Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (27)transporters (2) Show 29 proteins XML

enzymes (27)transporters (2) Show 29 proteins

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2025-05-29 18:10:13 UTC

HMDB ID

HMDB0001257

Secondary Accession Numbers

HMDB01257

Metabolite Identification

Common Name

Spermidine

Description

Spermidine, 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

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

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

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

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1,5,10-Triazadecane	ChEBI
4-Azaoctamethylenediamine	ChEBI
4-Azaoctane-1,8-diamine	ChEBI
N-(3-Aminopropyl)-1,4-butane-diamine	ChEBI
Spermidin	ChEBI
1,8-Diamino-4-azaoctane	HMDB
Aminopropylbutandiamine	HMDB
N-(3-Aminopropyl)-1,4-butanediamine	HMDB
N-(3-Aminopropyl)-1,4-diamino-butane	HMDB
N-(3-Aminopropyl)-1,4-diaminobutane	HMDB
N-(3-Aminopropyl)-4-aminobutylamine	HMDB
N-(4-Aminobutyl)-1,3-diaminopropane	HMDB
N-(gamma-Aminopropyl)tetramethylenediamine	HMDB
SPD	HMDB

Chemical Formula

C₇H₁₉N₃

Average Molecular Weight

145.2459

Monoisotopic Molecular Weight

145.157897623

IUPAC Name

(4-aminobutyl)(3-aminopropyl)amine

Traditional Name

spermidine

CAS Registry Number

124-20-9

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

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.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

Dialkylamines

Alternative Parents

Substituents

Secondary aliphatic amine
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary aliphatic amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

triamine (CHEBI:16610 )
polyazaalkane (CHEBI:16610 )

Ontology

Physiological effect

Health effect

Digestive system disorder

Hepatobiliary disorder

Hepatic disorder

Liver damage (PMID: 31434538)

Nervous system disorder

Nerve damage (PMID: 31434538)

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 22626821)
Saliva (PMID: 11419735)
Cerebrospinal Fluid (CSF) (PMID: 15745737)

Organ

Cell

Hematocyte

Platelet (HMDB: HMDB0001257)

Tissue

Epithelium

Epidermis (HMDB: HMDB0001257)

Excreta

Biofluid or Excreta

Urine (PMID: 19309105)
Feces (PMID: 20669995)

Cellular substructure

Cytoplasm (HMDB: HMDB0001257)
Extracellular (HMDB: HMDB0001257)

Source

Exogenous

Exogenous (HMDB: HMDB0001257)

Herbs and Spices (FooDB: FOOD00866)

Nut

Almond (FooDB: FOOD00148)
Brazil nut (FooDB: FOOD00024)
Cashew nut (FooDB: FOOD00011)
Chestnut (FooDB: FOOD00045)
Hazelnut (FooDB: FOOD00376)
Peanut (FooDB: FOOD00016)
Pecan nut (FooDB: FOOD00044)
Pine nut (FooDB: FOOD00138)
Pistachio (FooDB: FOOD00140)
Walnut (FooDB: FOOD00608)
Acorn (FooDB: FOOD00282)
Beech nut (FooDB: FOOD00299)
Butternut (FooDB: FOOD00316)
Chinese chestnut (FooDB: FOOD00331)
European chestnut (FooDB: FOOD00363)
Hickory nut (FooDB: FOOD00377)
Macadamia nut (FooDB: FOOD00525)
Mixed nuts (FooDB: FOOD00771)
Pili nut (FooDB: FOOD00432)
Colorado pinyon (FooDB: FOOD00433)
Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)
Japanese chestnut (FooDB: FOOD00385)
Common hazelnut (FooDB: FOOD00062)
Macadamia nut (M. tetraphylla) (FooDB: FOOD00225)
Japanese walnut (FooDB: FOOD00240)
Nuts (FooDB: FOOD00869)

Fruit

Pome

Drupe

Apricot (FooDB: FOOD00144)
Prunus (Cherry, Plum) (FooDB: FOOD00143)
Nectarine (FooDB: FOOD00229)
Peach (FooDB: FOOD00149)
European plum (FooDB: FOOD00147)
Sour cherry (FooDB: FOOD00146)
Sweet cherry (FooDB: FOOD00145)
Common chokecherry (FooDB: FOOD00562)
Peach (var.) (FooDB: FOOD00230)

