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Showing metabocard for 5-Amino-2-oxopentanoic acid (HMDB0006272)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2007-05-22 20:51:34 UTC
Update Date2023-02-21 17:17:16 UTC
HMDB IDHMDB0006272
Secondary Accession Numbers
  • HMDB06272
Metabolite Identification
Common Name5-Amino-2-oxopentanoic acid
Description5-Amino-2-oxopentanoic acid, also known as 2-oxo-5-amino-pentanoate or alpha-keto-delta-aminopentanoate, belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms. 5-Amino-2-oxopentanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 5-Amino-2-oxopentanoic acid exists in all living organisms, ranging from bacteria to humans. 5-amino-2-oxopentanoic acid can be biosynthesized from D-ornithine through the action of the enzyme D-amino-acid oxidase. The 2-oxo-5-amino derivative of valeric acid. In humans, 5-amino-2-oxopentanoic acid is involved in d-arginine and d-ornithine metabolism.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0006272 (5-Amino-2-oxopentanoic acid)

  Mrv0541 02231220352D          

  9  8  0  0  0  0            999 V2000
   18.3849   -4.9777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.8138   -4.1527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.0994   -2.9151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5271   -4.1527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.9560   -4.1527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6705   -3.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2416   -3.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3849   -4.1527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0994   -3.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  2  0  0  0  0
  2  9  1  0  0  0  0
  3  9  2  0  0  0  0
  4  7  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
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3D MOL for HMDB0006272 (5-Amino-2-oxopentanoic acid)

HMDB0006272
     RDKit          3D
5-Amino-2-oxopentanoic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -3.0608    0.1754   -0.0289 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6633    0.1139    0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8962   -0.7280   -0.5425 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5329   -0.8432   -0.1568 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2895    0.4290   -0.1145 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7607    1.5360   -0.4270 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6702    0.3803    0.2986 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1959   -0.6971    0.6059 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3982    1.5419    0.3482 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3813   -0.7366   -0.4206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0794    0.8599   -0.8256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5795   -0.2982    1.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3254    1.1653    0.4216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3406   -1.7534   -0.5941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9561   -0.3006   -1.5712 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6819   -1.3207    0.8427 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0772   -1.5035   -0.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6763    1.9796    1.2037 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  2  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  9 18  1  0
M  END
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3D SDF for HMDB0006272 (5-Amino-2-oxopentanoic acid)

  Mrv0541 02231220352D          

  9  8  0  0  0  0            999 V2000
   18.3849   -4.9777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.8138   -4.1527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.0994   -2.9151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5271   -4.1527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.9560   -4.1527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6705   -3.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2416   -3.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3849   -4.1527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0994   -3.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  2  0  0  0  0
  2  9  1  0  0  0  0
  3  9  2  0  0  0  0
  4  7  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006272

> <DATABASE_NAME>
hmdb

> <SMILES>
NCCCC(=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO3/c6-3-1-2-4(7)5(8)9/h1-3,6H2,(H,8,9)

> <INCHI_KEY>
BWHGMFYTDQEALD-UHFFFAOYSA-N

> <FORMULA>
C5H9NO3

> <MOLECULAR_WEIGHT>
131.1299

> <EXACT_MASS>
131.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.590688695983491

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-amino-2-oxopentanoic acid

> <ALOGPS_LOGP>
-2.46

> <JCHEM_LOGP>
-2.595682911607415

> <ALOGPS_LOGS>
-0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.74990300336155

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1122390128026995

> <JCHEM_PKA_STRONGEST_BASIC>
9.793079801179742

> <JCHEM_POLAR_SURFACE_AREA>
80.39

> <JCHEM_REFRACTIVITY>
30.803799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.61e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-amino-2-oxopentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0006272 (5-Amino-2-oxopentanoic acid)

HMDB0006272
     RDKit          3D
5-Amino-2-oxopentanoic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -3.0608    0.1754   -0.0289 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6633    0.1139    0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8962   -0.7280   -0.5425 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5329   -0.8432   -0.1568 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2895    0.4290   -0.1145 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7607    1.5360   -0.4270 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6702    0.3803    0.2986 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1959   -0.6971    0.6059 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3982    1.5419    0.3482 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3813   -0.7366   -0.4206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0794    0.8599   -0.8256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5795   -0.2982    1.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3254    1.1653    0.4216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3406   -1.7534   -0.5941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9561   -0.3006   -1.5712 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6819   -1.3207    0.8427 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0772   -1.5035   -0.8900 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6763    1.9796    1.2037 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  2  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  9 18  1  0
M  END
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PDB for HMDB0006272 (5-Amino-2-oxopentanoic acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      34.318  -9.292   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      36.986  -7.752   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      35.652  -5.442   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      28.984  -7.752   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      31.651  -7.752   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      32.985  -6.982   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      30.318  -6.982   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      34.318  -7.752   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      35.652  -6.982   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3    9                                                            
CONECT    4    7                                                            
CONECT    5    6    7                                                       
CONECT    6    5    8                                                       
CONECT    7    4    5                                                       
CONECT    8    1    6    9                                                  
CONECT    9    2    3    8                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0006272 (5-Amino-2-oxopentanoic acid)

