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Showing metabocard for N-Methylputrescine (HMDB0003661)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-08-13 02:46:53 UTC
Update Date2023-02-21 17:16:47 UTC
HMDB IDHMDB0003661
Secondary Accession Numbers
  • HMDB0060258
  • HMDB03661
  • HMDB60258
Metabolite Identification
Common NameN-Methylputrescine
DescriptionN-Methylputrescine is a byproduct of putrescine (a diamine), via methylation by putrescine N-methyltransferase (PMT; EC 2.1.1.53). N-methylputrescine is able to affect protein synthesis to a small extent in stimulated H-35 hepatoma cells, being an inhibitor of cellular insulin-induced ornithine decarboxylase activity. (PMID: 2051998 ). Putrescine is related to cadaverine (another polyamine). Both are produced by the breakdown of amino acids in living and dead organisms and both are toxic in large doses. Putrescine and cadaverine are largely responsible for the foul odor of putrefying flesh, but also contribute to the odor of such processes as bad breath and bacterial vaginosis. Putrescine is also found in semen. Putrescine attacks s-adenosyl methionine and converts it to spermidine. Spermidine in turn attacks another s-adenosyl methionine and converts it to spermine. Putrescine is synthesized in small quantities by healthy living cells by the action of ornithine decarboxylase. N-Methylputrescine is a microbial metabolite.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003661 (N-Methylputrescine)

  Mrv1652309042000302D          

  7  6  0  0  0  0            999 V2000
   13.4328  -13.5288    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0053  -13.1162    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.1474  -13.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2907  -13.5288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8618  -13.5288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5763  -13.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7183  -13.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for HMDB0003661 (N-Methylputrescine)

HMDB0003661
     RDKit          3D
N-Methylputrescine
 21 20  0  0  0  0  0  0  0  0999 V2000
   -3.0786    0.4067   -0.4081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4214   -0.8088   -0.1073 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1031   -0.9716   -0.5839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0907   -0.0623    0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2958   -0.2886   -0.4805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2524    0.6464    0.2293 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6048    0.5361   -0.2083 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1115    0.6660   -1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6608    1.2897    0.1405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1414    0.3294   -0.0815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0072   -1.6504   -0.0482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7874   -2.0233   -0.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0328   -0.8258   -1.6820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0371   -0.2675    1.1822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3835    1.0039   -0.0065 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6085   -1.3396   -0.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2686   -0.0493   -1.5842 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8176    1.6750    0.0966 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1507    0.4386    1.3264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7637   -0.1419   -0.9987 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0933    1.4374   -0.3292 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
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  0
  7 21  1  0
M  END
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3D SDF for HMDB0003661 (N-Methylputrescine)

  Mrv1652309042000302D          

  7  6  0  0  0  0            999 V2000
   13.4328  -13.5288    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0053  -13.1162    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.1474  -13.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2907  -13.5288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8618  -13.5288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5763  -13.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7183  -13.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003661

> <DATABASE_NAME>
hmdb

> <SMILES>
CNCCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C5H14N2/c1-7-5-3-2-4-6/h7H,2-6H2,1H3

> <INCHI_KEY>
RMIVMBYMDISYFZ-UHFFFAOYSA-N

> <FORMULA>
C5H14N2

> <MOLECULAR_WEIGHT>
102.1781

> <EXACT_MASS>
102.115698458

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.153058354365573

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4-aminobutyl)(methyl)amine

> <ALOGPS_LOGP>
-0.46

> <JCHEM_LOGP>
-0.4125398703333332

> <ALOGPS_LOGS>
0.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
10.706588962278609

> <JCHEM_POLAR_SURFACE_AREA>
38.05

> <JCHEM_REFRACTIVITY>
32.1532

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.74e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-methylputrescine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0003661 (N-Methylputrescine)

HMDB0003661
     RDKit          3D
N-Methylputrescine
 21 20  0  0  0  0  0  0  0  0999 V2000
   -3.0786    0.4067   -0.4081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4214   -0.8088   -0.1073 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1031   -0.9716   -0.5839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0907   -0.0623    0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2958   -0.2886   -0.4805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2524    0.6464    0.2293 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6048    0.5361   -0.2083 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1115    0.6660   -1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6608    1.2897    0.1405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1414    0.3294   -0.0815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0072   -1.6504   -0.0482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7874   -2.0233   -0.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0328   -0.8258   -1.6820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0371   -0.2675    1.1822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3835    1.0039   -0.0065 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6085   -1.3396   -0.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2686   -0.0493   -1.5842 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8176    1.6750    0.0966 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1507    0.4386    1.3264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7637   -0.1419   -0.9987 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0933    1.4374   -0.3292 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
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  0
  7 21  1  0
M  END
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PDB for HMDB0003661 (N-Methylputrescine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0      25.075 -25.254   0.000  0.00  0.00           N+0
HETATM    2  N   UNK     0      31.743 -24.484   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      26.408 -24.484   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      30.409 -25.254   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      27.742 -25.254   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      29.076 -24.484   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      23.741 -24.484   0.000  0.00  0.00           C+0
CONECT    1    3    7                                                       
CONECT    2    4                                                            
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5                                                       
CONECT    7    1                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0003661 (N-Methylputrescine)