Tropical fruit

Berry

Bilberry (FooDB: FOOD00193)
Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Elderberry (FooDB: FOOD00358)
Gooseberry (FooDB: FOOD00157)
Grape (FooDB: FOOD00369)
Lingonberry (FooDB: FOOD00194)
Loganberry (FooDB: FOOD00400)
Strawberry (FooDB: FOOD00083)
Boysenberry (FooDB: FOOD00542)
American cranberry (FooDB: FOOD00192)
Common grape (FooDB: FOOD00204)
Strawberry guava (FooDB: FOOD00482)
Black mulberry (FooDB: FOOD00117)
Red raspberry (FooDB: FOOD00162)
Muscadine grape (FooDB: FOOD00203)
Salmonberry (FooDB: FOOD00456)
Alaska blueberry (FooDB: FOOD00380)
Sea-buckthornberry (FooDB: FOOD00087)
Black elderberry (FooDB: FOOD00166)
Black crowberry (FooDB: FOOD00075)
Black huckleberry (FooDB: FOOD00084)
Mulberry (FooDB: FOOD00116)
Black chokeberry (FooDB: FOOD00136)
Cloudberry (FooDB: FOOD00161)
Black raspberry (FooDB: FOOD00163)
Rowanberry (FooDB: FOOD00176)
Lowbush blueberry (FooDB: FOOD00189)
Sparkleberry (FooDB: FOOD00190)
Highbush blueberry (FooDB: FOOD00191)
Arctic blackberry (FooDB: FOOD00207)
Bayberry (FooDB: FOOD00209)
Elliott's blueberry (FooDB: FOOD00210)
Canada blueberry (FooDB: FOOD00211)
Bog bilberry (FooDB: FOOD00212)
Buffalo currant (FooDB: FOOD00213)
European cranberry (FooDB: FOOD00217)
Deerberry (FooDB: FOOD00218)
Cascade huckleberry (FooDB: FOOD00220)
Oval-leaf huckleberry (FooDB: FOOD00221)
Evergreen huckleberry (FooDB: FOOD00222)
Red huckleberry (FooDB: FOOD00223)
Summer grape (FooDB: FOOD00227)
Fox grape (FooDB: FOOD00228)
Half-highbush blueberry (FooDB: FOOD00248)
Jostaberry (FooDB: FOOD00257)
Sweet rowanberry (FooDB: FOOD00265)
Skunk currant (FooDB: FOOD00267)
Squashberry (FooDB: FOOD00344)
Ohelo berry (FooDB: FOOD00419)
Chinese bayberry (FooDB: FOOD00852)
Saskatoon berry (FooDB: FOOD00884)
Nanking cherry (FooDB: FOOD00885)

Other fruit

Date (FooDB: FOOD00135)
Fig (FooDB: FOOD00081)
Jujube (FooDB: FOOD00388)

Citrus

Grapefruit (FooDB: FOOD00256)
Lemon (FooDB: FOOD00054)
Lime (FooDB: FOOD00053)
Sweet orange (FooDB: FOOD00057)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Persian lime (FooDB: FOOD00543)
Pummelo (FooDB: FOOD00055)
Grapefruit/Pummelo hybrid (FooDB: FOOD00255)
Citrus (FooDB: FOOD00859)

Fruits (FooDB: FOOD00871)

Vegetable

Shoot vegetable

Fruit vegetable

Eggplant (FooDB: FOOD00174)
Avocado (FooDB: FOOD00130)
Groundcherry (FooDB: FOOD00371)
Olive (FooDB: FOOD00121)
Pepper (FooDB: FOOD00040)
Garden tomato (FooDB: FOOD00171)
Mexican groundcherry (FooDB: FOOD00491)
Green bell pepper (FooDB: FOOD00877)
Yellow bell pepper (FooDB: FOOD00878)
Red bell pepper (FooDB: FOOD00880)
Italian sweet red pepper (FooDB: FOOD00881)
Garden tomato (var.) (FooDB: FOOD00173)
Cherry tomato (FooDB: FOOD00172)
Pepper (C. baccatum) (FooDB: FOOD00231)
Pepper (C. chinense) (FooDB: FOOD00232)
Pepper (Capsicum) (FooDB: FOOD00233)
Pepper (C. frutescens) (FooDB: FOOD00428)
Pepper (C. pubescens) (FooDB: FOOD00849)
Orange bell pepper (FooDB: FOOD00879)

Root vegetable

Cabbage

Leaf vegetable

Lettuce (FooDB: FOOD00095)
Swiss chard (FooDB: FOOD00237)
Garden cress (FooDB: FOOD00099)
Endive (FooDB: FOOD00048)
Spinach (FooDB: FOOD00178)
Common beet (FooDB: FOOD00025)
Garland chrysanthemum (FooDB: FOOD00333)
Jute (FooDB: FOOD00389)
Lambsquarters (FooDB: FOOD00394)
New Zealand spinach (FooDB: FOOD00415)
Swamp cabbage (FooDB: FOOD00091)
Rocket salad (ssp.) (FooDB: FOOD00077)
Yautia (FooDB: FOOD00510)
Romaine lettuce (FooDB: FOOD00888)
Rocket salad (FooDB: FOOD00244)
Chicory leaves (FooDB: FOOD00250)
Corn salad (FooDB: FOOD00340)
Malabar spinach (FooDB: FOOD00404)
Ostrich fern (FooDB: FOOD00556)
Green vegetables (FooDB: FOOD00872)

Mushroom

Tuber

Onion-family vegetable

Leek (FooDB: FOOD00007)
Allium (FooDB: FOOD00005)
Wild leek (FooDB: FOOD00396)
Shallot (FooDB: FOOD00243)
Garden onion (FooDB: FOOD00006)
Garden onion (var.) (FooDB: FOOD00226)
Onion-family vegetables (FooDB: FOOD00855)
Green onion (FooDB: FOOD00963)
Red onion (FooDB: FOOD00962)

Other vegetable

Okra (FooDB: FOOD00420)
Horseradish tree (FooDB: FOOD00379)
Sacred lotus (FooDB: FOOD00402)
Tree fern (FooDB: FOOD00797)
Chinese water chestnut (FooDB: FOOD00332)
Nopal (FooDB: FOOD00416)
Carob (FooDB: FOOD00321)
Agave (FooDB: FOOD00563)
Narrowleaf cattail (FooDB: FOOD00564)
Giant butterbur (FooDB: FOOD00314)
Sesbania flower (FooDB: FOOD00469)

Stalk vegetable

Brassica

Brassicas (FooDB: FOOD00857)

Cereal and cereal product

Other bread

Other bread (FooDB: FOOD00269)

Cereal

Cereal product

Dough

Sourdough (FooDB: FOOD00275)

Cereals and cereal products (FooDB: FOOD00858)

Pulse

Bean

Lentil

Lentils (FooDB: FOOD00098)

Pea

Other pulse

White lupine (FooDB: FOOD00403)
Lupine (FooDB: FOOD00104)