COMPND    HMDB0006272
HETATM    1  N1  UNL     1      -3.061   0.175  -0.029  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.663   0.114   0.412  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.896  -0.728  -0.543  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.533  -0.843  -0.157  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.289   0.429  -0.115  1.00  0.00           C  
HETATM    6  O1  UNL     1       0.761   1.536  -0.427  1.00  0.00           O  
HETATM    7  C5  UNL     1       2.670   0.380   0.299  1.00  0.00           C  
HETATM    8  O2  UNL     1       3.196  -0.697   0.606  1.00  0.00           O  
HETATM    9  O3  UNL     1       3.398   1.542   0.348  1.00  0.00           O  
HETATM   10  H1  UNL     1      -3.381  -0.737  -0.421  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.079   0.860  -0.826  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.580  -0.298   1.438  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.325   1.165   0.422  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.341  -1.753  -0.594  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.956  -0.301  -1.571  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.682  -1.321   0.843  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.077  -1.503  -0.890  1.00  0.00           H  
HETATM   18  H9  UNL     1       3.676   1.980   1.204  1.00  0.00           H  
CONECT    1    2   10   11
CONECT    2    3   12   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6    6    7
CONECT    7    8    8    9
CONECT    9   18
END
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SMILES for HMDB0006272 (5-Amino-2-oxopentanoic acid)

NCCCC(=O)C(O)=O
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INCHI for HMDB0006272 (5-Amino-2-oxopentanoic acid)

InChI=1S/C5H9NO3/c6-3-1-2-4(7)5(8)9/h1-3,6H2,(H,8,9)
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Synonyms
Chemical FormulaC5H9NO3
Average Molecular Weight131.1299
Monoisotopic Molecular Weight131.058243159
IUPAC Name5-amino-2-oxopentanoic acid
Traditional Name5-amino-2-oxopentanoic acid
CAS Registry NumberNot Available
SMILES
NCCCC(=O)C(O)=O
InChI Identifier
InChI=1S/C5H9NO3/c6-3-1-2-4(7)5(8)9/h1-3,6H2,(H,8,9)
InChI KeyBWHGMFYTDQEALD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassShort-chain keto acids and derivatives
Direct ParentShort-chain keto acids and derivatives
Alternative Parents
Substituents
  • Short-chain keto acid
  • Alpha-keto acid
  • Gamma-aminoketone
  • Alpha-hydroxy ketone
  • Amino acid or derivatives
  • Amino acid
  • Ketone
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organooxygen compound
  • Primary amine
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Organopnictogen compound
  • Amine
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
  • Peroxisome
Biospecimen Locations
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
    • Zerihun T. Dame, ...
 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023870
KNApSAcK IDNot Available
Chemspider ID388519
KEGG Compound IDC01110
BioCyc ID5-AMINO-2-OXOPENTANOATE
BiGG ID36830
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439402
PDB IDNot Available
ChEBI ID49268
Food Biomarker OntologyNot Available
VMH ID5A2OPNTN
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. 3-ketoacyl-CoA thiolase, mitochondrial
General function:
Involved in transferase activity, transferring acyl groups other than amino-acyl groups
Specific function:
Abolishes BNIP3-mediated apoptosis and mitochondrial damage.
Gene Name:
ACAA2
Uniprot ID:
P42765
Molecular weight:
41923.82
Enzyme Details
2. D-amino-acid oxidase
General function:
Involved in D-amino-acid oxidase activity
Specific function:
Regulates the level of the neuromodulator D-serine in the brain. Has high activity towards D-DOPA and contributes to dopamine synthesis. Could act as a detoxifying agent which removes D-amino acids accumulated during aging. Acts on a variety of D-amino acids with a preference for those having small hydrophobic side chains followed by those bearing polar, aromatic, and basic groups. Does not act on acidic amino acids.
Gene Name:
DAO
Uniprot ID:
P14920
Molecular weight:
39473.75
Reactions
D-Ornithine + Water + Oxygen → 5-Amino-2-oxopentanoic acid + Ammonia + Hydrogen peroxidedetails