COMPND    HMDB0003661
HETATM    1  C1  UNL     1      -3.079   0.407  -0.408  1.00  0.00           C  
HETATM    2  N1  UNL     1      -2.421  -0.809  -0.107  1.00  0.00           N  
HETATM    3  C2  UNL     1      -1.103  -0.972  -0.584  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.091  -0.062   0.078  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.296  -0.289  -0.480  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.252   0.646   0.229  1.00  0.00           C  
HETATM    7  N2  UNL     1       3.605   0.536  -0.208  1.00  0.00           N  
HETATM    8  H1  UNL     1      -3.112   0.666  -1.492  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.661   1.290   0.140  1.00  0.00           H  
HETATM   10  H3  UNL     1      -4.141   0.329  -0.081  1.00  0.00           H  
HETATM   11  H4  UNL     1      -3.007  -1.650  -0.048  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.787  -2.023  -0.393  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.033  -0.826  -1.682  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.037  -0.267   1.182  1.00  0.00           H  
HETATM   15  H8  UNL     1      -0.384   1.004  -0.007  1.00  0.00           H  
HETATM   16  H9  UNL     1       1.609  -1.340  -0.404  1.00  0.00           H  
HETATM   17  H10 UNL     1       1.269  -0.049  -1.584  1.00  0.00           H  
HETATM   18  H11 UNL     1       1.818   1.675   0.097  1.00  0.00           H  
HETATM   19  H12 UNL     1       2.151   0.439   1.326  1.00  0.00           H  
HETATM   20  H13 UNL     1       3.764  -0.142  -0.999  1.00  0.00           H  
HETATM   21  H14 UNL     1       4.093   1.437  -0.329  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5    6   16   17
CONECT    6    7   18   19
CONECT    7   20   21
END
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SMILES for HMDB0003661 (N-Methylputrescine)

CNCCCCN
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INCHI for HMDB0003661 (N-Methylputrescine)

InChI=1S/C5H14N2/c1-7-5-3-2-4-6/h7H,2-6H2,1H3
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Synonyms
ValueSource
1-Amino-4-methylaminobutaneHMDB
N-Methyl-1,4-butanediamineHMDB
N-Methyl-1,4-diaminobutaneHMDB
N-Methylbutane-1,4-diamineHMDB
N-MethylputresciniumHMDB
N1-Methyl-1,4-butanediamineHMDB
Chemical FormulaC5H14N2
Average Molecular Weight102.1781
Monoisotopic Molecular Weight102.115698458
IUPAC Name(4-aminobutyl)(methyl)amine
Traditional NameN-methylputrescine
CAS Registry Number14475-60-6
SMILES
CNCCCCN
InChI Identifier
InChI=1S/C5H14N2/c1-7-5-3-2-4-6/h7H,2-6H2,1H3
InChI KeyRMIVMBYMDISYFZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dialkylamines. These are organic compounds containing a dialkylamine group, characterized by two alkyl groups bonded to the amino nitrogen.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentDialkylamines
Alternative Parents
Substituents
  • Secondary aliphatic amine
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary amine
  • Primary aliphatic amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-0.051Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023211
KNApSAcK IDC00034611
Chemspider ID388845
KEGG Compound IDC02723
BioCyc IDCPD-394
BiGG ID40435
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439791
PDB IDNot Available
ChEBI ID17166
Food Biomarker OntologyNot Available
VMH IDNMPTRC
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceDudley, H. W.; Thorpe, W. V. Synthesis of N-methylputrescine and of putrescine. Biochemical Journal (1925), 19 845-9.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]
  2. Frydman J, Ruiz O, Robetto E, Dellacha JM, Frydman RB: Modulation of insulin induced ornithine decarboxylase by putrescine and methylputrescines in H-35 hepatoma cells. Mol Cell Biochem. 1991 Jan 16;100(1):9-23. [PubMed:2051998 ]

Enzymes

Enzyme Details
1. 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
N-Methylputrescine + Oxygen + Hydrogen Ion → 1-Methylpyrrolinium + Hydrogen peroxide + Ammoniadetails
Enzyme Details
2. 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
N-Methylputrescine + Oxygen + Hydrogen Ion → 1-Methylpyrrolinium + Hydrogen peroxide + Ammoniadetails