Pulses (FooDB: FOOD00867)

Soy

Soy bean (FooDB: FOOD00085)

Soy product

Other soy product (FooDB: FOOD00271)

Abalone (FooDB: FOOD00279)
Conch (FooDB: FOOD00611)

Gourd

Chayote (FooDB: FOOD00325)
Cucumber (FooDB: FOOD00065)
Muskmelon (FooDB: FOOD00064)
Cucurbita (FooDB: FOOD00066)
Watermelon (FooDB: FOOD00052)
Bitter gourd (FooDB: FOOD00115)
Calabash (FooDB: FOOD00318)
Towel gourd (FooDB: FOOD00492)
Winter squash (FooDB: FOOD00283)
Butternut squash (FooDB: FOOD00317)
Wax gourd (FooDB: FOOD00499)
Green zucchini (FooDB: FOOD00875)
Yellow zucchini (FooDB: FOOD00876)
Japanese pumpkin (FooDB: FOOD00886)
Sunburst squash (pattypan squash) (FooDB: FOOD00874)
Tinda (FooDB: FOOD00559)
Horned melon (FooDB: FOOD00761)

Milk and milk product

Unfermented milk

Milk (Cow) (FooDB: FOOD00618)

Tea

Herbal tea

Greenthread tea (FooDB: FOOD00820)

Coffee and coffee product

Coffee

Arabica coffee (FooDB: FOOD00059)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Endogenous

Endogenous (HMDB: HMDB0001257)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Methionine Metabolism (HMDB: HMDB0001257)
Spermidine and Spermine Biosynthesis (HMDB: HMDB0001257)
Spermidine Biosynthesis I (PathBank: SMP0122229)
Beta-Alanine metabolism (PathBank: SMP0002307)
S-Adenosyl-L-Methionine Biosynthesis (PathBank: SMP0121301)
Spermidine Biosynthesis and Metabolism (PathBank: SMP0002097)

Disease pathway

Methylenetetrahydrofolate Reductase Deficiency (MTHFRD) (PathBank: SMP0000340)
Cystathionine beta-Synthase Deficiency (PathBank: SMP0120471)
Hypermethioninemia (PathBank: SMP0120498)
Glycine N-Methyltransferase Deficiency (PathBank: SMP0120707)
Methionine Adenosyltransferase Deficiency (PathBank: SMP0120739)
Homocystinuria-Megaloblastic Anemia Due to Defect in Cobalamin Metabolism, cblG Complementation Type (PathBank: SMP0120853)
S-Adenosylhomocysteine (SAH) Hydrolase Deficiency (PathBank: SMP0120747)

Role

Biological role

Primary metabolite (HMDB: HMDB0001257)
Waste product (PMID: 35448883)

Industrial application

Manufacturing industry

Material processing agent

Solid material processing agent

Protective agent

Antioxidant (HMDB: HMDB0001257)
Antioxidant (HMDB: HMDB0001257)

Pharmaceutical industry

Biomarker

Leukemia (MarkerDB: MDB00000312)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	< 25 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	MetCCS_train_pos	131.891	30932474
[M+H]+	Not Available	131.7	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000537

