MiMeDB: Showing metabocard for Spermidine (MMDBc0000183)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:38:55 UTC

Update Date

2024-10-09 22:04:01 UTC

Metabolite ID

MMDBc0000183

Metabolite Identification

Common Name

Spermidine

Description

Spermidine is a polyamine formed from putrescine. It is found in almost all tissues in association with nucleic acids. It has been identified as a uremic toxin according to the European Uremic Toxin Working Group (PMID: 22626821 ). Spermidine is found as a cation at all pH values, and is thought to help stabilize some membranes and nucleic acid structures. It is a precursor of spermine.¬†

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

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

Molecular Formula

C₇H₁₉N₃

Average Mass

145.2459

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted 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

Spectra

Not Available

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Brain
Cerebrospinal Fluid (CSF)
Epidermis
Erythrocyte
Feces
Fibroblasts
Intestine
Liver
Neuron
Placenta
Platelet
Prostate
Saliva
Testis
Urine

Tissue Locations

Brain
Epidermis
Erythrocyte
Fibroblasts
Intestine
Liver
Neuron
Placenta
Platelet
Prostate
Testis

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191705	Diamine acetyltransferase 1	Enzyme	P21673	Homo sapiens
MMDBp0191707	3-ketoacyl-CoA thiolase, mitochondrial	Enzyme	P42765	Homo sapiens
MMDBp0191794	Peroxisomal N(1)-acetyl-spermine/spermidine oxidase	Unknown	Q6QHF9	Homo sapiens
MMDBp0191805	Thioredoxin reductase 1, cytoplasmic	Unknown	Q16881	Homo sapiens
MMDBp0191872	Choline dehydrogenase, mitochondrial	Unknown	Q8NE62	Homo sapiens
MMDBp0191874	Dimethylglycine dehydrogenase, mitochondrial	Unknown	Q9UI17	Homo sapiens
MMDBp0191887	Spermine synthase	Enzyme	P52788	Homo sapiens
MMDBp0191888	Spermidine synthase	Enzyme	P19623	Homo sapiens
MMDBp0191889	Deoxyhypusine synthase	Unknown	P49366	Homo sapiens
MMDBp0191929	Propionyl-CoA carboxylase alpha chain, mitochondrial	Enzyme	P05165	Homo sapiens
MMDBp0191961	4-trimethylaminobutyraldehyde dehydrogenase	Unknown	P49189	Homo sapiens
MMDBp0192049	Gamma-butyrobetaine dioxygenase	Unknown	O75936	Homo sapiens
MMDBp0192064	S-methyl-5'-thioadenosine phosphorylase	Enzyme	Q13126	Homo sapiens
MMDBp0192086	S-adenosylmethionine decarboxylase proenzyme	Unknown	P17707	Homo sapiens
MMDBp0192122	Glycine amidinotransferase, mitochondrial	Enzyme	P50440	Homo sapiens
MMDBp0192205	Betaine--homocysteine S-methyltransferase 1	Unknown	Q93088	Homo sapiens
MMDBp0192413	Sarcosine dehydrogenase, mitochondrial	Unknown	Q9UL12	Homo sapiens
MMDBp0192503	Histidine decarboxylase	Enzyme	P19113	Homo sapiens
MMDBp0192645	Ornithine decarboxylase	Enzyme	P11926	Homo sapiens
MMDBp0193543	Solute carrier family 22 member 4	Transporter	Q9H015	Homo sapiens
MMDBp0193588	Solute carrier family 22 member 1	Transporter	O15245	Homo sapiens
MMDBp0193618	Spermine oxidase	Unknown	Q9NWM0	Homo sapiens
MMDBp0193643	Agmatinase, mitochondrial	Unknown	Q9BSE5	Homo sapiens
MMDBp0193925	Trimethyllysine dioxygenase, mitochondrial	Unknown	Q9NVH6	Homo sapiens
MMDBp0193964	S-methylmethionine--homocysteine S-methyltransferase BHMT2	Unknown	Q9H2M3	Homo sapiens
MMDBp0195554	Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial	Unknown	Q8NCN5	Homo sapiens
MMDBp0196292	Ornithine decarboxylase antizyme 1	Enzyme	P54368	Homo sapiens
MMDBp0196362	Augmented expression in SLE 3	Unknown	A2VED4	Homo sapiens
MMDBp0196552	Polyamine-modulated factor 1	Unknown	Q6P1K2	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018850	Putrescine	Spermidine	Polyamine aminopropyltransferase	Synthesis	PathBank	31602464
MMDBr0018867	Spermidine	N8-Acetylspermidine	Spermidine N(1)-acetyltransferase	N-Acetylation	PathBank	31602464
MMDBr0019227	Putrescine	Spermidine	Polyamine aminopropyltransferase	Synthesis	PathBank	31602464
MMDBr0019423	Spermine	Spermidine	Polyamine oxidase FMS1	Oxidation	PathBank	31602464
MMDBr0019425	Putrescine	Spermidine	Spermidine synthase SPE3	Synthesis	PathBank	31602464
MMDBr0019428	Spermidine	Spermine	Spermine synthase SPE4	Synthesis	PathBank	31602464
MMDBr0024905	Spermidine	1,3-Diaminopropane	Probable deoxyhypusine synthase	Synthesis	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Alzheimer's disease		Association	Human Saliva	HMDB	23857558
Frontotemporal dementia		Association	Human Saliva	HMDB	23857558
Leukemia		Association	Human Urine	HMDB	9464484
Uremia	Decreased	Association	Human Blood	HMDB	22626821
Uremia	Increased	Association	Human Blood	HMDB	12675874

