Showing metabocard for Aminopropylcadaverine (MMDBc0029920)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:46:52 UTC
Update Date2022-08-31 17:37:37 UTC
Metabolite IDMMDBc0029920
Metabolite Identification
Common NameAminopropylcadaverine
DescriptionAminopropylcadaverine,a polyamine, is the final product of aminopropylcadaverine biosynthesis pathway. Polyamines are important for cell growth and are believed to be involved in many processes including DNA, RNA, and protein synthesis, as well as membrane integrity and resistance to stress, to name a few. Cadaverine and aminopropylcadaverine are alternative polyamines that can at least partially substitute for purtrescine and spermidine, the primary polyamines found in E. coli. Lysine is decarboxylated to form cadaverine which is then converted to aminopropylcadaverine by the aminopropyltransferase, SpeE.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645c9c2fd20>


  Mrv0541 02241203492D          

 11 10  0  0  0  0            999 V2000
   14.9516  -10.2273    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.6661   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3806  -10.2273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0951   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8096  -10.2273    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.5241   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2386  -10.2273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9530   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.6676  -10.2273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3820   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.0966  -10.2273    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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00005645c9c2fd20>

HMDB0012189
     RDKit          3D
Aminopropylcadaverine
 32 31  0  0  0  0  0  0  0  0999 V2000
    4.3757    1.2741   -0.1891 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4912    0.2018   -0.5880 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9950   -0.5538    0.6255 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0695   -1.6768    0.2535 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8437   -1.1710   -0.4938 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0939   -0.1942    0.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0722    0.3541   -0.2047 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1769   -0.4959   -0.4259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2836    0.3460   -1.0414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6168    1.4528   -0.0853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0635    0.9166    1.1636 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8409    2.1367    0.0378 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0023    1.0012    0.5780 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6118    0.6341   -1.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0398   -0.4473   -1.2933 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8819   -1.0276    1.1144 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5881    0.1506    1.3603 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6248   -2.4247   -0.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6913   -2.1085    1.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0998   -0.6857   -1.4484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1708   -2.0324   -0.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1907   -0.6754    1.3427 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7596    0.6769    0.6476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9830    1.1956   -0.7659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9947   -1.3166   -1.1543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5449   -0.9171    0.5161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1683   -0.2959   -1.2293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9311    0.7239   -2.0193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3871    2.1446   -0.5129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7304    2.1011    0.1307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2729    0.5259    1.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7642    0.1868    0.9882 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
 10 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
 11 32  1  0
M  END
Download

3D SDF for #<Metabolite:0x00005645c9c2fd20>


  Mrv0541 02241203492D          

 11 10  0  0  0  0            999 V2000
   14.9516  -10.2273    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.6661   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3806  -10.2273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0951   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8096  -10.2273    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.5241   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2386  -10.2273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9530   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.6676  -10.2273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3820   -9.8148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.0966  -10.2273    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
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029920

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCCCNCCCN

> <INCHI_IDENTIFIER>
InChI=1S/C8H21N3/c9-5-2-1-3-7-11-8-4-6-10/h11H,1-10H2

> <INCHI_KEY>
QZBYOYPROVGOGE-UHFFFAOYSA-N

> <FORMULA>
C8H21N3

> <MOLECULAR_WEIGHT>
159.2724

> <EXACT_MASS>
159.173547687

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
20.904693787528277

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5-aminopentyl)(3-aminopropyl)amine

> <ALOGPS_LOGP>
-0.09

> <JCHEM_LOGP>
-0.7049952750000001

> <ALOGPS_LOGS>
-1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA_STRONGEST_BASIC>
10.89817484046326

> <JCHEM_POLAR_SURFACE_AREA>
64.07

> <JCHEM_REFRACTIVITY>
49.5694

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.28e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
aminopropylcadaverine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00005645c9c2fd20>

HMDB0012189
     RDKit          3D
Aminopropylcadaverine
 32 31  0  0  0  0  0  0  0  0999 V2000
    4.3757    1.2741   -0.1891 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4912    0.2018   -0.5880 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9950   -0.5538    0.6255 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0695   -1.6768    0.2535 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8437   -1.1710   -0.4938 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0939   -0.1942    0.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0722    0.3541   -0.2047 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1769   -0.4959   -0.4259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2836    0.3460   -1.0414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6168    1.4528   -0.0853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0635    0.9166    1.1636 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8409    2.1367    0.0378 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0023    1.0012    0.5780 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6118    0.6341   -1.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0398   -0.4473   -1.2933 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8819   -1.0276    1.1144 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5881    0.1506    1.3603 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6248   -2.4247   -0.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6913   -2.1085    1.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0998   -0.6857   -1.4484 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1708   -2.0324   -0.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1907   -0.6754    1.3427 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7596    0.6769    0.6476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9830    1.1956   -0.7659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9947   -1.3166   -1.1543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5449   -0.9171    0.5161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1683   -0.2959   -1.2293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9311    0.7239   -2.0193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3871    2.1446   -0.5129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7304    2.1011    0.1307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2729    0.5259    1.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7642    0.1868    0.9882 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
 10 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 10 30  1  0
 11 31  1  0
 11 32  1  0
M  END
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PDB for #<Metabolite:0x00005645c9c2fd20>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  N   UNK     0      27.910 -19.091   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      29.243 -18.321   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      30.577 -19.091   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      31.911 -18.321   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      33.245 -19.091   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      34.578 -18.321   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      35.912 -19.091   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      37.246 -18.321   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      38.580 -19.091   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      39.913 -18.321   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      41.247 -19.091   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    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for #<Metabolite:0x00005645c9c2fd20>