Predicted Molecular Properties

Property	Value	Source
Water Solubility	32.7 g/L	ALOGPS
logP	-0.62	ALOGPS
logP	-1.1	ChemAxon
logS	-0.65	ALOGPS
pKa (Strongest Basic)	10.68	ChemAxon
Physiological Charge	3	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	64.07 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	44.97 m³·mol⁻¹	ChemAxon
Polarizability	18.8 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	132.807	31661259
DarkChem	[M-H]-	128.128	31661259
AllCCS	[M+H]+	132.393	32859911
AllCCS	[M-H]-	135.176	32859911
DeepCCS	[M+H]+	135.668	30932474
DeepCCS	[M-H]-	133.212	30932474
DeepCCS	[M-2H]-	169.357	30932474
DeepCCS	[M+Na]+	144.54	30932474
AllCCS	[M+H]+	132.4	32859911
AllCCS	[M+H-H2O]+	128.6	32859911
AllCCS	[M+NH4]+	136.0	32859911
AllCCS	[M+Na]+	137.0	32859911
AllCCS	[M-H]-	135.2	32859911
AllCCS	[M+Na-2H]-	137.6	32859911
AllCCS	[M+HCOO]-	140.2	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
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.	1.05 minutes	32390414
Predicted by Siyang on May 30, 2022	7.9516 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	8.09 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	477.4 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	289.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	245.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	52.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	173.4 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	61.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	283.6 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	224.0 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	1157.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	516.3 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	38.2 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	457.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	185.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	249.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	1149.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	810.7 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	349.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Spermidine	NCCCCNCCCN	2053.6	Standard polar	33892256
Spermidine	NCCCCNCCCN	1407.1	Standard non polar	33892256
Spermidine	NCCCCNCCCN	1305.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Spermidine,1TMS,isomer #1	C[Si](C)(C)NCCCCNCCCN	1629.0	Semi standard non polar	33892256
Spermidine,1TMS,isomer #1	C[Si](C)(C)NCCCCNCCCN	1646.9	Standard non polar	33892256
Spermidine,1TMS,isomer #1	C[Si](C)(C)NCCCCNCCCN	2557.9	Standard polar	33892256
Spermidine,1TMS,isomer #2	C[Si](C)(C)NCCCNCCCCN	1623.1	Semi standard non polar	33892256
Spermidine,1TMS,isomer #2	C[Si](C)(C)NCCCNCCCCN	1647.9	Standard non polar	33892256
Spermidine,1TMS,isomer #2	C[Si](C)(C)NCCCNCCCCN	2552.0	Standard polar	33892256
Spermidine,1TMS,isomer #3	C[Si](C)(C)N(CCCN)CCCCN	1549.1	Semi standard non polar	33892256
Spermidine,1TMS,isomer #3	C[Si](C)(C)N(CCCN)CCCCN	1591.5	Standard non polar	33892256
Spermidine,1TMS,isomer #3	C[Si](C)(C)N(CCCN)CCCCN	2903.4	Standard polar	33892256
Spermidine,2TMS,isomer #1	C[Si](C)(C)NCCCCNCCCN[Si](C)(C)C	1792.8	Semi standard non polar	33892256
Spermidine,2TMS,isomer #1	C[Si](C)(C)NCCCCNCCCN[Si](C)(C)C	1925.2	Standard non polar	33892256
Spermidine,2TMS,isomer #1	C[Si](C)(C)NCCCCNCCCN[Si](C)(C)C	2056.0	Standard polar	33892256
Spermidine,2TMS,isomer #2	C[Si](C)(C)N(CCCCNCCCN)[Si](C)(C)C	1836.2	Semi standard non polar	33892256
Spermidine,2TMS,isomer #2	C[Si](C)(C)N(CCCCNCCCN)[Si](C)(C)C	1872.5	Standard non polar	33892256
Spermidine,2TMS,isomer #2	C[Si](C)(C)N(CCCCNCCCN)[Si](C)(C)C	2482.0	Standard polar	33892256
Spermidine,2TMS,isomer #3	C[Si](C)(C)NCCCCN(CCCN)[Si](C)(C)C	1707.2	Semi standard non polar	33892256
Spermidine,2TMS,isomer #3	C[Si](C)(C)NCCCCN(CCCN)[Si](C)(C)C	1813.0	Standard non polar	33892256
Spermidine,2TMS,isomer #3	C[Si](C)(C)NCCCCN(CCCN)[Si](C)(C)C	2383.2	Standard polar	33892256
Spermidine,2TMS,isomer #4	C[Si](C)(C)N(CCCNCCCCN)[Si](C)(C)C	1824.7	Semi standard non polar	33892256
Spermidine,2TMS,isomer #4	C[Si](C)(C)N(CCCNCCCCN)[Si](C)(C)C	1869.8	Standard non polar	33892256
Spermidine,2TMS,isomer #4	C[Si](C)(C)N(CCCNCCCCN)[Si](C)(C)C	2475.3	Standard polar	33892256
Spermidine,2TMS,isomer #5	C[Si](C)(C)NCCCN(CCCCN)[Si](C)(C)C	1733.2	Semi standard non polar	33892256
Spermidine,2TMS,isomer #5	C[Si](C)(C)NCCCN(CCCCN)[Si](C)(C)C	1812.2	Standard non polar	33892256
Spermidine,2TMS,isomer #5	C[Si](C)(C)NCCCN(CCCCN)[Si](C)(C)C	2393.6	Standard polar	33892256
Spermidine,3TMS,isomer #1	C[Si](C)(C)NCCCNCCCCN([Si](C)(C)C)[Si](C)(C)C	1972.6	Semi standard non polar	33892256
Spermidine,3TMS,isomer #1	C[Si](C)(C)NCCCNCCCCN([Si](C)(C)C)[Si](C)(C)C	2082.2	Standard non polar	33892256
Spermidine,3TMS,isomer #1	C[Si](C)(C)NCCCNCCCCN([Si](C)(C)C)[Si](C)(C)C	1962.6	Standard polar	33892256
Spermidine,3TMS,isomer #2	C[Si](C)(C)NCCCCN(CCCN[Si](C)(C)C)[Si](C)(C)C	1824.5	Semi standard non polar	33892256
Spermidine,3TMS,isomer #2	C[Si](C)(C)NCCCCN(CCCN[Si](C)(C)C)[Si](C)(C)C	2040.2	Standard non polar	33892256
Spermidine,3TMS,isomer #2	C[Si](C)(C)NCCCCN(CCCN[Si](C)(C)C)[Si](C)(C)C	1969.1	Standard polar	33892256
Spermidine,3TMS,isomer #3	C[Si](C)(C)NCCCCNCCCN([Si](C)(C)C)[Si](C)(C)C	1961.7	Semi standard non polar	33892256
Spermidine,3TMS,isomer #3	C[Si](C)(C)NCCCCNCCCN([Si](C)(C)C)[Si](C)(C)C	2080.4	Standard non polar	33892256
Spermidine,3TMS,isomer #3	C[Si](C)(C)NCCCCNCCCN([Si](C)(C)C)[Si](C)(C)C	1960.1	Standard polar	33892256
Spermidine,3TMS,isomer #4	C[Si](C)(C)N(CCCN)CCCCN([Si](C)(C)C)[Si](C)(C)C	1931.4	Semi standard non polar	33892256
Spermidine,3TMS,isomer #4	C[Si](C)(C)N(CCCN)CCCCN([Si](C)(C)C)[Si](C)(C)C	2025.8	Standard non polar	33892256
Spermidine,3TMS,isomer #4	C[Si](C)(C)N(CCCN)CCCCN([Si](C)(C)C)[Si](C)(C)C	2285.6	Standard polar	33892256
Spermidine,3TMS,isomer #5	C[Si](C)(C)N(CCCCN)CCCN([Si](C)(C)C)[Si](C)(C)C	1961.2	Semi standard non polar	33892256
Spermidine,3TMS,isomer #5	C[Si](C)(C)N(CCCCN)CCCN([Si](C)(C)C)[Si](C)(C)C	2036.7	Standard non polar	33892256
Spermidine,3TMS,isomer #5	C[Si](C)(C)N(CCCCN)CCCN([Si](C)(C)C)[Si](C)(C)C	2292.2	Standard polar	33892256
Spermidine,4TMS,isomer #1	C[Si](C)(C)N(CCCCNCCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	2182.3	Semi standard non polar	33892256
Spermidine,4TMS,isomer #1	C[Si](C)(C)N(CCCCNCCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	2231.2	Standard non polar	33892256
Spermidine,4TMS,isomer #1	C[Si](C)(C)N(CCCCNCCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	1917.2	Standard polar	33892256
Spermidine,4TMS,isomer #2	C[Si](C)(C)NCCCN(CCCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	2045.8	Semi standard non polar	33892256
Spermidine,4TMS,isomer #2	C[Si](C)(C)NCCCN(CCCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	2202.4	Standard non polar	33892256
Spermidine,4TMS,isomer #2	C[Si](C)(C)NCCCN(CCCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	1947.4	Standard polar	33892256
Spermidine,4TMS,isomer #3	C[Si](C)(C)NCCCCN(CCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	2044.8	Semi standard non polar	33892256
Spermidine,4TMS,isomer #3	C[Si](C)(C)NCCCCN(CCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	2204.1	Standard non polar	33892256
Spermidine,4TMS,isomer #3	C[Si](C)(C)NCCCCN(CCCN([Si](C)(C)C)[Si](C)(C)C)[Si](C)(C)C	1944.5	Standard polar	33892256
Spermidine,5TMS,isomer #1	C[Si](C)(C)N(CCCCN([Si](C)(C)C)[Si](C)(C)C)CCCN([Si](C)(C)C)[Si](C)(C)C	2296.3	Semi standard non polar	33892256
