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Showing metabocard for Pyroglutamine (HMDB0062558)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2017-03-23 04:24:35 UTC
Update Date2021-09-14 15:25:44 UTC
HMDB IDHMDB0062558
Secondary Accession Numbers
  • HMDB62558
Metabolite Identification
Common NamePyroglutamine
DescriptionPyroglutamine (CAS: 2353-44-8), also known as alpha-aminoglutarimide or 3-amino-1,6-dioxopiperidine, 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. Pyroglutamine is considered to be soluble (in water) and acidic. Pyroglutamine has been identified in the human placenta (PMID: 32033212 ).
Structure
Data?1571244723
MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0062558 (Pyroglutamine)


  Mrv1652305052017412D          

  9  9  0  0  0  0            999 V2000
    0.2455    1.5170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4689    1.1045    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4689    0.2793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2455   -0.1330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9601    0.2793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9601    1.1045    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2455    2.3421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6745   -0.1331    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1835    1.5170    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  1  0  0  0  0
  1  6  1  0  0  0  0
  5  6  1  0  0  0  0
  2  9  1  6  0  0  0
  1  7  2  0  0  0  0
  5  8  2  0  0  0  0
M  END
Download

3D MOL for HMDB0062558 (Pyroglutamine)

Download
3D SDF for HMDB0062558 (Pyroglutamine)

  Mrv1652305052017412D          

  9  9  0  0  0  0            999 V2000
    0.2455    1.5170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4689    1.1045    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4689    0.2793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2455   -0.1330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9601    0.2793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9601    1.1045    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2455    2.3421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6745   -0.1331    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1835    1.5170    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  1  0  0  0  0
  1  6  1  0  0  0  0
  5  6  1  0  0  0  0
  2  9  1  6  0  0  0
  1  7  2  0  0  0  0
  5  8  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0062558

> <DATABASE_NAME>
hmdb

> <SMILES>
N[C@H]1CCC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8N2O2/c6-3-1-2-4(8)7-5(3)9/h3H,1-2,6H2,(H,7,8,9)/t3-/m0/s1

> <INCHI_KEY>
NPWMTBZSRRLQNJ-VKHMYHEASA-N

> <FORMULA>
C5H8N2O2

> <MOLECULAR_WEIGHT>
128.131

> <EXACT_MASS>
128.058577506

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.066753635700708

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-3-aminopiperidine-2,6-dione

> <ALOGPS_LOGP>
-1.59

> <JCHEM_LOGP>
-1.5268506133333333

> <ALOGPS_LOGS>
0.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.622134907298863

> <JCHEM_PKA_STRONGEST_BASIC>
6.71184693973515

> <JCHEM_POLAR_SURFACE_AREA>
72.19

> <JCHEM_REFRACTIVITY>
30.032100000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.59e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-3-aminopiperidine-2,6-dione

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for HMDB0062558 (Pyroglutamine)
https://cactus.nci.nih.gov/chemical/structure/N%5BC@H%5D1CCC(=O)NC1=O/file?fo...
 OpenBabel09142113323D
Jmol version 14.31.45  2021-07-21 05:08 EXTRACT: ({0:16})
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.5107    0.7222   -0.2088 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1693    0.5731    0.3712 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2165    0.7429    1.4468 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2193    1.5922   -0.2670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1945    1.3439    0.2694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5789   -0.0880    0.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7469   -0.3699   -0.1551 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6540   -1.0576   -0.0552 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6570   -0.8174    0.1033 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4432   -1.7370    0.0266 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1550    0.0590    0.1951 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4823    0.6330   -1.2134 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5373    2.6018   -0.0071 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2263    1.4708   -1.3502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2158    1.5351    1.3423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8970    2.0082   -0.2338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9439   -1.9685   -0.2193 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  2  3  1  1  0  0  0
  2  4  1  0  0  0  0
  2  9  1  0  0  0  0
  4  5  1  0  0  0  0
  4 13  1  0  0  0  0
  4 14  1  0  0  0  0
  5  6  1  0  0  0  0
  5 15  1  0  0  0  0
  5 16  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 17  1  0  0  0  0
  9 10  2  0  0  0  0
M  END
$$$$

Download
PDB for HMDB0062558 (Pyroglutamine)
HEADER    PROTEIN                                 05-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-MAY-20         0                                  
HETATM    1  C   UNK     0       0.458   2.832   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.875   2.062   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.875   0.521   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.458  -0.248   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.792   0.521   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.792   2.062   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       0.458   4.372   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.126  -0.248   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      -2.209   2.832   0.000  0.00  0.00           N+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    1    5                                                       
CONECT    7    1                                                            
CONECT    8    5                                                            
CONECT    9    2                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

