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Showing metabocard for Amino (2S)-2,5-diamino-5-oxopentanoate (HMDB0257701)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 18:44:20 UTC
Update Date2021-09-26 23:14:14 UTC
HMDB IDHMDB0257701
Secondary Accession NumbersNone
Metabolite Identification
Common NameAmino (2S)-2,5-diamino-5-oxopentanoate
DescriptionAmino (2S)-2,5-diamino-5-oxopentanoate, also known as 4-amino-5-(aminooxy)-5-oxopentanimidate, belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. Based on a literature review very few articles have been published on Amino (2S)-2,5-diamino-5-oxopentanoate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Amino (2s)-2,5-diamino-5-oxopentanoate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Amino (2S)-2,5-diamino-5-oxopentanoate is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0257701 (Amino (2S)-2,5-diamino-5-oxopentanoate)

  Mrv1652309112120442D          

 11 10  0  0  0  0            999 V2000
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    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  2  0  0  0  0
  3  5  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6 11  1  0  0  0  0
M  END
Download

3D MOL for HMDB0257701 (Amino (2S)-2,5-diamino-5-oxopentanoate)

HMDB0257701
     RDKit          3D
Amino (2S)-2,5-diamino-5-oxopentanoate
 22 21  0  0  0  0  0  0  0  0999 V2000
    3.0183    1.7946    0.4166 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2515    0.9993   -0.3995 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7641   -0.1880    0.0700 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0332   -0.5282    1.2541 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9279   -1.1282   -0.7142 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6661   -0.6714   -2.0479 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4029   -1.2493    0.0003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0575    0.0977    0.0764 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3671    0.0234    0.7707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1668    1.2016    0.9552 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7426   -1.0995    1.1854 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9182    1.5563    1.4236 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0045    1.8102    0.1108 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3793   -2.1575   -0.7278 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9876    0.2826   -2.2557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3005   -0.8885   -2.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0851   -1.9381   -0.5272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2335   -1.6153    1.0443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4375    0.8442    0.6181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2354    0.4429   -0.9785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1048    1.7698    1.8360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8169    1.5009    0.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  2  0
  1 12  1  0
  1 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
  8 20  1  0
 10 21  1  0
 10 22  1  0
M  END
Download

3D SDF for HMDB0257701 (Amino (2S)-2,5-diamino-5-oxopentanoate)

  Mrv1652309112120442D          

 11 10  0  0  0  0            999 V2000
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    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  2  0  0  0  0
  3  5  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0257701

> <DATABASE_NAME>
hmdb

> <SMILES>
NOC(=O)C(N)CCC(N)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11N3O3/c6-3(5(10)11-8)1-2-4(7)9/h3H,1-2,6,8H2,(H2,7,9)

> <INCHI_KEY>
FWBDAHSKNXCJMX-UHFFFAOYSA-N

> <FORMULA>
C5H11N3O3

> <MOLECULAR_WEIGHT>
161.161

> <EXACT_MASS>
161.080041226

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
15.342377842408974

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
amino 2-amino-4-carbamoylbutanoate

> <ALOGPS_LOGP>
-1.78

> <JCHEM_LOGP>
-2.1130623359999996

> <ALOGPS_LOGS>
-0.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.101900214306003

> <JCHEM_PKA_STRONGEST_BASIC>
6.836080805619484

> <JCHEM_POLAR_SURFACE_AREA>
121.42999999999999

> <JCHEM_REFRACTIVITY>
37.4664

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.27e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
amino 2-amino-4-carbamoylbutanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0257701 (Amino (2S)-2,5-diamino-5-oxopentanoate)

HMDB0257701
     RDKit          3D
Amino (2S)-2,5-diamino-5-oxopentanoate
 22 21  0  0  0  0  0  0  0  0999 V2000
    3.0183    1.7946    0.4166 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2515    0.9993   -0.3995 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7641   -0.1880    0.0700 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0332   -0.5282    1.2541 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9279   -1.1282   -0.7142 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6661   -0.6714   -2.0479 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4029   -1.2493    0.0003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0575    0.0977    0.0764 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3671    0.0234    0.7707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1668    1.2016    0.9552 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7426   -1.0995    1.1854 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9182    1.5563    1.4236 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0045    1.8102    0.1108 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3793   -2.1575   -0.7278 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9876    0.2826   -2.2557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3005   -0.8885   -2.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0851   -1.9381   -0.5272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2335   -1.6153    1.0443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4375    0.8442    0.6181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2354    0.4429   -0.9785 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1048    1.7698    1.8360 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8169    1.5009    0.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  2  0
  1 12  1  0
  1 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
  8 20  1  0
 10 21  1  0
 10 22  1  0
M  END
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PDB for HMDB0257701 (Amino (2S)-2,5-diamino-5-oxopentanoate)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.953   2.667   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       3.286   4.977   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       9.955   2.667   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      11.288   3.437   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       7.287   1.127   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    1    7   11                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
CONECT   11    6                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0257701 (Amino (2S)-2,5-diamino-5-oxopentanoate)