Spermidine,5TMS,isomer #1	C[Si](C)(C)N(CCCCN([Si](C)(C)C)[Si](C)(C)C)CCCN([Si](C)(C)C)[Si](C)(C)C	2343.9	Standard non polar	33892256
Spermidine,5TMS,isomer #1	C[Si](C)(C)N(CCCCN([Si](C)(C)C)[Si](C)(C)C)CCCN([Si](C)(C)C)[Si](C)(C)C	1912.9	Standard polar	33892256
Spermidine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCCNCCCN	1837.9	Semi standard non polar	33892256
Spermidine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCCNCCCN	1836.0	Standard non polar	33892256
Spermidine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCCNCCCN	2601.6	Standard polar	33892256
Spermidine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCNCCCCN	1832.9	Semi standard non polar	33892256
Spermidine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCNCCCCN	1839.1	Standard non polar	33892256
Spermidine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCNCCCCN	2598.0	Standard polar	33892256
Spermidine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N(CCCN)CCCCN	1794.5	Semi standard non polar	33892256
Spermidine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N(CCCN)CCCCN	1786.9	Standard non polar	33892256
Spermidine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N(CCCN)CCCCN	2970.1	Standard polar	33892256
Spermidine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCCNCCCN[Si](C)(C)C(C)(C)C	2247.0	Semi standard non polar	33892256
Spermidine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCCNCCCN[Si](C)(C)C(C)(C)C	2273.6	Standard non polar	33892256
Spermidine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCCNCCCN[Si](C)(C)C(C)(C)C	2173.9	Standard polar	33892256
Spermidine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(CCCCNCCCN)[Si](C)(C)C(C)(C)C	2260.8	Semi standard non polar	33892256
Spermidine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(CCCCNCCCN)[Si](C)(C)C(C)(C)C	2247.1	Standard non polar	33892256
Spermidine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N(CCCCNCCCN)[Si](C)(C)C(C)(C)C	2440.4	Standard polar	33892256
Spermidine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NCCCCN(CCCN)[Si](C)(C)C(C)(C)C	2194.9	Semi standard non polar	33892256
Spermidine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NCCCCN(CCCN)[Si](C)(C)C(C)(C)C	2221.0	Standard non polar	33892256
Spermidine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NCCCCN(CCCN)[Si](C)(C)C(C)(C)C	2406.9	Standard polar	33892256
Spermidine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N(CCCNCCCCN)[Si](C)(C)C(C)(C)C	2244.4	Semi standard non polar	33892256
Spermidine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N(CCCNCCCCN)[Si](C)(C)C(C)(C)C	2249.0	Standard non polar	33892256
Spermidine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N(CCCNCCCCN)[Si](C)(C)C(C)(C)C	2437.7	Standard polar	33892256
Spermidine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)NCCCN(CCCCN)[Si](C)(C)C(C)(C)C	2215.0	Semi standard non polar	33892256
Spermidine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)NCCCN(CCCCN)[Si](C)(C)C(C)(C)C	2222.7	Standard non polar	33892256
Spermidine,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)NCCCN(CCCCN)[Si](C)(C)C(C)(C)C	2417.4	Standard polar	33892256
Spermidine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCNCCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2649.9	Semi standard non polar	33892256
Spermidine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCNCCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2611.2	Standard non polar	33892256
Spermidine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NCCCNCCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2248.5	Standard polar	33892256
Spermidine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCCN(CCCN[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2562.6	Semi standard non polar	33892256
Spermidine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCCN(CCCN[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2575.0	Standard non polar	33892256
Spermidine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCCN(CCCN[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2280.7	Standard polar	33892256
Spermidine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NCCCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2643.6	Semi standard non polar	33892256
Spermidine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NCCCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2610.6	Standard non polar	33892256
Spermidine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NCCCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2247.5	Standard polar	33892256
Spermidine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N(CCCN)CCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2594.7	Semi standard non polar	33892256
Spermidine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N(CCCN)CCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2555.8	Standard non polar	33892256
Spermidine,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N(CCCN)CCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2425.8	Standard polar	33892256
Spermidine,3TBDMS,isomer #5	CC(C)(C)[Si](C)(C)N(CCCCN)CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2615.0	Semi standard non polar	33892256
Spermidine,3TBDMS,isomer #5	CC(C)(C)[Si](C)(C)N(CCCCN)CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2563.6	Standard non polar	33892256
Spermidine,3TBDMS,isomer #5	CC(C)(C)[Si](C)(C)N(CCCCN)CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2431.0	Standard polar	33892256
Spermidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CCCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2994.9	Semi standard non polar	33892256
Spermidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CCCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2899.5	Standard non polar	33892256
Spermidine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CCCCNCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2311.4	Standard polar	33892256
Spermidine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCN(CCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2957.8	Semi standard non polar	33892256
Spermidine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCN(CCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2856.5	Standard non polar	33892256
Spermidine,4TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NCCCN(CCCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2360.9	Standard polar	33892256
Spermidine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NCCCCN(CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2959.7	Semi standard non polar	33892256
Spermidine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NCCCCN(CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2862.3	Standard non polar	33892256
Spermidine,4TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NCCCCN(CCCN([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2359.3	Standard polar	33892256
Spermidine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CCCCN([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)C	3305.9	Semi standard non polar	33892256
Spermidine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CCCCN([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)C	3087.5	Standard non polar	33892256
Spermidine,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CCCCN([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)C	2418.6	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Feces
Saliva
Urine