COMPND    HMDB0012189
HETATM    1  N1  UNL     1       4.376   1.274  -0.189  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.491   0.202  -0.588  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.995  -0.554   0.626  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.069  -1.677   0.253  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.844  -1.171  -0.494  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.094  -0.194   0.376  1.00  0.00           C  
HETATM    7  N2  UNL     1      -1.072   0.354  -0.205  1.00  0.00           N  
HETATM    8  C6  UNL     1      -2.177  -0.496  -0.426  1.00  0.00           C  
HETATM    9  C7  UNL     1      -3.284   0.346  -1.041  1.00  0.00           C  
HETATM   10  C8  UNL     1      -3.617   1.453  -0.085  1.00  0.00           C  
HETATM   11  N3  UNL     1      -4.063   0.917   1.164  1.00  0.00           N  
HETATM   12  H1  UNL     1       3.841   2.137   0.038  1.00  0.00           H  
HETATM   13  H2  UNL     1       5.002   1.001   0.578  1.00  0.00           H  
HETATM   14  H3  UNL     1       2.612   0.634  -1.112  1.00  0.00           H  
HETATM   15  H4  UNL     1       4.040  -0.447  -1.293  1.00  0.00           H  
HETATM   16  H5  UNL     1       3.882  -1.028   1.114  1.00  0.00           H  
HETATM   17  H6  UNL     1       2.588   0.151   1.360  1.00  0.00           H  
HETATM   18  H7  UNL     1       2.625  -2.425  -0.322  1.00  0.00           H  
HETATM   19  H8  UNL     1       1.691  -2.108   1.216  1.00  0.00           H  
HETATM   20  H9  UNL     1       1.100  -0.686  -1.448  1.00  0.00           H  
HETATM   21  H10 UNL     1       0.171  -2.032  -0.683  1.00  0.00           H  
HETATM   22  H11 UNL     1      -0.191  -0.675   1.343  1.00  0.00           H  
HETATM   23  H12 UNL     1       0.760   0.677   0.648  1.00  0.00           H  
HETATM   24  H13 UNL     1      -0.983   1.196  -0.766  1.00  0.00           H  
HETATM   25  H14 UNL     1      -1.995  -1.317  -1.154  1.00  0.00           H  
HETATM   26  H15 UNL     1      -2.545  -0.917   0.516  1.00  0.00           H  
HETATM   27  H16 UNL     1      -4.168  -0.296  -1.229  1.00  0.00           H  
HETATM   28  H17 UNL     1      -2.931   0.724  -2.019  1.00  0.00           H  
HETATM   29  H18 UNL     1      -4.387   2.145  -0.513  1.00  0.00           H  
HETATM   30  H19 UNL     1      -2.730   2.101   0.131  1.00  0.00           H  
HETATM   31  H20 UNL     1      -3.273   0.526   1.714  1.00  0.00           H  
HETATM   32  H21 UNL     1      -4.764   0.187   0.988  1.00  0.00           H  
CONECT    1    2   12   13
CONECT    2    3   14   15
CONECT    3    4   16   17
CONECT    4    5   18   19
CONECT    5    6   20   21
CONECT    6    7   22   23
CONECT    7    8   24
CONECT    8    9   25   26
CONECT    9   10   27   28
CONECT   10   11   29   30
CONECT   11   31   32
END
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SMILES for #<Metabolite:0x00005645c9c2fd20>

NCCCCCNCCCN
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INCHI for #<Metabolite:0x00005645c9c2fd20>

InChI=1S/C8H21N3/c9-5-2-1-3-7-11-8-4-6-10/h11H,1-10H2
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Synonyms
ValueSource
3-ApcadChEBI
N-(3-Aminopropyl)-1,5-pentanediamineChEBI
N-(3-Aminopropyl)cadaverineChEBI
N-3-Aminopropyl-1,5-diaminopentaneChEBI
Molecular FormulaC8H21N3
Average Mass159.2724
Monoisotopic Mass159.173547687
IUPAC Name(5-aminopentyl)(3-aminopropyl)amine
Traditional Nameaminopropylcadaverine
CAS Registry Number56-19-9
SMILES
NCCCCCNCCCN
InChI Identifier
InChI=1S/C8H21N3/c9-5-2-1-3-7-11-8-4-6-10/h11H,1-10H2
InChI KeyQZBYOYPROVGOGE-UHFFFAOYSA-N