Showing metabocard for 5-Aminopentanamide (MMDBc0049942)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:46:44 UTC
Update Date2025-01-15 22:50:19 UTC
Metabolite IDMMDBc0049942
Metabolite Identification
Common Name5-Aminopentanamide
Description5-Aminopentanamide is involved in the lysine degradation IV pathway. It can be generated from the enzymatic reduction of 5-aminopentanoate or enzymatic oxidation of L-lysine. Pseudomonas putida can catabolize L-lysine via the δ-aminovalerate (AMV) (5-aminopentanoate) pathway to glutarate. In this pathway, L-lysine is transported into the cell by basic amino acid transport systems. It is oxidatively decarboxylated to 5-aminopentanamide, which is then hydrolyzed to 5-aminopentanoate and ammonia. The conversion of 5-aminopentanoate to glutarate involves gene products of the davDT operon. Activation of glutarate to glutaryl-CoA by an as yet uncharacterized reaction(s) and further metabolism of glutaryl-CoA to carbon dioxide and acetyl-CoA have been demonstrated in Pseudomonas fluorescens.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923c4bfb60>


  Mrv0541 02241203482D          

  8  7  0  0  0  0            999 V2000
   10.0559   -6.7988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3415   -7.2113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7704   -7.2113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6270   -6.7988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4848   -6.7988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9126   -7.2113    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.1993   -7.2113    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.4848   -5.9738    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  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  7  1  0  0  0  0
  5  8  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f923c4bfb60>

HMDB0012176
     RDKit          3D
5-Aminopentanamide
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.6945   -0.0457   -1.0539 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2993   -0.6669    0.1963 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8589   -0.3293    0.5296 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0987   -0.7919   -0.5105 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4939   -0.4316   -0.1202 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7602    1.0066    0.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0272    1.4051    0.5166 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9119    1.8881   -0.2595 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9560    0.5148   -1.4940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4921    0.6294   -0.8593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9146   -0.2662    1.0321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4606   -1.7665    0.1333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5560   -0.8156    1.4934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8098    0.7566    0.7239 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0399   -1.9157   -0.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1677   -0.4662   -1.5381 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7249   -0.9920    0.8344 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1787   -0.8120   -0.9264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6523    1.9692   -0.0770 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3217    1.1300    1.4652 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
  6  8  2  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  7 19  1  0
  7 20  1  0
M  END
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3D SDF for #<Metabolite:0x00007f923c4bfb60>


  Mrv0541 02241203482D          

  8  7  0  0  0  0            999 V2000
   10.0559   -6.7988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3415   -7.2113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7704   -7.2113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6270   -6.7988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4848   -6.7988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9126   -7.2113    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.1993   -7.2113    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.4848   -5.9738    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  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  7  1  0  0  0  0
  5  8  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049942

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCCC(N)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H12N2O/c6-4-2-1-3-5(7)8/h1-4,6H2,(H2,7,8)

> <INCHI_KEY>
OTIAVLWNTIXJDO-UHFFFAOYSA-N

> <FORMULA>
C5H12N2O

> <MOLECULAR_WEIGHT>
116.1616

> <EXACT_MASS>
116.094963016

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
13.025910755151

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-aminopentanamide

> <ALOGPS_LOGP>
-2.00

> <JCHEM_LOGP>
-0.9841755643333333

> <ALOGPS_LOGS>
0.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.94112919095558

> <JCHEM_PKA_STRONGEST_BASIC>
9.905080622222428

> <JCHEM_POLAR_SURFACE_AREA>
69.11

> <JCHEM_REFRACTIVITY>
31.881

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
aminopentamide

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f923c4bfb60>

HMDB0012176
     RDKit          3D
5-Aminopentanamide
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.6945   -0.0457   -1.0539 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2993   -0.6669    0.1963 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8589   -0.3293    0.5296 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0987   -0.7919   -0.5105 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4939   -0.4316   -0.1202 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7602    1.0066    0.0289 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0272    1.4051    0.5166 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9119    1.8881   -0.2595 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9560    0.5148   -1.4940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4921    0.6294   -0.8593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9146   -0.2662    1.0321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4606   -1.7665    0.1333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5560   -0.8156    1.4934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8098    0.7566    0.7239 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0399   -1.9157   -0.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1677   -0.4662   -1.5381 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7249   -0.9920    0.8344 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1787   -0.8120   -0.9264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6523    1.9692   -0.0770 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3217    1.1300    1.4652 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
  6  8  2  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  7 19  1  0
  7 20  1  0
M  END
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PDB for #<Metabolite:0x00007f923c4bfb60>

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  C   UNK     0      18.771 -12.691   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.437 -13.461   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      20.105 -13.461   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.104 -12.691   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      21.438 -12.691   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      14.770 -13.461   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      22.772 -13.461   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      21.438 -11.151   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7    8                                                  
CONECT    6    4                                                            
CONECT    7    5                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00007f923c4bfb60>

COMPND    HMDB0012176
HETATM    1  N1  UNL     1      -2.694  -0.046  -1.054  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.299  -0.667   0.196  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.859  -0.329   0.530  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.099  -0.792  -0.511  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.494  -0.432  -0.120  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.760   1.007   0.029  1.00  0.00           C  
HETATM    7  N2  UNL     1       3.027   1.405   0.517  1.00  0.00           N  
HETATM    8  O1  UNL     1       0.912   1.888  -0.259  1.00  0.00           O  
HETATM    9  H1  UNL     1      -1.956   0.515  -1.494  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.492   0.629  -0.859  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.915  -0.266   1.032  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.461  -1.766   0.133  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.556  -0.816   1.493  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.810   0.757   0.724  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.040  -1.916  -0.544  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.168  -0.466  -1.538  1.00  0.00           H  
HETATM   17  H9  UNL     1       1.725  -0.992   0.834  1.00  0.00           H  
HETATM   18  H10 UNL     1       2.179  -0.812  -0.926  1.00  0.00           H  
HETATM   19  H11 UNL     1       3.652   1.969  -0.077  1.00  0.00           H  
HETATM   20  H12 UNL     1       3.322   1.130   1.465  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3   11   12
CONECT    3    4   13   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7    8    8
CONECT    7   19   20
END
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SMILES for #<Metabolite:0x00007f923c4bfb60>

NCCCCC(N)=O
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INCHI for #<Metabolite:0x00007f923c4bfb60>

InChI=1S/C5H12N2O/c6-4-2-1-3-5(7)8/h1-4,6H2,(H2,7,8)
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Synonyms
ValueSource
5-AminovaleramideChEBI
5-Aminovaleric acid amideChEBI
5-Aminovalerate amideGenerator
Molecular FormulaC5H12N2O
Average Mass116.1616
Monoisotopic Mass116.094963016
IUPAC Name5-aminopentanamide
Traditional Nameaminopentamide
CAS Registry NumberNot Available
SMILES
NCCCCC(N)=O
InChI Identifier
InChI=1S/C5H12N2O/c6-4-2-1-3-5(7)8/h1-4,6H2,(H2,7,8)
InChI KeyOTIAVLWNTIXJDO-UHFFFAOYSA-N