Tissue Locations

Brain
Epidermis
Erythrocyte
Fibroblasts
Intestine
Liver
Neuron
Placenta
Platelet
Prostate
Testis

Pathways

Name	SMPDB/PathBank	KEGG
Methionine Metabolism
Spermidine and Spermine Biosynthesis		Not Available
Cystathionine Beta-Synthase Deficiency		Not Available
Hypermethioninemia		Not Available
S-Adenosylhomocysteine (SAH) Hydrolase Deficiency		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	9.99 ± 3.57 uM	Adult (>18 years old)	Both	Normal	Quantitative comp...	details
Blood	Detected and Quantified	10.3 +/- 3.78 uM	Adult (>18 years old)	Male	Normal	Geigy Scientific ...	details
Blood	Detected and Quantified	8.47 +/- 2.02 uM	Adult (>18 years old)	Female	Normal	Geigy Scientific ...	details
Blood	Detected and Quantified	0.09 ± 0.03 uM	Adult (>18 years old)	Both	Normal	Quantitative comp...	details
Blood	Detected and Quantified	0.17 ± 0.05 uM	Adult (>18 years old)	Both	Normal	Quantitative comp...	details
Blood	Detected and Quantified	7.99 ± 2.58 uM	Adult (>18 years old)	Both	Normal	Quantitative comp...	details
Blood	Detected and Quantified	0.19 ± 0.09 uM	Adult (>18 years old)	Both	Normal	Quantitative comp...	details
Blood	Detected and Quantified	0.2 ± 0.06 uM	Adult (>18 years old)	Both	Normal	Quantitative comp...	details
Blood	Detected and Quantified	0.07 +/- 0.04 uM	Adult (>18 years old)	Both	Normal	22626821	details
Blood	Detected and Quantified	8.13 ± 4.85 uM	Adult (>18 years old)	Both	Normal	Quantitative comp...	details
Blood	Detected and Quantified	0.38 ± 0.29 uM	Adult (>18 years old)	Both	Normal	Quantitative comp...	details
Blood	Detected and Quantified	0.29 ± 0.11 uM	Adult (>18 years old)	Both	Normal	Quantitative comp...	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Blood	Detected and Quantified	0.13-0.40 uM	Adult (>18 years old)	Both	Normal	Molecular You	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	0.12 +/- 0.04 uM	Adult (>18 years old)	Both	Normal	15745737	details
Feces	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	20669995	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Normal	27609529	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Feces	Detected and Quantified	10 +/- 20 nmol/g wet feces	Adult (>18 years old)	Both	Normal	27624970	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Saliva	Detected and Quantified	0.552 +/- 0.329 uM	Adult (>18 years old)	Both	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.05 uM	Adult (>18 years old)	Both	Normal	11419735	details
Saliva	Detected and Quantified	3.21 +/- 6.80 uM	Adult (>18 years old)	Both	Normal	Zerihun T. Dame, ...	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Not Specified	Normal	22727327	details
Saliva	Detected and Quantified	1.78 +/- 1.65 uM	Adult (>18 years old)	Female	Normal	23857558	details
Saliva	Detected and Quantified	0.331 +/- 0.265 uM	Adult (>18 years old)	Both	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.402 +/- 0.320 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	1.38 +/- 2.59 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	1.27 +/- 1.70 uM	Adult (>18 years old)	Male	Normal	Sugimoto et al. (...	details
Saliva	Detected and Quantified	0.487 +/- 1.02 uM	Adult (>18 years old)	Female	Normal	Sugimoto et al. (...	details
Urine	Detected and Quantified	0.06(0.02-0.33) umol/mmol creatinine	Newborn (0-30 days old)	Female	Normal	32340350	details
Urine	Detected and Quantified	0.04(0.01-0.19) umol/mmol creatinine	Newborn (0-30 days old)	Male	Normal	32340350	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Urine	Detected and Quantified	0.02-0.3 umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	32340350	details
Urine	Detected and Quantified	0.112 +/- 0.008 umol/mmol creatinine	Adult (>18 years old)	Both	Not Available	9464484	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	9464484	details
Urine	Detected and Quantified	0.05 (0.01-0.09) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	3757213	details
Urine	Detected and Quantified	0.026 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	19309105	details
Urine	Detected and Quantified	1.1 +/- 0.2 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Geigy Scientific ... West Cadwell, N.J... Basel, Switzerlan...	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.069 +/- 0.053 uM	Adult (>18 years old)	Both	uremia	22626821	details
Blood	Detected and Quantified	0.670 +/- 0.310 uM	Adult (>18 years old)	Both	Uremia	12675874	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Crohns disease	27609529	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Ulcerative colitis	27609529	details
Feces	Detected but not Quantified	Not Quantified	Children (6 - 18 years old)	Not Specified	Unclassified IBD	27609529	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Saliva	Detected and Quantified	0.46 +/- 0.14 uM	Adult (>18 years old)	Male	Alzheimer's disease	23857558	details
Saliva	Detected and Quantified	0.72 +/- 0.39 uM	Adult (>18 years old)	Male	Frontotemporal lobe dementia	23857558	details
Saliva	Detected and Quantified	1.19 +/- 1.70 uM	Adult (>18 years old)	Both	Lewy body disease	23857558	details
Saliva	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Male	Tooth Decay	31026179	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Leukemia	9464484	details
Urine	Detected and Quantified	0.347 +/- 0.147 umol/mmol creatinine	Adult (>18 years old)	Both	Leukemia	9464484	details

