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Showing metabocard for pyroglutamylmethionine (HMDB0341384)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:49:58 UTC
Update Date2022-09-22 18:34:52 UTC
HMDB IDHMDB0341384
Secondary Accession NumbersNone
Metabolite Identification
Common Namepyroglutamylmethionine
DescriptionPyroGlu-Met 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 PyroGlu-Met.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341384 (pyroglutamylmethionine)


  Mrv1652309092223282D          

 17 17  0  0  0  0            999 V2000
   -0.5192   -5.1626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1067   -4.4481    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7183   -4.4481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1308   -3.7336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9558   -3.7336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3683   -3.0191    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1933   -3.0191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6058   -3.7336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6058   -2.3047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2703   -1.5510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8834   -0.9990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5978   -1.4115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3515   -1.0759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4263   -2.2184    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3683   -4.4481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1933   -4.4481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9558   -5.1626    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  4  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  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
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
  9 14  1  0  0  0  0
  5 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
M  END
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3D MOL for HMDB0341384 (pyroglutamylmethionine)

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3D SDF for HMDB0341384 (pyroglutamylmethionine)

  Mrv1652309092223282D          

 17 17  0  0  0  0            999 V2000
   -0.5192   -5.1626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1067   -4.4481    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7183   -4.4481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1308   -3.7336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9558   -3.7336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3683   -3.0191    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1933   -3.0191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6058   -3.7336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6058   -2.3047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2703   -1.5510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8834   -0.9990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5978   -1.4115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3515   -1.0759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4263   -2.2184    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3683   -4.4481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1933   -4.4481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9558   -5.1626    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  4  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  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
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
  9 14  1  0  0  0  0
  5 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341384

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H16N2O4S/c1-17-5-4-7(10(15)16)12-9(14)6-2-3-8(13)11-6/h6-7H,2-5H2,1H3,(H,11,13)(H,12,14)(H,15,16)

> <INCHI_KEY>
FKWGLFXEKQAERS-UHFFFAOYSA-N

> <FORMULA>
C10H16N2O4S

> <MOLECULAR_WEIGHT>
260.31

> <EXACT_MASS>
260.083078177

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
26.036201300653847

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
0.6989754984495047

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.39250125101261

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.52475096574581

> <JCHEM_PKA_STRONGEST_BASIC>
1.9640987620114183

> <JCHEM_POLAR_SURFACE_AREA>
102.48000000000002

> <JCHEM_REFRACTIVITY>
63.51730000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for HMDB0341384 (pyroglutamylmethionine)
Download
PDB for HMDB0341384 (pyroglutamylmethionine)
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      -0.969  -9.637   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0      -0.199  -8.303   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       1.341  -8.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.111  -6.969   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.651  -6.969   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       4.421  -5.636   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       5.961  -5.636   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.731  -6.969   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.731  -4.302   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.105  -2.895   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.249  -1.865   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.583  -2.635   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.990  -2.008   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0       8.262  -4.141   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       4.421  -8.303   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.961  -8.303   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.651  -9.637   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   15                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    9                                                       
CONECT   15    5   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

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3D PDB for HMDB0341384 (pyroglutamylmethionine)
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SMILES for HMDB0341384 (pyroglutamylmethionine)
CSCCC(N=C(O)C1CCC(O)=N1)C(O)=O
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INCHI for HMDB0341384 (pyroglutamylmethionine)
InChI=1S/C10H16N2O4S/c1-17-5-4-7(10(15)16)12-9(14)6-2-3-8(13)11-6/h6-7H,2-5H2,1H3,(H,11,13)(H,12,14)(H,15,16)
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC10H16N2O4S
Average Molecular Weight260.31
Monoisotopic Molecular Weight260.083078177
IUPAC Name2-{[hydroxy(5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl)methylidene]amino}-4-(methylsulfanyl)butanoic acid
Traditional Name2-{[hydroxy(5-hydroxy-3,4-dihydro-2H-pyrrol-2-yl)methylidene]amino}-4-(methylsulfanyl)butanoic acid
CAS Registry NumberNot Available
SMILES
CSCCC(N=C(O)C1CCC(O)=N1)C(O)=O
InChI Identifier
InChI=1S/C10H16N2O4S/c1-17-5-4-7(10(15)16)12-9(14)6-2-3-8(13)11-6/h6-7H,2-5H2,1H3,(H,11,13)(H,12,14)(H,15,16)
InChI KeyFKWGLFXEKQAERS-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
    • 

  • Methionine or derivatives
    • 

  • N-acyl-alpha-amino acid
    • 

  • Proline or derivatives
    • 

  • N-acyl-alpha amino acid or derivatives
    • 

  • Alpha-amino acid amide
    • 

  • Alpha-amino acid or derivatives
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • Pyrrolidine-2-carboxamide
    • 

  • Heterocyclic fatty acid
    • 

  • Thia fatty acid
    • 

  • Fatty acyl
    • 

  • Pyrrolidone
    • 

  • 2-pyrrolidone
    • 

  • Fatty acid
    • 

  • Pyrrolidine
    • 

  • Secondary carboxylic acid amide
    • 

  • Carboxamide group
    • 

  • Lactam
    • 

  • Organoheterocyclic compound
    • 

  • Dialkylthioether
    • 

  • Sulfenyl compound
    • 

  • Thioether
    • 

  • Azacycle
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organonitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Organooxygen compound
    • 

  • Organosulfur compound
    • 

  • Organic nitrogen 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
logP0.7ChemAxon
pKa (Strongest Acidic)3.52ChemAxon
pKa (Strongest Basic)1.96ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area102.48 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity63.52 m³·mol⁻¹ChemAxon
Polarizability26.04 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
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 ID24014033  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound24695092  
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  ]