Showing metabocard for 5-Aminopentanoic acid (MMDBc0000234)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:40:46 UTC
Update Date2024-10-15 16:52:54 UTC
Metabolite IDMMDBc0000234
Metabolite Identification
Common Name5-Aminopentanoic acid
Description5-Aminopentanoic acid (or 5-aminovalerate) is a lysine degradation product. It can be produced both endogenously or through bacterial catabolism of lysine. 5-aminovalerate is formed via the following multi-step reaction: L-lysine leads to cadverine leads to L-piperideine leads 5-aminovalerate (PMID: 405455 ). In other words it is a metabolite of cadaverine which is formed via the intermediate, 1-piperideine (PMID: 6436440 ). Cadaverine is a foul-smelling diamine compound produced by protein hydrolysis during putrefaction of animal tissue. High levels of 5-aminovalerate in biofluids may indicate bacterial overgrowth or endogenous tissue necrosis. In most cases endogenous 5-aminovalerate is thought to be primarily a microbial metabolite produced by the gut or oral microflora, although it can be produced endogenously. 5-aminovalerate is a normal metabolite present in human saliva, with a tendency to elevated concentration in patients with chronic periodontitis. Bacterial contamination and decomposition of salivary proteins is primarily responsible for elevated salivary levels (PMID 3481959 ). Beyond being a general waste product, 5-aminovalerate is also believed to act as a methylene homologue of gamma-aminobutyric acid (GABA) and functions as a weak GABA agonist (PMID: 4031870 ). It is also known as an antifibrinolytic amino acid analog and so it functions as a weak inhibitor of the blood clotting pathway (PMID: 6703712 ). 5- aminovalerate is an in vivo substrate of 4-aminobutyrate:2-oxoglutarate aminotransferase (PMID: 4031870 ). It can be found in Corynebacterium (PMID: 27717386 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9202771000>


  Mrv1652305271900002D          

  8  7  0  0  0  0            999 V2000
   23.2152  -11.1336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.9297  -12.3711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.5021  -11.1336    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.7877  -11.5461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.0731  -11.1336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3587  -11.5461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6442  -11.1336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9297  -11.5461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  8  2  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
M  END
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3D MOL for #<Metabolite:0x00007f9202771000>

HMDB0003355
     RDKit          3D
5-Aminopentanoic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    3.0127   -0.8049   -0.0629 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0477    0.2293    0.1562 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6675   -0.2759   -0.2781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3017    0.8324   -0.0327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7175    0.5310   -0.3985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3027   -0.5956    0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7065   -1.2608    1.2046 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6241   -0.9974    0.0688 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4110   -1.2070    0.8167 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7058   -0.6214   -0.7936 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0160    0.4477    1.2476 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2884    1.1837   -0.3414 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4041   -1.1842    0.2691 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7212   -0.5581   -1.3566 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    1.7455   -0.5770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2376    1.0876    1.0597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7693    0.3174   -1.4970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3209    1.4504   -0.1627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3434   -0.3197    0.3465 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  2  0
  6  8  1  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
  8 19  1  0
M  END
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3D SDF for #<Metabolite:0x00007f9202771000>


  Mrv1652305271900002D          

  8  7  0  0  0  0            999 V2000
   23.2152  -11.1336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.9297  -12.3711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.5021  -11.1336    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.7877  -11.5461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.0731  -11.1336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3587  -11.5461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6442  -11.1336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9297  -11.5461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  8  2  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
M  END
> <DATABASE_ID>
MMDBc0000234

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO2/c6-4-2-1-3-5(7)8/h1-4,6H2,(H,7,8)

> <INCHI_KEY>
JJMDCOVWQOJGCB-UHFFFAOYSA-N

> <FORMULA>
C5H11NO2

> <MOLECULAR_WEIGHT>
117.1463

> <EXACT_MASS>
117.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.65225454504008

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-aminopentanoic acid

> <ALOGPS_LOGP>
-2.75

> <JCHEM_LOGP>
-2.441462136430473

> <ALOGPS_LOGS>
0.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.6510543313288055

