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Showing metabocard for cyclo(gly-gly) (HMDB0341300)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:16:10 UTC
Update Date2022-09-22 18:34:46 UTC
HMDB IDHMDB0341300
Secondary Accession NumbersNone
Metabolite Identification
Common Namecyclo(gly-gly)
Descriptionpiperazine-2,5-dione, also known as diketopiperazine or glycine anhydride, 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. A cyclic peptide that is piperazine in which the hydrogens at positions 2 and 5 are replaced by oxo groups. piperazine-2,5-dione is a very strong basic compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341300 (cyclo(gly-gly))


  Mrv0541 09041212392D          

  8  8  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   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   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  4  2  0  0  0  0
  6  2  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
M  END
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3D MOL for HMDB0341300 (cyclo(gly-gly))

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3D SDF for HMDB0341300 (cyclo(gly-gly))

  Mrv0541 09041212392D          

  8  8  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   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   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   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
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  4  2  0  0  0  0
  6  2  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341300

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=NCC(O)=NC1

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

> <INCHI_KEY>
BXRNXXXXHLBUKK-UHFFFAOYSA-N

> <FORMULA>
C4H6N2O2

> <MOLECULAR_WEIGHT>
114.1026

> <EXACT_MASS>
114.042927446

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
10.17358401412922

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,6-dihydropyrazine-2,5-diol

> <ALOGPS_LOGP>
-1.26

> <JCHEM_LOGP>
-1.1489690839980826

> <ALOGPS_LOGS>
-1.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.405764960415763

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.069394103866179

> <JCHEM_PKA_STRONGEST_BASIC>
5.640931412336054

> <JCHEM_POLAR_SURFACE_AREA>
65.18

> <JCHEM_REFRACTIVITY>
26.650399999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.51e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,6-dihydropyrazine-2,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341300 (cyclo(gly-gly))
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PDB for HMDB0341300 (cyclo(gly-gly))
HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    6    7                                                  
CONECT    4    2    5    8                                                  
CONECT    5    1    4                                                       
CONECT    6    2    3                                                       
CONECT    7    3                                                            
CONECT    8    4                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

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3D PDB for HMDB0341300 (cyclo(gly-gly))
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SMILES for HMDB0341300 (cyclo(gly-gly))
OC1=NCC(O)=NC1
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INCHI for HMDB0341300 (cyclo(gly-gly))
InChI=1S/C4H6N2O2/c7-3-1-5-4(8)2-6-3/h1-2H2,(H,5,8)(H,6,7)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,5-Diazacyclohexane-1,4-dioneChEBI
2,5-DioxopiperazineChEBI
2,5-PiperazinedioneChEBI
Cyclo-(gly-gly)ChEBI
DiketopiperazineChEBI
Glycine anhydrideChEBI
cyclo(Glycylglycyl)MeSH
cyclo(Gly-gly)MeSH
2,5-DiketopiperazineMeSH
Chemical FormulaC4H6N2O2
Average Molecular Weight114.1026
Monoisotopic Molecular Weight114.042927446
IUPAC Name3,6-dihydropyrazine-2,5-diol
Traditional Name3,6-dihydropyrazine-2,5-diol
CAS Registry NumberNot Available
SMILES
OC1=NCC(O)=NC1
InChI Identifier
InChI=1S/C4H6N2O2/c7-3-1-5-4(8)2-6-3/h1-2H2,(H,5,8)(H,6,7)
InChI KeyBXRNXXXXHLBUKK-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
    • 

  • 2,5-dioxopiperazine
    • 

  • 1,4-diazinane
    • 

  • Piperazine
    • 

  • Secondary carboxylic acid amide
    • 

  • Lactam
    • 

  • Carboxamide group
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Organopnictogen compound
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot 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
PropertyValueSource
logP-1.3ALOGPS
logP-1.1ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)4.07ChemAxon
pKa (Strongest Basic)5.64ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area65.18 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.65 m³·mol⁻¹ChemAxon
Polarizability10.17 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
GC-MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - cyclo(gly-gly) GC-MS (2 TMS)splash10-100c-3930000000-68c7f02cf5f5b5c11fe92014-06-16HMDB team, MONA, MassBankView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00014894  
Chemspider IDNot Available
KEGG Compound IDC02777  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDiketopiperazine  
METLIN IDNot Available
PubChem Compound7817  
PDB IDNot Available
ChEBI ID16535  
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. Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920  ]