COMPND    HMDB0257701
HETATM    1  N1  UNL     1       3.018   1.795   0.417  1.00  0.00           N  
HETATM    2  O1  UNL     1       2.251   0.999  -0.400  1.00  0.00           O  
HETATM    3  C1  UNL     1       1.764  -0.188   0.070  1.00  0.00           C  
HETATM    4  O2  UNL     1       2.033  -0.528   1.254  1.00  0.00           O  
HETATM    5  C2  UNL     1       0.928  -1.128  -0.714  1.00  0.00           C  
HETATM    6  N2  UNL     1       0.666  -0.671  -2.048  1.00  0.00           N  
HETATM    7  C3  UNL     1      -0.403  -1.249   0.000  1.00  0.00           C  
HETATM    8  C4  UNL     1      -1.057   0.098   0.076  1.00  0.00           C  
HETATM    9  C5  UNL     1      -2.367   0.023   0.771  1.00  0.00           C  
HETATM   10  N3  UNL     1      -3.167   1.202   0.955  1.00  0.00           N  
HETATM   11  O3  UNL     1      -2.743  -1.099   1.185  1.00  0.00           O  
HETATM   12  H1  UNL     1       2.918   1.556   1.424  1.00  0.00           H  
HETATM   13  H2  UNL     1       4.004   1.810   0.111  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.379  -2.158  -0.728  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.988   0.283  -2.256  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.301  -0.889  -2.322  1.00  0.00           H  
HETATM   17  H6  UNL     1      -1.085  -1.938  -0.527  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.234  -1.615   1.044  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.437   0.844   0.618  1.00  0.00           H  
HETATM   20  H9  UNL     1      -1.235   0.443  -0.979  1.00  0.00           H  
HETATM   21  H10 UNL     1      -3.105   1.770   1.836  1.00  0.00           H  
HETATM   22  H11 UNL     1      -3.817   1.501   0.211  1.00  0.00           H  
CONECT    1    2   12   13
CONECT    2    3
CONECT    3    4    4    5
CONECT    5    6    7   14
CONECT    6   15   16
CONECT    7    8   17   18
CONECT    8    9   19   20
CONECT    9   10   11   11
CONECT   10   21   22
END
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SMILES for HMDB0257701 (Amino (2S)-2,5-diamino-5-oxopentanoate)

NOC(=O)C(N)CCC(N)=O
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INCHI for HMDB0257701 (Amino (2S)-2,5-diamino-5-oxopentanoate)

InChI=1S/C5H11N3O3/c6-3(5(10)11-8)1-2-4(7)9/h3H,1-2,6,8H2,(H2,7,9)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Amino (2S)-2,5-diamino-5-oxopentanoic acidGenerator
4-Amino-5-(aminooxy)-5-oxopentanimidateHMDB
Chemical FormulaC5H11N3O3
Average Molecular Weight161.161
Monoisotopic Molecular Weight161.080041226
IUPAC Nameamino 2-amino-4-carbamoylbutanoate
Traditional Nameamino 2-amino-4-carbamoylbutanoate
CAS Registry NumberNot Available
SMILES
NOC(=O)C(N)CCC(N)=O
InChI Identifier
InChI=1S/C5H11N3O3/c6-3(5(10)11-8)1-2-4(7)9/h3H,1-2,6,8H2,(H2,7,9)
InChI KeyFWBDAHSKNXCJMX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Monocarboxylic acid or derivatives
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Amino (2S)-2,5-diamino-5-oxopentanoate GC-MS (Non-derivatized) - 70eV, Positivesplash10-0udi-8900000000-f88b6efb2f0105cbbfe72021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Amino (2S)-2,5-diamino-5-oxopentanoate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID14170905
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound22417575
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]