Hmdb loader

Showing metabocard for 1,3-Diaminopropane (HMDB0000002)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (7) Show 7 proteinsXML
enzymes (7) Show 7 proteins
Show more...Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:27 UTC
HMDB IDHMDB0000002
Secondary Accession Numbers
  • HMDB00002
  • HMDB0060172
  • HMDB60172
Metabolite Identification
Common Name1,3-Diaminopropane
Description1,3-Diaminopropane, also known as DAP or trimethylenediamine, belongs to the class of organic compounds known as monoalkylamines. These are organic compounds containing a primary aliphatic amine group. 1,3-Diaminopropane is a stable, flammable, and highly hygroscopic fluid. It is a polyamine that is normally quite toxic if swallowed, inhaled, or absorbed through the skin. It is a catabolic byproduct of spermidine. It is also a precursor in the enzymatic synthesis of beta-alanine. 1,3-Diaminopropane is involved in the arginine/proline metabolic pathways and the beta-alanine metabolic pathway. 1,3-Diaminopropane has been detected, but not quantified in, several different foods, such as cassava, shiitakes, oyster mushrooms, muscadine grapes, and cinnamons. This could make 1,3-diaminopropane a potential biomarker for the consumption of these foods.
Structure
Data?1676999666
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000002 (1,3-Diaminopropane)

  Mrv1652309032023462D          

  5  4  0  0  0  0            999 V2000
    1.2375   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9519   -0.3019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -0.3019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7144    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914   -0.7144    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000002 (1,3-Diaminopropane)

HMDB0000002
     RDKit          3D
1,3-Diaminopropane
 15 14  0  0  0  0  0  0  0  0999 V2000
    2.3332   -0.0746    0.5309 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0490    0.5049    0.1915 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1014   -0.6258   -0.0898 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2856   -0.1577   -0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8510    0.6261    0.6358 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2742   -1.0844    0.7710 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0916    0.1710   -0.1100 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7458    1.1454    1.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1850    1.1566   -0.7047 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0147   -1.2290    0.8202 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5016   -1.2123   -0.9412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9101   -1.0701   -0.5698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3284    0.3768   -1.4136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4041    1.4142    0.2399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5173    0.0591    1.2086 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
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
M  END
Download

3D SDF for HMDB0000002 (1,3-Diaminopropane)

  Mrv1652309032023462D          

  5  4  0  0  0  0            999 V2000
    1.2375   -0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9519   -0.3019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -0.3019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7144    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914   -0.7144    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000002

> <DATABASE_NAME>
hmdb

> <SMILES>
NCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C3H10N2/c4-2-1-3-5/h1-5H2

> <INCHI_KEY>
XFNJVJPLKCPIBV-UHFFFAOYSA-N

> <FORMULA>
C3H10N2

> <MOLECULAR_WEIGHT>
74.1249

> <EXACT_MASS>
74.08439833

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
9.059383875573538

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
propane-1,3-diamine

> <ALOGPS_LOGP>
-1.41

> <JCHEM_LOGP>
-1.362482935

> <ALOGPS_LOGS>
0.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
10.169241483553524

> <JCHEM_POLAR_SURFACE_AREA>
52.04

> <JCHEM_REFRACTIVITY>
22.734

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.37e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α,ω-propanediamine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000002 (1,3-Diaminopropane)

HMDB0000002
     RDKit          3D
1,3-Diaminopropane
 15 14  0  0  0  0  0  0  0  0999 V2000
    2.3332   -0.0746    0.5309 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0490    0.5049    0.1915 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1014   -0.6258   -0.0898 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2856   -0.1577   -0.4595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8510    0.6261    0.6358 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2742   -1.0844    0.7710 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0916    0.1710   -0.1100 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7458    1.1454    1.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1850    1.1566   -0.7047 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0147   -1.2290    0.8202 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5016   -1.2123   -0.9412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9101   -1.0701   -0.5698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3284    0.3768   -1.4136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4041    1.4142    0.2399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5173    0.0591    1.2086 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
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
M  END
Download

