspermidine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2541.0Semi standard non polar33892256
Norspermidine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2512.8Standard non polar33892256
Norspermidine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)NCCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2166.2Standard polar33892256
Norspermidine,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)NCCCN(CCCN[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2470.4Semi standard non polar33892256
Norspermidine,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)NCCCN(CCCN[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2476.4Standard non polar33892256
Norspermidine,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)NCCCN(CCCN[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2199.7Standard polar33892256
Norspermidine,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)N(CCCN)CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2501.0Semi standard non polar33892256
Norspermidine,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)N(CCCN)CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2470.0Standard non polar33892256
Norspermidine,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)N(CCCN)CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2329.6Standard polar33892256
Norspermidine,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2888.9Semi standard non polar33892256
Norspermidine,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2808.2Standard non polar33892256
Norspermidine,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2236.4Standard polar33892256
Norspermidine,4TBDMS,isomer #2CC(C)(C)[Si](C)(C)NCCCN(CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2863.8Semi standard non polar33892256
Norspermidine,4TBDMS,isomer #2CC(C)(C)[Si](C)(C)NCCCN(CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2771.6Standard non polar33892256
Norspermidine,4TBDMS,isomer #2CC(C)(C)[Si](C)(C)NCCCN(CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2284.8Standard polar33892256
Norspermidine,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3205.1Semi standard non polar33892256
Norspermidine,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C3003.9Standard non polar33892256
Norspermidine,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)N(CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C2349.0Standard polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028332
KNApSAcK IDNot Available
Chemspider ID5729
KEGG Compound IDC03375
BioCyc IDNORSPERMIDINE
BiGG IDNot Available
Wikipedia LinkNorspermidine
METLIN IDNot Available
PubChem Compound5942
PDB IDNSD
ChEBI ID16841
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General ReferencesNot Available

Only showing the first 10 proteins. There are 20 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Diamine acetyltransferase 1
General function:
Involved in N-acetyltransferase activity
Specific function:
Enzyme which catalyzes the acetylation of polyamines. Substrate specificity: norspermidine = spermidine >> spermine > N(1)-acetylspermine > putrescine. This highly regulated enzyme allows a fine attenuation of the intracellular concentration of polyamines. Also involved in the regulation of polyamine transport out of cells. Acts on 1,3-diaminopropane, 1,5-diaminopentane, putrescine, spermidine (forming N(1)- and N(8)-acetylspermidine), spermine, N(1)-acetylspermidine and N(8)-acetylspermidine.
Gene Name:
SAT1
Uniprot ID:
P21673
Molecular weight:
20023.8
Enzyme Details
2. Choline dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity, acting on CH-OH group of donors
Specific function:
Not Available
Gene Name:
CHDH
Uniprot ID:
Q8NE62
Molecular weight:
65358.005
Enzyme Details
3. Dimethylglycine dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
DMGDH
Uniprot ID:
Q9UI17
Molecular weight:
96810.135
Enzyme Details
4. Spermine synthase
General function:
Involved in spermine synthase activity
Specific function:
Catalyzes the production of spermine from spermidine and decarboxylated S-adenosylmethionine (dcSAM).
Gene Name:
SMS
Uniprot ID:
P52788
Molecular weight:
35278.2
Enzyme Details
5. 4-trimethylaminobutyraldehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Converts gamma-trimethylaminobutyraldehyde into gamma-butyrobetaine. Catalyzes the irreversible oxidation of a broad range of aldehydes to the corresponding acids in an NAD-dependent reaction.
Gene Name:
ALDH9A1
Uniprot ID:
P49189
Molecular weight:
56291.485
Enzyme Details
6. Gamma-butyrobetaine dioxygenase
General function:
Involved in iron ion binding
Specific function:
Catalyzes the formation of L-carnitine from gamma-butyrobetaine.
Gene Name:
BBOX1
Uniprot ID:
O75936
Molecular weight:
44714.6
Enzyme Details
7. S-methyl-5'-thioadenosine phosphorylase
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the reversible phosphorylation of S-methyl-5'-thioadenosine (MTA) to adenine and 5-methylthioribose-1-phosphate. Involved in the breakdown of MTA, a major by-product of polyamine biosynthesis. Responsible for the first step in the methionine salvage pathway after MTA has been generated from S-adenosylmethionine. Has broad substrate specificity with 6-aminopurine nucleosides as preferred substrates.
Gene Name:
MTAP
Uniprot ID:
Q13126
Molecular weight:
31235.76
Enzyme Details
8. S-adenosylmethionine decarboxylase proenzyme
General function:
Involved in adenosylmethionine decarboxylase activity
Specific function:
Not Available
Gene Name:
AMD1
Uniprot ID:
P17707
Molecular weight:
21301.015
Enzyme Details
9. Glycine amidinotransferase, mitochondrial
General function:
Amino acid transport and metabolism
Specific function:
Catalyzes the biosynthesis of guanidinoacetate, the immediate precursor of creatine. Creatine plays a vital role in energy metabolism in muscle tissues. May play a role in embryonic and central nervous system development. May be involved in the response to heart failure by elevating local creatine synthesis.
Gene Name:
GATM
Uniprot ID:
P50440
Molecular weight:
48455.01
Enzyme Details
10. Betaine--homocysteine S-methyltransferase 1
General function:
Involved in zinc ion binding
Specific function:
Involved in the regulation of homocysteine metabolism. Converts betaine and homocysteine to dimethylglycine and methionine, respectively. This reaction is also required for the irreversible oxidation of choline.
Gene Name:
BHMT
Uniprot ID:
Q93088
Molecular weight:
44998.205

Only showing the first 10 proteins. There are 20 proteins in total.

Show all enzymes and transporters