Np mrd loader

Showing NP-Card for Spermidine (NP0000632)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 23:58:17 UTC
NP-MRD IDNP0000632
Secondary Accession NumbersNone
Natural Product Identification
Common NameSpermidine
DescriptionSpermidine, also known as SPD, 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. Abnormal bleeding, such as bleeding spontaneously or profusely from a very minor injury can also occur. Spermidine exists in all living species, ranging from bacteria to humans. Within humans, spermidine participates in a number of enzymatic reactions. In particular, 5'-methylthioadenosine and spermidine can be biosynthesized from S-adenosylmethioninamine and putrescine by the enzyme spermidine synthase. In addition, S-adenosylmethioninamine and spermidine can be converted into 5'-methylthioadenosine and spermine through the action of the enzyme spermine synthase. In humans, spermidine is involved in spermidine and spermine biosynthesis. Outside of the human body, spermidine is found, on average, in the highest concentration within cow milk and oats. Spermidine has also been detected, but not quantified in several different foods, such as common chokecherries, watercress, agars, strawberry guava, and bog bilberries. This could make spermidine a potential biomarker for the consumption of these foods. Spermidine is consideres as an uremic toxine. Increased levels of uremic toxins can stimulate the production of reactive oxygen species. Chronic exposure to uremic toxins can lead to a number of conditions including renal damage, chronic kidney disease and cardiovascular disease. As a uremic toxin, this compound can cause uremic syndrome. Uremic toxins such as spermidine are actively transported into the kidneys via organic ion transporters (especially OAT3).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000632 (Spermidine)


  Mrv1652309042000202D          

 10  9  0  0  0  0            999 V2000
    2.2836    2.1434    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0000632 (Spermidine)

HMDB0001257
     RDKit          3D
Spermidine
 29 28  0  0  0  0  0  0  0  0999 V2000
    5.1063    0.5322   -0.0635 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8090   -0.0973    0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7271    0.9253    0.1595 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3497    0.4240    0.4739 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8785   -0.6996   -0.4136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4652   -1.1335   -0.0640 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4907   -0.1948   -0.3803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8358   -0.7416    0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9332    0.2508   -0.2328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2004   -0.2428    0.2486 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9811    1.5471    0.1736 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8612    0.1466    0.5746 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7159   -0.8994   -0.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9207   -0.5787    1.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9353    1.7315    0.9202 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7801    1.4093   -0.8457 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3257    0.1042    1.5554 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5833    1.2474    0.3768 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9592   -0.4342   -1.4887 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5463   -1.5729   -0.2739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4453   -1.2906    0.9641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6430   -0.1110   -1.4960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3472    0.7675    0.1125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8540   -0.8580    1.2018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0456   -1.6965   -0.3794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0025    0.3241   -1.3427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7648    1.2572    0.1644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5219    0.2060    1.1360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9299   -0.3223   -0.4657 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
  9 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  0
  8 25  1  0
  9 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
M  END
Download

3D SDF for NP0000632 (Spermidine)


  Mrv1652309042000202D          

 10  9  0  0  0  0            999 V2000
    2.2836    2.1434    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000632

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCCCNCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2

> <INCHI_KEY>
ATHGHQPFGPMSJY-UHFFFAOYSA-N

> <FORMULA>
C7H19N3

> <MOLECULAR_WEIGHT>
145.2459

> <EXACT_MASS>
145.157897623

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
18.802478340004217

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4-aminobutyl)(3-aminopropyl)amine

> <ALOGPS_LOGP>
-0.62

> <JCHEM_LOGP>
-1.1495639400000002

> <ALOGPS_LOGS>
-0.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA_STRONGEST_BASIC>
10.676624477088431

> <JCHEM_POLAR_SURFACE_AREA>
64.07

> <JCHEM_REFRACTIVITY>
44.968399999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.27e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
spermidine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000632 (Spermidine)

HMDB0001257
     RDKit          3D
Spermidine
 29 28  0  0  0  0  0  0  0  0999 V2000
    5.1063    0.5322   -0.0635 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8090   -0.0973    0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7271    0.9253    0.1595 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3497    0.4240    0.4739 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8785   -0.6996   -0.4136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4652   -1.1335   -0.0640 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4907   -0.1948   -0.3803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8358   -0.7416    0.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9332    0.2508   -0.2328 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2004   -0.2428    0.2486 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9811    1.5471    0.1736 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8612    0.1466    0.5746 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7159   -0.8994   -0.5163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9207   -0.5787    1.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9353    1.7315    0.9202 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7801    1.4093   -0.8457 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3257    0.1042    1.5554 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5833    1.2474    0.3768 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9592   -0.4342   -1.4887 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5463   -1.5729   -0.2739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4453   -1.2906    0.9641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6430   -0.1110   -1.4960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3472    0.7675    0.1125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8540   -0.8580    1.2018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0456   -1.6965   -0.3794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0025    0.3241   -1.3427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7648    1.2572    0.1644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5219    0.2060    1.1360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9299   -0.3223   -0.4657 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
  9 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
  8 24  1  0
  8 25  1  0
  9 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
M  END
Download

