Showing NP-Card for 5-Aminopentanoic acid (NP0001412)

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Record Information
Version2.0
Created at2006-08-12 19:17:39 UTC
Updated at2021-10-07 20:40:59 UTC
NP-MRD IDNP0001412
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001412 (5-Aminopentanoic acid)

  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 NP0001412 (5-Aminopentanoic acid)

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 NP0001412 (5-Aminopentanoic acid)

  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>
NP0001412

> <DATABASE_NAME>
NP-MRD

> <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 NP0001412 (5-Aminopentanoic acid)

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 NP0001412 (5-Aminopentanoic acid)

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 NP0001412 (5-Aminopentanoic acid)

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 NP0001412 (5-Aminopentanoic acid)

NCCCCC(O)=O
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INCHI for NP0001412 (5-Aminopentanoic acid)

InChI=1S/C5H11NO2/c6-4-2-1-3-5(7)8/h1-4,6H2,(H,7,8)
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Synonyms
Chemical FormulaC5H11NO2
Average Mass117.1463 Da
Monoisotopic Mass117.07898 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as delta amino acids and derivatives. Delta amino acids and derivatives are compounds containing a carboxylic acid group and an amino group at the C5 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentDelta amino acids and derivatives
Alternative Parents
Substituents
  • Delta amino acid or derivatives
  • Straight chain fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point157.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mL at 20 °CNot Available
LogP-2.63Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility206 g/LALOGPS
logP-2.8ALOGPS
logP-2.4ChemAxon
logS0.24ALOGPS
pKa (Strongest Acidic)4.65ChemAxon
pKa (Strongest Basic)10.21ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.06 m³·mol⁻¹ChemAxon
Polarizability12.65 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0003355
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023151
KNApSAcK IDC00052162
Chemspider ID135
KEGG Compound IDC00431
BioCyc ID5-AMINOPENTANOATE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6902
PubChem Compound138
PDB IDNot Available
ChEBI ID15887
Good Scents IDNot Available
References
General References