> <JCHEM_PKA_STRONGEST_BASIC>
10.205972024771656

> <JCHEM_POLAR_SURFACE_AREA>
63.31999999999999

> <JCHEM_REFRACTIVITY>
30.058799999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.06e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-aminovaleric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9202771000>

HMDB0003355
     RDKit          3D
5-Aminopentanoic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    3.0127   -0.8049   -0.0629 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0477    0.2293    0.1562 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6675   -0.2759   -0.2781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3017    0.8324   -0.0327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7175    0.5310   -0.3985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3027   -0.5956    0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7065   -1.2608    1.2046 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6241   -0.9974    0.0688 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4110   -1.2070    0.8167 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7058   -0.6214   -0.7936 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0160    0.4477    1.2476 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2884    1.1837   -0.3414 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4041   -1.1842    0.2691 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7212   -0.5581   -1.3566 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493    1.7455   -0.5770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2376    1.0876    1.0597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7693    0.3174   -1.4970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3209    1.4504   -0.1627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3434   -0.3197    0.3465 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  2  0
  6  8  1  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
  8 19  1  0
M  END
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PDB for #<Metabolite:0x00007f9202771000>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      43.335 -20.783   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      44.669 -23.093   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      51.337 -20.783   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      50.004 -21.553   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      48.670 -20.783   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      47.336 -21.553   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      46.003 -20.783   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      44.669 -21.553   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    8                                                            
CONECT    3    4                                                            
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    1    2    7                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00007f9202771000>

COMPND    HMDB0003355
HETATM    1  N1  UNL     1       3.013  -0.805  -0.063  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.048   0.229   0.156  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.667  -0.276  -0.278  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.302   0.832  -0.033  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.718   0.531  -0.399  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.303  -0.596   0.331  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.707  -1.261   1.205  1.00  0.00           O  
HETATM    8  O2  UNL     1      -3.624  -0.997   0.069  1.00  0.00           O  
HETATM    9  H1  UNL     1       3.411  -1.207   0.817  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.706  -0.621  -0.794  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.016   0.448   1.248  1.00  0.00           H  
HETATM   12  H4  UNL     1       2.288   1.184  -0.341  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.404  -1.184   0.269  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.721  -0.558  -1.357  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.049   1.746  -0.577  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.238   1.088   1.060  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.769   0.317  -1.497  1.00  0.00           H  
HETATM   18  H10 UNL     1      -2.321   1.450  -0.163  1.00  0.00           H  
HETATM   19  H11 UNL     1      -4.343  -0.320   0.347  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    7    8
CONECT    8   19
END
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SMILES for #<Metabolite:0x00007f9202771000>

NCCCCC(O)=O
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INCHI for #<Metabolite:0x00007f9202771000>

InChI=1S/C5H11NO2/c6-4-2-1-3-5(7)8/h1-4,6H2,(H,7,8)
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Synonyms
ValueSource
5-Amino-N-valeric acidChEBI
5-AminopentanoateChEBI
5-Aminovaleric acidChEBI
DANVAChEBI
delta-Amino-N-valeric acidChEBI
delta-Aminovaleric acidChEBI
5-Amino-N-valerateGenerator
5-AminovalerateGenerator
delta-Amino-N-valerateGenerator
Δ-amino-N-valerateGenerator
Δ-amino-N-valeric acidGenerator
delta-AminovalerateGenerator
Δ-aminovalerateGenerator
Δ-aminovaleric acidGenerator
5-Aminovaleric acid hydrochlorideMeSH
5-Aminopentanoic acidKEGG
5-Amino-pentanoateGenerator, HMDB
Molecular FormulaC5H11NO2
Average Mass117.1463
Monoisotopic Mass117.078978601
IUPAC Name5-aminopentanoic acid
Traditional Name5-aminovaleric acid
CAS Registry Number660-88-8
SMILES
NCCCCC(O)=O
InChI Identifier
InChI=1S/C5H11NO2/c6-4-2-1-3-5(7)8/h1-4,6H2,(H,7,8)
InChI KeyJJMDCOVWQOJGCB-UHFFFAOYSA-N