Showing metabocard for Putrescine (MMDBc0000193)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:39:16 UTC
Update Date2022-08-31 00:00:25 UTC
Metabolite IDMMDBc0000193
Metabolite Identification
Common NamePutrescine
DescriptionPutrescine is a polyamine. 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 has been identified as a uremic toxin according to the European Uremic Toxin Working Group (PMID: 22626821 ). It 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. The polyamines, of which putrescine is one of the simplest, appear to be growth factors necessary for cell division. Putrescine apparently has specific role in skin physiology and neuroprotection. (PMID: 15009201 , 16364196 ). Pharmacological interventions have demonstrated convincingly that a steady supply of polyamines is a prerequisite for cell proliferation to occur. Genetic engineering of polyamine metabolism in transgenic rodents has shown that polyamines play a role in spermatogenesis, skin physiology, promotion of tumorigenesis and organ hypertrophy as well as neuronal protection. Transgenic activation of polyamine catabolism not only profoundly disturbs polyamine homeostasis in most tissues, but also creates a complex phenotype affecting skin, female fertility, fat depots, pancreatic integrity and regenerative growth. Transgenic expression of ornithine decarboxylase antizyme has suggested that this unique protein may act as a general tumor suppressor. Homozygous deficiency of the key biosynthetic enzymes of the polyamines, ornithine and S-adenosylmethionine decarboxylase is not compatible with murine embryogenesis. Putrescine can be found in Citrobacter, Corynebacterium, Cronobacter and Enterobacter (PMID: 27872963 ) (https://onlinelibrary.wiley.com/doi/full/10.1111/1541-4337.12099).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f5a9401d510>


  Mrv1652309042000232D          

  6  5  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f5a9401d510>

HMDB0001414
     RDKit          3D
Putrescine
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.9022    0.3545    0.0023 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7671   -0.1068    0.7310 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4723   -0.0171   -0.0839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6179   -0.5294    0.8008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9785   -0.5170    0.1630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4362    0.7649   -0.2433 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1770    1.3373    0.2052 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9185    0.1092   -1.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8594   -1.1425    1.1129 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6172    0.5630    1.6047 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5888   -0.6922   -0.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3392    1.0289   -0.3982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6625   -0.0024    1.7768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3787   -1.6056    1.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6914   -0.9136    0.9254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0202   -1.2108   -0.6971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8047    1.3195   -0.8221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0516    1.2601    0.3955 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
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
M  END
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3D SDF for #<Metabolite:0x00007f5a9401d510>


  Mrv1652309042000232D          

  6  5  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000193

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C4H12N2/c5-3-1-2-4-6/h1-6H2

> <INCHI_KEY>
KIDHWZJUCRJVML-UHFFFAOYSA-N

> <FORMULA>
C4H12N2

> <MOLECULAR_WEIGHT>
88.1515

> <EXACT_MASS>
88.100048394

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
11.070241676529026

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
butane-1,4-diamine

> <ALOGPS_LOGP>
-0.98

> <JCHEM_LOGP>
-0.845120264

> <ALOGPS_LOGS>
0.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
10.505115467408618

> <JCHEM_POLAR_SURFACE_AREA>
52.04

> <JCHEM_REFRACTIVITY>
27.3786

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.36e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
putrescine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f5a9401d510>

HMDB0001414
     RDKit          3D
Putrescine
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.9022    0.3545    0.0023 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7671   -0.1068    0.7310 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4723   -0.0171   -0.0839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6179   -0.5294    0.8008 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9785   -0.5170    0.1630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4362    0.7649   -0.2433 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1770    1.3373    0.2052 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9185    0.1092   -1.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8594   -1.1425    1.1129 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6172    0.5630    1.6047 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5888   -0.6922   -0.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3392    1.0289   -0.3982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6625   -0.0024    1.7768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3787   -1.6056    1.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6914   -0.9136    0.9254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0202   -1.2108   -0.6971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8047    1.3195   -0.8221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0516    1.2601    0.3955 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
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
M  END
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PDB for #<Metabolite:0x00007f5a9401d510>

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      -0.357   1.334   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       6.311   2.104   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for #<Metabolite:0x00007f5a9401d510>

COMPND    HMDB0001414
HETATM    1  N1  UNL     1       2.902   0.355   0.002  1.00  0.00           N  
HETATM    2  C1  UNL     1       1.767  -0.107   0.731  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.472  -0.017  -0.084  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.618  -0.529   0.801  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.978  -0.517   0.163  1.00  0.00           C  
HETATM    6  N2  UNL     1      -2.436   0.765  -0.243  1.00  0.00           N  
HETATM    7  H1  UNL     1       3.177   1.337   0.205  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.919   0.109  -1.000  1.00  0.00           H  
HETATM    9  H3  UNL     1       1.859  -1.142   1.113  1.00  0.00           H  
HETATM   10  H4  UNL     1       1.617   0.563   1.605  1.00  0.00           H  
HETATM   11  H5  UNL     1       0.589  -0.692  -0.943  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.339   1.029  -0.398  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.662  -0.002   1.777  1.00  0.00           H  
HETATM   14  H8  UNL     1      -0.379  -1.606   1.016  1.00  0.00           H  
HETATM   15  H9  UNL     1      -2.691  -0.914   0.925  1.00  0.00           H  
HETATM   16  H10 UNL     1      -2.020  -1.211  -0.697  1.00  0.00           H  
HETATM   17  H11 UNL     1      -1.805   1.320  -0.822  1.00  0.00           H  
HETATM   18  H12 UNL     1      -3.052   1.260   0.395  1.00  0.00           H  
CONECT    1    2    7    8
CONECT    2    3    9   10
CONECT    3    4   11   12
CONECT    4    5   13   14
CONECT    5    6   15   16
CONECT    6   17   18
END
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SMILES for #<Metabolite:0x00007f5a9401d510>

NCCCCN
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INCHI for #<Metabolite:0x00007f5a9401d510>

InChI=1S/C4H12N2/c5-3-1-2-4-6/h1-6H2
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Synonyms
ValueSource
1,4-ButanediamineChEBI
1,4-ButylenediamineChEBI
1,4-DIAMINOBUTANEChEBI
1,4-TetramethylenediamineChEBI
Butane-1,4-diamineChEBI
ButylenediamineChEBI
H2N(CH2)4nh2ChEBI
PutrescinChEBI
PutrescinaChEBI
PutreszinChEBI
TetramethylendiaminChEBI
TetramethylenediamineChEBI
1,4-ButanediammoniumHMDB
TetramethyldiamineHMDB
1,4 DiaminobutaneHMDB
1,4 ButanediamineHMDB
Molecular FormulaC4H12N2
Average Mass88.1515
Monoisotopic Mass88.100048394
IUPAC Namebutane-1,4-diamine
Traditional Nameputrescine
CAS Registry Number110-60-1
SMILES
NCCCCN
InChI Identifier
InChI=1S/C4H12N2/c5-3-1-2-4-6/h1-6H2
InChI KeyKIDHWZJUCRJVML-UHFFFAOYSA-N