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Showing metabocard for piperazine-2,3-dione (HMDB0256573)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:05:40 UTC
Update Date2021-09-26 23:12:20 UTC
HMDB IDHMDB0256573
Secondary Accession NumbersNone
Metabolite Identification
Common Namepiperazine-2,3-dione
Descriptionpiperazine-2,3-dione 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 a small amount of articles have been published on piperazine-2,3-dione. This compound has been identified in human blood as reported by (PMID: 31557052 ). Piperazine-2,3-dione is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically piperazine-2,3-dione 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 HMDB0256573 (piperazine-2,3-dione)

  Mrv1652309112119052D          

  8  8  0  0  0  0            999 V2000
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
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3D MOL for HMDB0256573 (piperazine-2,3-dione)

HMDB0256573
     RDKit          3D
piperazine-2,3-dione
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.0098   -1.9227    0.2474 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1172   -1.0284    0.1371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2556   -1.3685   -0.0058 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2255   -0.3345    0.2864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8198    0.8746   -0.5300 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4476    1.3304    0.0278 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4977    0.3806    0.1561 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7059    0.6893    0.2817 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5498   -2.3190   -0.3068 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1166   -0.1215    1.3904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2619   -0.6566    0.0675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5919    0.5115   -1.5649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5822    1.6591   -0.5221 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6251    2.3056    0.3351 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  2  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
M  END
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3D SDF for HMDB0256573 (piperazine-2,3-dione)

  Mrv1652309112119052D          

  8  8  0  0  0  0            999 V2000
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  1  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256573

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1NCCNC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H6N2O2/c7-3-4(8)6-2-1-5-3/h1-2H2,(H,5,7)(H,6,8)

> <INCHI_KEY>
JTHRRMFZHSDGNJ-UHFFFAOYSA-N

> <FORMULA>
C4H6N2O2

> <MOLECULAR_WEIGHT>
114.104

> <EXACT_MASS>
114.042927441

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.110690600482876

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
piperazine-2,3-dione

> <ALOGPS_LOGP>
-1.70

> <JCHEM_LOGP>
-1.6018096086666664

> <ALOGPS_LOGS>
-0.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.14953016578848

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.084113935856015

> <JCHEM_PKA_STRONGEST_BASIC>
-4.001973556622865

> <JCHEM_POLAR_SURFACE_AREA>
58.2

> <JCHEM_REFRACTIVITY>
25.907400000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.65e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
piperazine-2,3-dione

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0256573 (piperazine-2,3-dione)

HMDB0256573
     RDKit          3D
piperazine-2,3-dione
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.0098   -1.9227    0.2474 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1172   -1.0284    0.1371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2556   -1.3685   -0.0058 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2255   -0.3345    0.2864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8198    0.8746   -0.5300 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4476    1.3304    0.0278 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4977    0.3806    0.1561 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7059    0.6893    0.2817 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5498   -2.3190   -0.3068 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1166   -0.1215    1.3904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2619   -0.6566    0.0675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5919    0.5115   -1.5649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5822    1.6591   -0.5221 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6251    2.3056    0.3351 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  2  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
M  END
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PDB for HMDB0256573 (piperazine-2,3-dione)

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       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.000   0.000   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    1                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0256573 (piperazine-2,3-dione)

COMPND    HMDB0256573
HETATM    1  O1  UNL     1       2.010  -1.923   0.247  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.117  -1.028   0.137  1.00  0.00           C  
HETATM    3  N1  UNL     1      -0.256  -1.369  -0.006  1.00  0.00           N  
HETATM    4  C2  UNL     1      -1.225  -0.335   0.286  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.820   0.875  -0.530  1.00  0.00           C  
HETATM    6  N2  UNL     1       0.448   1.330   0.028  1.00  0.00           N  
HETATM    7  C4  UNL     1       1.498   0.381   0.156  1.00  0.00           C  
HETATM    8  O2  UNL     1       2.706   0.689   0.282  1.00  0.00           O  
HETATM    9  H1  UNL     1      -0.550  -2.319  -0.307  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.117  -0.121   1.390  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.262  -0.657   0.067  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.592   0.511  -1.565  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.582   1.659  -0.522  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.625   2.306   0.335  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    9
CONECT    4    5   10   11
CONECT    5    6   12   13
CONECT    6    7   14
CONECT    7    8    8
END
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SMILES for HMDB0256573 (piperazine-2,3-dione)

O=C1NCCNC1=O
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INCHI for HMDB0256573 (piperazine-2,3-dione)

InChI=1S/C4H6N2O2/c7-3-4(8)6-2-1-5-3/h1-2H2,(H,5,7)(H,6,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC4H6N2O2
Average Molecular Weight114.104
Monoisotopic Molecular Weight114.042927441
IUPAC Namepiperazine-2,3-dione
Traditional Namepiperazine-2,3-dione
CAS Registry NumberNot Available
SMILES
O=C1NCCNC1=O
InChI Identifier
InChI=1S/C4H6N2O2/c7-3-4(8)6-2-1-5-3/h1-2H2,(H,5,7)(H,6,8)
InChI KeyJTHRRMFZHSDGNJ-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
  • Dioxopiperazine
  • 1,4-diazinane
  • Piperazine
  • Secondary carboxylic acid amide
  • Lactam
  • Carboxamide group
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic oxide
  • Organopnictogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
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 ID65599
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound72761
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 ]