Showing metabocard for 1,5-Diaminopentane (MMDBc0049943)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:46:45 UTC
Update Date2022-12-15 22:52:19 UTC
Metabolite IDMMDBc0049943
Metabolite Identification
Common Name1,5-Diaminopentane
Description1,5-Diaminopentane, also known as cadaverine, is a foul-smelling diamine formed by bacterial decarboxylation of lysine that occurs during protein hydrolysis during putrefaction of animal tissue. However, this diamine is not purely associated with putrefaction. 1,5-Diaminopentane is a toxic diamine with the formula NH2(CH2)5NH2, which is similar to putrescine's NH2(CH2)4NH2. 1,5-Diaminopentane is also known by the names 1,5-pentanediamine and pentamethylenediamine. It is also produced in small quantities by mammals. In particular, it is partially responsible for the distinctive smell of urine and semen. Elevated levels of 1,5-diaminopentane have been found in the urine of some patients with defects in lysine metabolism. 1,5-Diaminopentane is toxic in large doses. In rats it had a low acute oral toxicity of more than 2000 mg/kg body weight. 1,5-Diaminopentane can be found in Corynebacterium (PMID:27872963 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fecab91d5a8>


  Mrv1652309042000272D          

  7  6  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    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
  6  7  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fecab91d5a8>

HMDB0002322
     RDKit          3D
Cadaverine
 21 20  0  0  0  0  0  0  0  0999 V2000
    3.6692   -0.1381   -0.4731 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4220    0.4262    0.0583 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2331   -0.4037   -0.4379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0017    0.2389    0.1492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2667   -0.4806   -0.2589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4193    0.2816    0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6962   -0.3210    0.0871 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1442   -0.7322    0.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2575    0.5883   -0.9071 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2485    1.4538   -0.3002 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5117    0.3451    1.1602 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2180   -0.4662   -1.5295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3500   -1.4056    0.0357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1226    0.2760    1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0873    1.2834   -0.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2650   -1.5453    0.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4308   -0.3530   -1.3488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2432    0.2612    1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3433    1.3221    0.0724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0705   -0.9243    0.8360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3531    0.3622   -0.3043 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
  2 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 #<Metabolite:0x00007fecab91d5a8>


  Mrv1652309042000272D          

  7  6  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    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
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049943

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C5H14N2/c6-4-2-1-3-5-7/h1-7H2

> <INCHI_KEY>
VHRGRCVQAFMJIZ-UHFFFAOYSA-N

> <FORMULA>
C5H14N2

> <MOLECULAR_WEIGHT>
102.1781

> <EXACT_MASS>
102.115698458

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.112767429733221

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentane-1,5-diamine

> <ALOGPS_LOGP>
-0.27

> <JCHEM_LOGP>
-0.4005515990000003

> <ALOGPS_LOGS>
-0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
10.506503804690274

> <JCHEM_POLAR_SURFACE_AREA>
52.04

> <JCHEM_REFRACTIVITY>
31.979599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.91e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cadaverine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fecab91d5a8>

HMDB0002322
     RDKit          3D
Cadaverine
 21 20  0  0  0  0  0  0  0  0999 V2000
    3.6692   -0.1381   -0.4731 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4220    0.4262    0.0583 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2331   -0.4037   -0.4379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0017    0.2389    0.1492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2667   -0.4806   -0.2589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4193    0.2816    0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6962   -0.3210    0.0871 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1442   -0.7322    0.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2575    0.5883   -0.9071 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2485    1.4538   -0.3002 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5117    0.3451    1.1602 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2180   -0.4662   -1.5295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3500   -1.4056    0.0357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1226    0.2760    1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0873    1.2834   -0.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2650   -1.5453    0.0269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4308   -0.3530   -1.3488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2432    0.2612    1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3433    1.3221    0.0724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0705   -0.9243    0.8360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3531    0.3622   -0.3043 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
  2 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 #<Metabolite:0x00007fecab91d5a8>

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       3.286   3.437   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      11.288   3.437   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    7                                                       
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for #<Metabolite:0x00007fecab91d5a8>

COMPND    HMDB0002322
HETATM    1  N1  UNL     1       3.669  -0.138  -0.473  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.422   0.426   0.058  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.233  -0.404  -0.438  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.002   0.239   0.149  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.267  -0.481  -0.259  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.419   0.282   0.408  1.00  0.00           C  
HETATM    7  N2  UNL     1      -3.696  -0.321   0.087  1.00  0.00           N  
HETATM    8  H1  UNL     1       4.144  -0.732   0.218  1.00  0.00           H  
HETATM    9  H2  UNL     1       4.258   0.588  -0.907  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.249   1.454  -0.300  1.00  0.00           H  
HETATM   11  H4  UNL     1       2.512   0.345   1.160  1.00  0.00           H  
HETATM   12  H5  UNL     1       1.218  -0.466  -1.530  1.00  0.00           H  
HETATM   13  H6  UNL     1       1.350  -1.406   0.036  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.123   0.276   1.249  1.00  0.00           H  
HETATM   15  H8  UNL     1      -0.087   1.283  -0.234  1.00  0.00           H  
HETATM   16  H9  UNL     1      -1.265  -1.545   0.027  1.00  0.00           H  
HETATM   17  H10 UNL     1      -1.431  -0.353  -1.349  1.00  0.00           H  
HETATM   18  H11 UNL     1      -2.243   0.261   1.492  1.00  0.00           H  
HETATM   19  H12 UNL     1      -2.343   1.322   0.072  1.00  0.00           H  
HETATM   20  H13 UNL     1      -4.071  -0.924   0.836  1.00  0.00           H  
HETATM   21  H14 UNL     1      -4.353   0.362  -0.304  1.00  0.00           H  
CONECT    1    2    8    9
CONECT    2    3   10   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 #<Metabolite:0x00007fecab91d5a8>

NCCCCCN
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INCHI for #<Metabolite:0x00007fecab91d5a8>

InChI=1S/C5H14N2/c6-4-2-1-3-5-7/h1-7H2
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Synonyms
ValueSource
1,5-DiaminopentaneChEBI
1,5-PentamethylenediamineChEBI
1,5-PentanediamineChEBI
DAPEChEBI
PentamethylenediamineChEBI
PENTANE-1,5-diamineChEBI
1,5-Diaminopentane dihydrochlorideHMDB
CadaverinHMDB
Cadaverine dihydrochlorideHMDB
Pentamethylenediamine dihydrochlorideHMDB
BioDex 1HMDB
1,5 PentanediamineHMDB
Molecular FormulaC5H14N2
Average Mass102.1781
Monoisotopic Mass102.115698458
IUPAC Namepentane-1,5-diamine
Traditional Namecadaverine
CAS Registry Number462-94-2
SMILES
NCCCCCN
InChI Identifier
InChI=1S/C5H14N2/c6-4-2-1-3-5-7/h1-7H2
InChI KeyVHRGRCVQAFMJIZ-UHFFFAOYSA-N