Download
3D PDB for HMDB0062558 (Pyroglutamine)
COMPND    https://cactus.nci.nih.gov/chemical/structure/N%5BC@H%5D1CCC(=O)NC1=O/file?fo... 
AUTHOR    GENERATED BY OPEN BABEL 3.1.0
HETATM    1  N   UNL     1       2.511   0.722  -0.209  1.00  0.00           N  
HETATM    2  C   UNL     1       1.169   0.573   0.371  1.00  0.00           C  
HETATM    3  H   UNL     1       1.216   0.743   1.447  1.00  0.00           H  
HETATM    4  C   UNL     1       0.219   1.592  -0.267  1.00  0.00           C  
HETATM    5  C   UNL     1      -1.194   1.344   0.269  1.00  0.00           C  
HETATM    6  C   UNL     1      -1.579  -0.088   0.006  1.00  0.00           C  
HETATM    7  O   UNL     1      -2.747  -0.370  -0.155  1.00  0.00           O  
HETATM    8  N   UNL     1      -0.654  -1.058  -0.055  1.00  0.00           N  
HETATM    9  C   UNL     1       0.657  -0.817   0.103  1.00  0.00           C  
HETATM   10  O   UNL     1       1.443  -1.737   0.027  1.00  0.00           O  
HETATM   11  H   UNL     1       3.155   0.059   0.195  1.00  0.00           H  
HETATM   12  H   UNL     1       2.482   0.633  -1.213  1.00  0.00           H  
HETATM   13  H   UNL     1       0.537   2.602  -0.007  1.00  0.00           H  
HETATM   14  H   UNL     1       0.226   1.471  -1.350  1.00  0.00           H  
HETATM   15  H   UNL     1      -1.216   1.535   1.342  1.00  0.00           H  
HETATM   16  H   UNL     1      -1.897   2.008  -0.234  1.00  0.00           H  
HETATM   17  H   UNL     1      -0.944  -1.968  -0.219  1.00  0.00           H  
CONECT    1    2   11   12                                            
CONECT    2    1    3    4    9                                       
CONECT    3    2                                                      
CONECT    4    2    5   13   14                                       
CONECT    5    4    6   15   16                                       
CONECT    6    5    7    7    8                                       
CONECT    7    6    6                                                 
CONECT    8    6    9   17                                            
CONECT    9    8    2   10   10                                       
CONECT   10    9    9                                                 
CONECT   11    1                                                      
CONECT   12    1                                                      
CONECT   13    4                                                      
CONECT   14    4                                                      
CONECT   15    5                                                      
CONECT   16    5                                                      
CONECT   17    8                                                      
MASTER        0    0    0    0    0    0    0    0   17    0   17    0
END

Download
SMILES for HMDB0062558 (Pyroglutamine)
N[C@H]1CCC(=O)NC1=O
Download
INCHI for HMDB0062558 (Pyroglutamine)
InChI=1S/C5H8N2O2/c6-3-1-2-4(8)7-5(3)9/h3H,1-2,6H2,(H,7,8,9)/t3-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(3S)-3-Amino-2,6-piperidinedioneHMDB
(3S)-3-Aminohexahydro-2,6-pyridinedioneHMDB
(3S)-3-Aminopiperidine-2,6-dioneHMDB
3-Amino-2,6-dioxopiperidineHMDB
3-Amino-2,6-piperidinedioneHMDB
3-AminoglutarimideHMDB
3-Aminopiperidine-2,6-dioneHMDB
Glutamic acid imideHMDB
GlutamimideHMDB
alpha-AminoglutarimideHMDB
α-AminoglutarimideHMDB
Chemical FormulaC5H8N2O2
Average Molecular Weight128.131
Monoisotopic Molecular Weight128.058577506
IUPAC Name(3S)-3-aminopiperidine-2,6-dione
Traditional Name(3S)-3-aminopiperidine-2,6-dione
CAS Registry Number29883-25-8
SMILES
N[C@H]1CCC(=O)NC1=O
InChI Identifier
InChI=1S/C5H8N2O2/c6-3-1-2-4(8)7-5(3)9/h3H,1-2,6H2,(H,7,8,9)/t3-/m0/s1
InChI KeyNPWMTBZSRRLQNJ-VKHMYHEASA-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
    • 

  • Piperidinedione
    • 

  • 3-aminopiperidine
    • 

  • Delta-lactam
    • 

  • Piperidinone
    • 

  • Piperidine
    • 

  • Carboxylic acid imide
    • 

  • Dicarboximide
    • 

  • Carboxylic acid imide, n-unsubstituted
    • 

  • Lactam
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Organic nitrogen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organooxygen compound
    • 

  • Primary amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Health effect:
Disposition
Biological location:
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility259 g/lALOGPS
LogP-1.59ALOGPS
Predicted Molecular Properties
PropertyValueSource
logP-1.6ALOGPS
logP-1.5ChemAxon
logS0.3ALOGPS
pKa (Strongest Acidic)11.62ChemAxon
pKa (Strongest Basic)6.71ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area72.19 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.03 m³·mol⁻¹ChemAxon
Polarizability12.07 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties
Collision Cross Sections
NameAdductTypeData SourceValueReference
Retention Indices
Underivatized
Not Available
Derivatized
Not Available
Spectra
LC-MS/MS
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum -  10V, Positivesplash10-004i-0900000000-aa6e270ef32f54b8f6382021-09-09View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum -  20V, Positivesplash10-08i0-4900000000-90ecea5e09f13233e4602021-09-09View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum -  40V, Positivesplash10-0006-9000000000-afb1c6887d6398dc18902021-09-09View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum -  10V, Negativesplash10-004i-2900000000-adb87a3c568530b4cd9d2021-09-09View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum -  20V, Negativesplash10-002f-9400000000-9c174d94cdc25eb9a59d2021-09-09View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum -  40V, Negativesplash10-0006-9000000000-8618561fa1ab375b39512021-09-09View Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
    • 

  • Saliva
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
 
Normal		  details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
 
Normal		  details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)MaleAttachment loss   details
Associated Disorders and Diseases
Disease References
Attachment loss
  1. Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr  26. [PubMed:31026179  ] 
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11984188  
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212  ]