PDB for NP0000632 (Spermidine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       4.263   4.001   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      10.931   4.771   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      16.266   4.771   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   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
Download

3D PDB for NP0000632 (Spermidine)

COMPND    HMDB0001257
HETATM    1  N1  UNL     1       5.106   0.532  -0.063  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.809  -0.097   0.255  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.727   0.925   0.159  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.350   0.424   0.474  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.878  -0.700  -0.414  1.00  0.00           C  
HETATM    6  N2  UNL     1      -0.465  -1.134  -0.064  1.00  0.00           N  
HETATM    7  C5  UNL     1      -1.491  -0.195  -0.380  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.836  -0.742   0.116  1.00  0.00           C  
HETATM    9  C7  UNL     1      -3.933   0.251  -0.233  1.00  0.00           C  
HETATM   10  N3  UNL     1      -5.200  -0.243   0.249  1.00  0.00           N  
HETATM   11  H1  UNL     1       4.981   1.547   0.174  1.00  0.00           H  
HETATM   12  H2  UNL     1       5.861   0.147   0.575  1.00  0.00           H  
HETATM   13  H3  UNL     1       3.716  -0.899  -0.516  1.00  0.00           H  
HETATM   14  H4  UNL     1       3.921  -0.579   1.241  1.00  0.00           H  
HETATM   15  H5  UNL     1       2.935   1.731   0.920  1.00  0.00           H  
HETATM   16  H6  UNL     1       2.780   1.409  -0.846  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.326   0.104   1.555  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.583   1.247   0.377  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.959  -0.434  -1.489  1.00  0.00           H  
HETATM   20  H10 UNL     1       1.546  -1.573  -0.274  1.00  0.00           H  
HETATM   21  H11 UNL     1      -0.445  -1.291   0.964  1.00  0.00           H  
HETATM   22  H12 UNL     1      -1.643  -0.111  -1.496  1.00  0.00           H  
HETATM   23  H13 UNL     1      -1.347   0.767   0.113  1.00  0.00           H  
HETATM   24  H14 UNL     1      -2.854  -0.858   1.202  1.00  0.00           H  
HETATM   25  H15 UNL     1      -3.046  -1.697  -0.379  1.00  0.00           H  
HETATM   26  H16 UNL     1      -4.003   0.324  -1.343  1.00  0.00           H  
HETATM   27  H17 UNL     1      -3.765   1.257   0.164  1.00  0.00           H  
HETATM   28  H18 UNL     1      -5.522   0.206   1.136  1.00  0.00           H  
HETATM   29  H19 UNL     1      -5.930  -0.322  -0.466  1.00  0.00           H  
CONECT    1    2   11   12
CONECT    2    3   13   14
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6   19   20
CONECT    6    7   21
CONECT    7    8   22   23
CONECT    8    9   24   25
CONECT    9   10   26   27
CONECT   10   28   29
END
Download

SMILES for NP0000632 (Spermidine)

NCCCCNCCCN
Download

INCHI for NP0000632 (Spermidine)

InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
Download
View in JSmol
Synonyms
ValueSource
1,5,10-TriazadecaneChEBI
4-AzaoctamethylenediamineChEBI
4-Azaoctane-1,8-diamineChEBI
N-(3-Aminopropyl)-1,4-butane-diamineChEBI
SpermidinChEBI
1,8-Diamino-4-azaoctaneHMDB
AminopropylbutandiamineHMDB
N-(3-Aminopropyl)-1,4-butanediamineHMDB
N-(3-Aminopropyl)-1,4-diamino-butaneHMDB
N-(3-Aminopropyl)-1,4-diaminobutaneHMDB
N-(3-Aminopropyl)-4-aminobutylamineHMDB
N-(4-Aminobutyl)-1,3-diaminopropaneHMDB
N-(gamma-Aminopropyl)tetramethylenediamineHMDB
SPDHMDB
Chemical FormulaC7H19N3
Average Mass145.2459 Da
Monoisotopic Mass145.15790 Da
IUPAC Name(4-aminobutyl)(3-aminopropyl)amine
Traditional Namespermidine
CAS Registry Number124-20-9
SMILES
NCCCCNCCCN
InChI Identifier
InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
InChI KeyATHGHQPFGPMSJY-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Agaricus bisporusFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Apis ceranaLOTUS Database
Arabidopsis thalianaKNApSAcK Database
Arachis hypogaeaKNApSAcK Database
Avena sativaKNApSAcK Database
Avena sativa L.FooDB
Bombyx moriLOTUS Database
Brugmansia x candidaLOTUS Database
Camellia sinensisLOTUS Database
Canavalia bonariensisKNApSAcK Database
Canavalia ensiformisKNApSAcK Database
Canavalia gladiataLOTUS Database
Cannabis sativaCannabisDB
      Not Available
Cicer arietinumLOTUS Database
Cichorium intybusLOTUS Database
Coffea arabica L.FooDB
Cucumis sativusLOTUS Database
Cucumis sativus L.FooDB
Cyanidium caldariumLOTUS Database
Glycine maxKNApSAcK Database
Heliotropium angiospermumLOTUS Database
Hydrilla verticillataLOTUS Database
Ipomoea batatasKNApSAcK Database
Lathyrus sativusKNApSAcK Database
Lotus corniculatusLOTUS Database
Lyallia kerguelensisKNApSAcK Database
Malus domesticaLOTUS Database
Malus pumilaFooDB
Mus musculusLOTUS Database
Musa x paradisiacaFooDB
Nicotiana alataLOTUS Database
Nicotiana tabacumKNApSAcK Database
Panax ginsengKNApSAcK Database
Peucedanum palustreLOTUS Database
Phaseolus coccineusKNApSAcK Database
Phaseolus lunatusKNApSAcK Database
Phaseolus vulgarisKNApSAcK Database
Picea glaucaLOTUS Database
Pisum sativumKNApSAcK Database
Pleurotus ostreatusFooDB
    • Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Populus tremulaLOTUS Database
Pseudomonas hydrogenovoraLOTUS Database
Psophocarpus tetragonolobusKNApSAcK Database
Salmonella entericaLOTUS Database
Senecio congestusLOTUS Database
Senecio vulgarisLOTUS Database
Solanum lycopersicumKNApSAcK Database
Solanum lycopersicum var. lycopersicumFooDB
Streptomyces nigraLOTUS Database
Synechococcus elongatusLOTUS Database
Trifolium subterraneumKNApSAcK Database
Trypanosoma bruceiLOTUS Database
Utricularia intermediaLOTUS Database
Vicia fabaKNApSAcK Database
Vicia sativaKNApSAcK Database
Vigna angularisKNApSAcK Database
Vigna mungoKNApSAcK Database
Vigna radiataKNApSAcK Database
Vigna unguiculataKNApSAcK Database
Vitis viniferaLOTUS Database
Wisteria floribundaKNApSAcK Database
Zea maysLOTUS Database
Zea mays L.FooDB
Species Where Detected
Species NameSourceReference
Coprinus comatusKNApSAcK Database
Escherichia coliKNApSAcK Database
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point< 25 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility32.7 g/LALOGPS
logP-0.62ALOGPS
logP-1.1ChemAxon
logS-0.65ALOGPS
pKa (Strongest Basic)10.68ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area64.07 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity44.97 m³·mol⁻¹ChemAxon
Polarizability18.8 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001257
DrugBank IDDB03566
Phenol Explorer Compound IDNot Available
FoodDB IDFDB008042
KNApSAcK IDC00001431
Chemspider ID1071
KEGG Compound IDC00315
BioCyc IDSPERMIDINE
BiGG ID34593
Wikipedia LinkSpermidine
METLIN ID254
PubChem Compound1102
PDB IDNot Available
ChEBI ID16610
Good Scents IDrw1284261
References
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
  2. Venza M, Visalli M, Cicciu D, Teti D: Determination of polyamines in human saliva by high-performance liquid chromatography with fluorescence detection. J Chromatogr B Biomed Sci Appl. 2001 Jun 5;757(1):111-7. [PubMed:11419735 ]
  3. Uehara N, Shirakawa S, Uchino H, Saeki Y: Elevated contents of spermidine and spermine in the erythrocytes of cancer patients. Cancer. 1980 Jan 1;45(1):108-11. [PubMed:7350997 ]
  4. Proctor MS, Fletcher HV Jr, Shukla JB, Rennert OM: Elevated spermidine and spermine levels in the blood of psoriasis patients. J Invest Dermatol. 1975 Oct;65(4):409-11. [PubMed:1176793 ]
  5. El Baze P, Milano G, Verrando P, Renee N, Ortonne JP: Polyamine levels in normal human skin. A comparative study of pure epidermis, pure dermis, and suction blister fluid. Arch Dermatol Res. 1983;275(4):218-21. [PubMed:6625645 ]
  6. Mirzoian PA, Promyslov MSh: [Contents of putrescine, spermidine and spermine in tissue of the human brain glial tumors]. Ukr Biokhim Zh (1978). 1979 Sep-Oct;51(5):474-6. [PubMed:516181 ]
  7. Chaisiri P, Harper ME, Blamey RW, Peeling WB, Griffiths K: Plasma spermidine concentrations in patients with tumours of the breast or prostate or testis. Clin Chim Acta. 1980 Jul 1;104(3):367-75. [PubMed:6156039 ]
  8. Martinet N, Beninati S, Nigra TP, Folk JE: N1N8-bis(gamma-glutamyl)spermidine cross-linking in epidermal-cell envelopes. Comparison of cross-link levels in normal and psoriatic cell envelopes. Biochem J. 1990 Oct 15;271(2):305-8. [PubMed:2241917 ]