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota	Euglenozoa	1		Microbial culture
Bacteria/Eubacteria	Deinococcus-thermus	3		Microbial culture
Archaea	Euryarchaeota	1		Microbial culture
Bacteria/Eubacteria	Firmicutes	705	Human feces; Human stool; Human ; Human pleural fluid plaque; Pig ; Human sputum; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	236	Human feces; Human stool; Human saliva; Human appendix biopsy; Human ; Human gastric fluid; Human subgingival plaque; Human supragingival plaque	Microbial culture; Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	409	Human ; Human feces; Human stool; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Lion ; Cattle	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	3	Human feces; Human stool; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Actinobacteria	27	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human saliva; Human subgingival plaque; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	177	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human saliva; Human subgingival plaque; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	5	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	54	Human feces; Human stool; Human ; Human pleural fluid plaque; Pig ; Human sputum; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	19	Human ; Human feces; Human stool; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Lion ; Cattle	Microbial culture; Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	6	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	2		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	39	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	10		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	2	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	8	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	2		Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Archaea/Archaea	Crenarchaeota	15		Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	10		Metabolic reconstruction
Bacteria/Eubacteria	Aquificae	2
Archaea/Archaea	Korarchaeota	1
Eukaryota/Fungi	Ascomycota	4	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Cyanobacteria	17
Bacteria/Eubacteria	Thermotogae	3

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Saliva	Detected and Quantified	0.46	0.14			uM	Adult (>18 years old)	Male	Alzheimer's disease	HMDB	23857558
Human Saliva	Detected and Quantified	0.72	0.39			uM	Adult (>18 years old)	Male	Frontotemporal lobe dementia	HMDB	23857558
Human Urine	Detected and Quantified	0.347	0.147			umol/mmol creatinine	Adult (>18 years old)	Both	Leukemia	HMDB	9464484
Human Saliva	Detected and Quantified	1.19	1.70			uM	Adult (>18 years old)	Both	Lewy body disease	HMDB	23857558
Human Blood	Detected and Quantified	0.069	0.053			uM	Adult (>18 years old)	Both	uremia	HMDB	22626821
Human Blood	Detected and Quantified	0.670	0.310			uM	Adult (>18 years old)	Both	Uremia	HMDB	12675874
Human Urine	Detected and Quantified	0.026				umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	19309105
Human Saliva	Detected and Quantified	0.05				uM	Adult (>18 years old)	Both	Normal	HMDB	11419735
Human Urine	Detected and Quantified			0.02	0.3	umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	HMDB	32340350
Human Urine	Detected and Quantified	0.04		0.01	0.19	umol/mmol creatinine	Newborn (0-30 days old)	Male	Normal	HMDB	32340350
Human Urine	Detected and Quantified	0.05		0.01	0.09	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	3757213
Human Urine	Detected and Quantified	0.06		0.02	0.33	umol/mmol creatinine	Newborn (0-30 days old)	Female	Normal	HMDB	32340350
Human Blood	Detected and Quantified	0.07	0.04			uM	Adult (>18 years old)	Both	Normal	HMDB	22626821
Human Urine	Detected and Quantified	0.112	0.008			umol/mmol creatinine	Adult (>18 years old)	Both		HMDB	9464484
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.12	0.04			uM	Adult (>18 years old)	Both	Normal	HMDB	15745737
Human Saliva	Detected and Quantified	1.78	1.65			uM	Adult (>18 years old)	Female	Normal	HMDB	23857558
Human Feces	Detected and Quantified	10	20			nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	27624970
Human Urine	Detected and Quantified	1.1	0.2			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Blood	Detected and Quantified	10.3	3.78			uM	Adult (>18 years old)	Male	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Blood	Detected and Quantified	8.47	2.02			uM	Adult (>18 years old)	Female	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Saliva	Detected and Quantified	0.331	0.265			uM	Adult (>18 years old)	Both	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.402	0.320			uM	Adult (>18 years old)	Female	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.487	1.02			uM	Adult (>18 years old)	Female	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	0.552	0.329			uM	Adult (>18 years old)	Both	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	1.27	1.70			uM	Adult (>18 years old)	Male	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	1.38	2.59			uM	Adult (>18 years old)	Female	Normal	HMDB	Sugimoto et al. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles.
Human Saliva	Detected and Quantified	3.21	6.80			uM	Adult (>18 years old)	Both	Normal	HMDB	https://doi.org/10.1007/s11306-015-0840-5
Human Blood	Detected and Quantified			0.13	0.40	uM	Adult (>18 years old)	Both	Normal	HMDB	Molecular You (https://molecularyou.com)
Human Brain	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Epidermis	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Erythrocyte	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Fibroblasts	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Intestine	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Neuron	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Platelet	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Prostate	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Testis	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	9464484
Human Saliva	Detected but not Quantified						Adult (>18 years old)	Not Specified	Normal	HMDB	22727327
Human Feces	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	20669995
Human Feces	Detected but not Quantified						Children (6 - 18 years old)	Not Specified	Normal	HMDB	27609529
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0001257

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

References

Synthesis Reference

Not Available

General References

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 ]
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. doi: 10.1111/1523-1747.ep12607659. [PubMed:1176793 ]
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. doi: 10.1042/bj2710305. [PubMed:2241917 ]
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. doi: 10.1016/0009-8981(80)90395-2. [PubMed:6156039 ]
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. doi: 10.1007/BF00416663. [PubMed:6625645 ]
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. doi: 10.1002/1097-0142(19800101)45:1<108::aid-cncr2820450120>3.0.co;2-w. [PubMed:7350997 ]
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. doi: 10.1016/s0378-4347(01)00130-x. [PubMed:11419735 ]
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 ]
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 ]

Showing metabocard for Spermidine (MMDBc0000183)

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