PDB for HMDB0000002 (1,3-Diaminopropane)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.644  -0.564   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.976  -0.564   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       4.977  -1.334   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      -0.357  -1.334   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2                                                            
CONECT    5    3                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
Download

3D PDB for HMDB0000002 (1,3-Diaminopropane)

COMPND    HMDB0000002
HETATM    1  N1  UNL     1       2.333  -0.075   0.531  1.00  0.00           N  
HETATM    2  C1  UNL     1       1.049   0.505   0.191  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.101  -0.626  -0.090  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.286  -0.158  -0.460  1.00  0.00           C  
HETATM    5  N2  UNL     1      -1.851   0.626   0.636  1.00  0.00           N  
HETATM    6  H1  UNL     1       2.274  -1.084   0.771  1.00  0.00           H  
HETATM    7  H2  UNL     1       3.092   0.171  -0.110  1.00  0.00           H  
HETATM    8  H3  UNL     1       0.746   1.145   1.017  1.00  0.00           H  
HETATM    9  H4  UNL     1       1.185   1.157  -0.705  1.00  0.00           H  
HETATM   10  H5  UNL     1       0.015  -1.229   0.820  1.00  0.00           H  
HETATM   11  H6  UNL     1       0.502  -1.212  -0.941  1.00  0.00           H  
HETATM   12  H7  UNL     1      -1.910  -1.070  -0.570  1.00  0.00           H  
HETATM   13  H8  UNL     1      -1.328   0.377  -1.414  1.00  0.00           H  
HETATM   14  H9  UNL     1      -2.404   1.414   0.240  1.00  0.00           H  
HETATM   15  H10 UNL     1      -2.517   0.059   1.209  1.00  0.00           H  
CONECT    1    2    6    7
CONECT    2    3    8    9
CONECT    3    4   10   11
CONECT    4    5   12   13
CONECT    5   14   15
END
Download

SMILES for HMDB0000002 (1,3-Diaminopropane)

NCCCN
Download

INCHI for HMDB0000002 (1,3-Diaminopropane)

InChI=1S/C3H10N2/c4-2-1-3-5/h1-5H2
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
1,3-PropanediamineChEBI
1,3-PropylenediamineChEBI
Propane-1,3-diamineChEBI
tnChEBI
TrimethylenediamineKegg
1,3-DiaminepropaneMeSH
Trimethylenediamine dihydrochlorideMeSH
Trimethylenediamine hydrochlorideMeSH
1,3-diamino-N-PropaneHMDB
1,3-TrimethylenediamineHMDB
3-AminopropylamineHMDB
a,W-PropanediamineHMDB
1,3-DiaminopropaneChEBI
Chemical FormulaC3H10N2
Average Molecular Weight74.1249
Monoisotopic Molecular Weight74.08439833
IUPAC Namepropane-1,3-diamine
Traditional Nameα,ω-propanediamine
CAS Registry Number109-76-2
SMILES
NCCCN
InChI Identifier
InChI=1S/C3H10N2/c4-2-1-3-5/h1-5H2
InChI KeyXFNJVJPLKCPIBV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monoalkylamines. These are organic compounds containing an primary aliphatic amine group.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentMonoalkylamines
Alternative Parents
Substituents
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Industrial application
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-12 °CNot Available
Boiling Point139.80 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-1.43HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.04 +/- 0.03 uMAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified0.16 (0.02-0.69) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified2.55 (0.18-5.85) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.015 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified1.2 umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.13 +/- 0.13 uMAdult (>18 years old)FemaleBreast cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
UrineDetected and Quantified0.96 (0.12-2.11) umol/mmol creatinineAdult (>18 years old)Both
Leukemia		 details
Associated Disorders and Diseases
Disease References
Perillyl alcohol administration for cancer treatment
  1. Byun JA, Lee SH, Jung BH, Choi MH, Moon MH, Chung BC: Analysis of polyamines as carbamoyl derivatives in urine and serum by liquid chromatography-tandem mass spectrometry. Biomed Chromatogr. 2008 Jan;22(1):73-80. [PubMed:17668437 ]
Colorectal cancer
  1. 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 ]
Leukemia
  1. 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
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB005274
KNApSAcK IDC00007404
Chemspider ID415
KEGG Compound IDC00986
BioCyc IDCPD-313
BiGG IDNot Available
Wikipedia Link1,3-Diaminopropane
METLIN IDNot Available
PubChem Compound428
PDB IDNot Available
ChEBI ID15725
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000002
Good Scents IDrw1146991
References
Synthesis ReferenceTakayanagi, Yasuyuki; Oohinata, Takahiro. Preparation of 1,3-diaminopropane from acrylonitrile and ammonia. Jpn. Kokai Tokkyo Koho (1994), 5 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References