Associated Disorders and Diseases

Disease References

Uremia
Duranton F, Cohen G, De Smet R, Rodriguez M, Jankowski J, Vanholder R, Argiles A: Normal and pathologic concentrations of uremic toxins. J Am Soc Nephrol. 2012 Jul;23(7):1258-70. doi: 10.1681/ASN.2011121175. Epub 2012 May 24. [PubMed:22626821 ] Vanholder R, De Smet R, Glorieux G, Argiles A, Baurmeister U, Brunet P, Clark W, Cohen G, De Deyn PP, Deppisch R, Descamps-Latscha B, Henle T, Jorres A, Lemke HD, Massy ZA, Passlick-Deetjen J, Rodriguez M, Stegmayr B, Stenvinkel P, Tetta C, Wanner C, Zidek W: Review on uremic toxins: classification, concentration, and interindividual variability. Kidney Int. 2003 May;63(5):1934-43. doi: 10.1046/j.1523-1755.2003.00924.x. [PubMed:12675874 ]
Colorectal cancer
Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ] Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Crohn's disease
Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Ulcerative colitis
Kolho KL, Pessia A, Jaakkola T, de Vos WM, Velagapudi V: Faecal and Serum Metabolomics in Paediatric Inflammatory Bowel Disease. J Crohns Colitis. 2017 Mar 1;11(3):321-334. doi: 10.1093/ecco-jcc/jjw158. [PubMed:27609529 ]
Alzheimer's disease
Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Frontotemporal dementia
Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Lewy body disease
Tsuruoka M, Hara J, Hirayama A, Sugimoto M, Soga T, Shankle WR, Tomita M: Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 2013 Oct;34(19):2865-72. doi: 10.1002/elps.201300019. Epub 2013 Sep 6. [PubMed:23857558 ]
Tooth Decay
Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Leukemia
Lee SH, Suh JW, Chung BC, Kim SO: Polyamine profiles in the urine of patients with leukemia. Cancer Lett. 1998 Jan 9;122(1-2):1-8. [PubMed:9464484 ]

Associated OMIM IDs

114500 (Colorectal cancer)
266600 (Crohn's disease)
104300 (Alzheimer's disease)
600274 (Frontotemporal dementia)

External Links

DrugBank ID

DB03566

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

16610

Food Biomarker Ontology

Not Available

VMH ID

SPMD

MarkerDB ID

MDB00000312

Good Scents ID

Not Available

References

Synthesis Reference

Bergeron, Raymond J., Jr. Preparation and formulation spermidine analogues for pharmaceutical use as tumor growth inhibitors. U.S. (2001), 31 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
Duranton F, Cohen G, De Smet R, Rodriguez M, Jankowski J, Vanholder R, Argiles A: Normal and pathologic concentrations of uremic toxins. J Am Soc Nephrol. 2012 Jul;23(7):1258-70. doi: 10.1681/ASN.2011121175. Epub 2012 May 24. [PubMed:22626821 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Only showing the first 10 proteins. There are 29 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. 3-ketoacyl-CoA thiolase, mitochondrial

General function:: Involved in transferase activity, transferring acyl groups other than amino-acyl groups
Specific function:: Abolishes BNIP3-mediated apoptosis and mitochondrial damage.
Gene Name:: ACAA2
Uniprot ID:: P42765
Molecular weight:: 41923.82

Enzyme Details

3. Peroxisomal N(1)-acetyl-spermine/spermidine oxidase

General function:: Amino acid transport and metabolism
Specific function:: Flavoenzyme which catalyzes the oxidation of N(1)-acetylspermine to spermidine and is thus involved in the polyamine back-conversion. Can also oxidize N(1)-acetylspermidine to putrescine. Substrate specificity: N(1)-acetylspermine = N(1)-acetylspermidine > N(1),N(12)-diacylspermine >> spermine. Does not oxidize spermidine. Plays an important role in the regulation of polyamine intracellular concentration and has the potential to act as a determinant of cellular sensitivity to the antitumor polyamine analogs.
Gene Name:: PAOX
Uniprot ID:: Q6QHF9
Molecular weight:: 55512.64

Reactions

N1-Acetylspermine + Oxygen + Water → Spermidine + Acetamidopropanal + Hydrogen peroxide	details

