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Showing metabocard for pyroglutamylthreonine (HMDB0341387)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:51:07 UTC
Update Date2022-09-22 18:34:52 UTC
HMDB IDHMDB0341387
Secondary Accession NumbersNone
Metabolite Identification
Common Namepyroglutamylthreonine
Descriptionpyroglutamylthreonine belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Based on a literature review very few articles have been published on pyroglutamylthreonine.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341387 (pyroglutamylthreonine)


  Mrv1652309092223292D          

 16 16  0  0  0  0            999 V2000
    1.9967    4.4143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    3.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7112    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    3.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    3.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    4.4143    0.0000 O   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
  2  4  1  0  0  0  0
  5  4  1  4  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
  8 13  1  0  0  0  0
  4 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
M  END
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3D MOL for HMDB0341387 (pyroglutamylthreonine)

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3D SDF for HMDB0341387 (pyroglutamylthreonine)

  Mrv1652309092223292D          

 16 16  0  0  0  0            999 V2000
    1.9967    4.4143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    3.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7112    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    3.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    3.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    4.4143    0.0000 O   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
  2  4  1  0  0  0  0
  5  4  1  4  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
  8 13  1  0  0  0  0
  4 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341387

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)C(N=C(O)C1CCC(O)=N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N2O5/c1-4(12)7(9(15)16)11-8(14)5-2-3-6(13)10-5/h4-5,7,12H,2-3H2,1H3,(H,10,13)(H,11,14)(H,15,16)

> <INCHI_KEY>
IDUPFOZIWWNGFZ-UHFFFAOYSA-N

> <FORMULA>
C9H14N2O5

> <MOLECULAR_WEIGHT>
230.22

> <EXACT_MASS>
230.090271559

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
21.87602737066083

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-2-{[hydroxy(5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl)methylidene]amino}butanoic acid

> <JCHEM_LOGP>
-0.6229209052444277

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.061140303926934

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.334511040148679

> <JCHEM_PKA_STRONGEST_BASIC>
1.7783856642522746

> <JCHEM_POLAR_SURFACE_AREA>
122.71000000000001

> <JCHEM_REFRACTIVITY>
52.39110000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-2-{[hydroxy(5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl)methylidene]amino}butanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341387 (pyroglutamylthreonine)
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PDB for HMDB0341387 (pyroglutamylthreonine)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0       3.727   8.240   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.727   6.700   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       5.061   5.930   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.393   5.930   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.393   4.390   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       1.060   6.700   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.274   5.930   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.060   8.240   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   14                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    8                                                       
CONECT   14    4   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

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3D PDB for HMDB0341387 (pyroglutamylthreonine)
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SMILES for HMDB0341387 (pyroglutamylthreonine)
CC(O)C(N=C(O)C1CCC(O)=N1)C(O)=O
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INCHI for HMDB0341387 (pyroglutamylthreonine)
InChI=1S/C9H14N2O5/c1-4(12)7(9(15)16)11-8(14)5-2-3-6(13)10-5/h4-5,7,12H,2-3H2,1H3,(H,10,13)(H,11,14)(H,15,16)
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC9H14N2O5
Average Molecular Weight230.22
Monoisotopic Molecular Weight230.090271559
IUPAC Name3-hydroxy-2-{[hydroxy(5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl)methylidene]amino}butanoic acid
Traditional Name3-hydroxy-2-{[hydroxy(5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl)methylidene]amino}butanoic acid
CAS Registry NumberNot Available
SMILES
CC(O)C(N=C(O)C1CCC(O)=N1)C(O)=O
InChI Identifier
InChI=1S/C9H14N2O5/c1-4(12)7(9(15)16)11-8(14)5-2-3-6(13)10-5/h4-5,7,12H,2-3H2,1H3,(H,10,13)(H,11,14)(H,15,16)
InChI KeyIDUPFOZIWWNGFZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentDipeptides  
Alternative Parents
Substituents
  • Alpha-dipeptide
    • 

  • Proline or derivatives
    • 

  • N-acyl-alpha-amino acid
    • 

  • N-acyl-alpha amino acid or derivatives
    • 

  • Alpha-amino acid amide
    • 

  • Alpha-amino acid or derivatives
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • Pyrrolidine-2-carboxamide
    • 

  • Beta-hydroxy acid
    • 

  • Heterocyclic fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Short-chain hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Pyrrolidone
    • 

  • 2-pyrrolidone
    • 

  • Pyrrolidine
    • 

  • Secondary carboxylic acid amide
    • 

  • Secondary alcohol
    • 

  • Carboxamide group
    • 

  • Lactam
    • 

  • Organoheterocyclic compound
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Azacycle
    • 

  • Alcohol
    • 

  • Organic oxide
    • 

  • Organic nitrogen compound
    • 

  • Organonitrogen compound
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
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-0.62ChemAxon
pKa (Strongest Acidic)3.33ChemAxon
pKa (Strongest Basic)1.78ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area122.71 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity52.39 m³·mol⁻¹ChemAxon
Polarizability21.88 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
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 IDNot Available
Chemspider ID24091775  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound24701336  
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. 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  ]