Enzymes

Enzyme Details
1. 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
References
  1. Oredsson SM, Anehus S, Heby O: Reversal of the growth inhibitory effect of alpha-difluoromethylornithine by putrescine but not by other divalent cations. Mol Cell Biochem. 1984 Sep;64(2):163-72. [PubMed:6438490 ]
Enzyme Details
2. 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-Diaminopropanedetails
References
  1. Park JH, Wolff EC, Folk JE, Park MH: Reversal of the deoxyhypusine synthesis reaction. Generation of spermidine or homospermidine from deoxyhypusine by deoxyhypusine synthase. J Biol Chem. 2003 Aug 29;278(35):32683-91. Epub 2003 Jun 4. [PubMed:12788913 ]
Enzyme Details
3. Amiloride-sensitive amine oxidase [copper-containing]
General function:
Involved in copper ion binding
Specific function:
Catalyzes the degradation of compounds such as putrescine, histamine, spermine, and spermidine, substances involved in allergic and immune responses, cell proliferation, tissue differentiation, tumor formation, and possibly apoptosis. Placental DAO is thought to play a role in the regulation of the female reproductive function.
Gene Name:
ABP1
Uniprot ID:
P19801
Molecular weight:
85377.1
Enzyme Details
4. Membrane primary amine oxidase
General function:
Involved in copper ion binding
Specific function:
Cell adhesion protein that participates in lymphocyte recirculation by mediating the binding of lymphocytes to peripheral lymph node vascular endothelial cells in an L-selectin-independent fashion. Has a monoamine oxidase activity. May play a role in adipogenesis.
Gene Name:
AOC3
Uniprot ID:
Q16853
Molecular weight:
84621.27
Reactions
1,3-Diaminopropane + Oxygen + Water → 3-Aminopropionaldehyde + Ammonia + Hydrogen peroxidedetails
Enzyme Details
5. Retina-specific copper amine oxidase
General function:
Involved in copper ion binding
Specific function:
Has a monoamine oxidase activity with substrate specificity for 2-phenylethylamine and tryptamine. May play a role in adipogenesis. May be a critical modulator of signal transmission in retina.
Gene Name:
AOC2
Uniprot ID:
O75106
Molecular weight:
80515.11
Reactions
1,3-Diaminopropane + Oxygen + Water → 3-Aminopropionaldehyde + Ammonia + Hydrogen peroxidedetails
Enzyme Details
6. S-adenosylmethionine decarboxylase proenzyme
General function:
Involved in adenosylmethionine decarboxylase activity
Specific function:
Not Available
Gene Name:
AMD1
Uniprot ID:
P17707
Molecular weight:
21301.015
References
  1. Pegg AE, Shuttleworth K, Hibasami H: Specificity of mammalian spermidine synthase and spermine synthase. Biochem J. 1981 Aug 1;197(2):315-20. [PubMed:6798961 ]
Enzyme Details
7. Ornithine decarboxylase
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
ODC1
Uniprot ID:
P11926
Molecular weight:
51147.73