Enzyme Details

4. Thioredoxin reductase 1, cytoplasmic

General function:: Involved in oxidoreductase activity
Specific function:: Isoform 1 may possess glutaredoxin activity as well as thioredoxin reductase activity and induces actin and tubulin polymerization, leading to formation of cell membrane protrusions. Isoform 4 enhances the transcriptional activity of estrogen receptors alpha and beta while isoform 5 enhances the transcriptional activity of the beta receptor only. Isoform 5 also mediates cell death induced by a combination of interferon-beta and retinoic acid.
Gene Name:: TXNRD1
Uniprot ID:: Q16881
Molecular weight:: 70905.58

References

Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]

Enzyme Details

5. 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

6. 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

7. 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

Reactions

S-Adenosylmethioninamine + Spermidine → 5'-Methylthioadenosine + Spermine	details

Enzyme Details

8. Spermidine synthase

General function:: Involved in catalytic activity
Specific function:: Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM). Has a strong preference for putrescine as substrate, and has very low activity towards 1,3-diaminopropane. Has extremely low activity towards spermidine.
Gene Name:: SRM
Uniprot ID:: P19623
Molecular weight:: 33824.455

Reactions

S-Adenosylmethioninamine + Putrescine → 5'-Methylthioadenosine + Spermidine	details
S-Adenosylmethioninamine + Spermidine → 5'-Methylthioadenosine + Spermine	details

Enzyme Details

9. Deoxyhypusine synthase

General function:: Involved in peptidyl-lysine modification to hypusine
Specific function:: Catalyzes the NAD-dependent oxidative cleavage of spermidine and the subsequent transfer of the butylamine moiety of spermidine to the epsilon-amino group of a specific lysine residue of the eIF-5A precursor protein to form the intermediate deoxyhypusine residue.
Gene Name:: DHPS
Uniprot ID:: P49366
Molecular weight:: 40970.28

Reactions

[eIF5A-precursor]-lysine + Spermidine → [eIF5A-precursor]-deoxyhypusine + 1,3-Diaminopropane	details

Enzyme Details

10. Propionyl-CoA carboxylase alpha chain, mitochondrial

General function:: Involved in catalytic activity
Specific function:: Not Available
Gene Name:: PCCA
Uniprot ID:: P05165
Molecular weight:: 80058.295

Transporters

Enzyme Details

1. Solute carrier family 22 member 4

General function:: Involved in ion transmembrane transporter activity
Specific function:: Sodium-ion dependent, low affinity carnitine transporter. Probably transports one sodium ion with one molecule of carnitine. Also transports organic cations such as tetraethylammonium (TEA) without the involvement of sodium. Relative uptake activity ratio of carnitine to TEA is 1.78. A key substrate of this transporter seems to be ergothioneine (ET)
Gene Name:: SLC22A4
Uniprot ID:: Q9H015
Molecular weight:: 62154.5

References

Yabuuchi H, Tamai I, Nezu J, Sakamoto K, Oku A, Shimane M, Sai Y, Tsuji A: Novel membrane transporter OCTN1 mediates multispecific, bidirectional, and pH-dependent transport of organic cations. J Pharmacol Exp Ther. 1999 May;289(2):768-73. [PubMed:10215651 ]

Enzyme Details

2. Solute carrier family 22 member 1

General function:: Involved in ion transmembrane transporter activity
Specific function:: Translocates a broad array of organic cations with various structures and molecular weights including the model compounds 1-methyl-4-phenylpyridinium (MPP), tetraethylammonium (TEA), N-1-methylnicotinamide (NMN), 4-(4-(dimethylamino)styryl)- N-methylpyridinium (ASP), the endogenous compounds choline, guanidine, histamine, epinephrine, adrenaline, noradrenaline and dopamine, and the drugs quinine, and metformin. The transport of organic cations is inhibited by a broad array of compounds like tetramethylammonium (TMA), cocaine, lidocaine, NMDA receptor antagonists, atropine, prazosin, cimetidine, TEA and NMN, guanidine, cimetidine, choline, procainamide, quinine, tetrabutylammonium, and tetrapentylammonium. Translocates organic cations in an electrogenic and pH-independent manner. Translocates organic cations across the plasma membrane in both directions. Transports the polyamines spermine and spermidine. Transports pramipexole across the basolateral membrane of the proximal tubular epithelial cells. The choline transport is activated by MMTS. Regulated by various intracellular signaling pathways including inhibition by protein kinase A activation, and endogenously activation by the calmodulin complex, the calmodulin- dependent kinase II and LCK tyrosine kinase
Gene Name:: SLC22A1
Uniprot ID:: O15245
Molecular weight:: 61187.4

References

Busch AE, Quester S, Ulzheimer JC, Waldegger S, Gorboulev V, Arndt P, Lang F, Koepsell H: Electrogenic properties and substrate specificity of the polyspecific rat cation transporter rOCT1. J Biol Chem. 1996 Dec 20;271(51):32599-604. [PubMed:8955087 ]

Only showing the first 10 proteins. There are 29 proteins in total.

Show all enzymes and transporters

Showing metabocard for Spermidine (HMDB0001257)

MOL for HMDB0001257 (Spermidine)

3D MOL for HMDB0001257 (Spermidine)

3D SDF for HMDB0001257 (Spermidine)

3D-SDF for HMDB0001257 (Spermidine)

PDB for HMDB0001257 (Spermidine)

3D PDB for HMDB0001257 (Spermidine)

SMILES for HMDB0001257 (Spermidine)

INCHI for HMDB0001257 (Spermidine)

Structure for HMDB0001257 (Spermidine)

3D Structure for HMDB0001257 (Spermidine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

Reactions

References

Reactions

Reactions

Reactions

Transporters

References

References