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Showing metabocard for pyroglutamyllysine (HMDB0341383)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:49:35 UTC
Update Date2022-09-22 18:34:52 UTC
HMDB IDHMDB0341383
Secondary Accession NumbersNone
Metabolite Identification
Common Namepyroglutamyllysine
Descriptionpyroglutamyllysine 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 pyroglutamyllysine.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for HMDB0341383 (pyroglutamyllysine)


  Mrv1652309092223272D          

 18 18  0  0  0  0            999 V2000
    0.6264    0.4894    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0744    1.1025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4869    1.8170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1513    2.5707    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2938    1.6455    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3801    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0945    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0945   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8090    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5235    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2380    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6669    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3814    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0958    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5235   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2380   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8090   -0.8250    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  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
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 10 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
M  END
Download

3D MOL for HMDB0341383 (pyroglutamyllysine)

Download
3D SDF for HMDB0341383 (pyroglutamyllysine)

  Mrv1652309092223272D          

 18 18  0  0  0  0            999 V2000
    0.6264    0.4894    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0744    1.1025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4869    1.8170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1513    2.5707    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2938    1.6455    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3801    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0945    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0945   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8090    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5235    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2380    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6669    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3814    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0958    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5235   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2380   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8090   -0.8250    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  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
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 10 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341383

> <DATABASE_NAME>
hmdb

> <SMILES>
NCCCCC(NC(=O)C1CCC(=O)N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H19N3O4/c12-6-2-1-3-8(11(17)18)14-10(16)7-4-5-9(15)13-7/h7-8H,1-6,12H2,(H,13,15)(H,14,16)(H,17,18)

> <INCHI_KEY>
NJNKDMFTMAKPIE-UHFFFAOYSA-N

> <FORMULA>
C11H19N3O4

> <MOLECULAR_WEIGHT>
257.29

> <EXACT_MASS>
257.137556104

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
26.49776033391334

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-amino-2-[(5-oxopyrrolidin-2-yl)formamido]hexanoic acid

> <JCHEM_LOGP>
-3.8210917867306637

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.576007703730781

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6496347640299893

> <JCHEM_PKA_STRONGEST_BASIC>
10.165107632406736

> <JCHEM_POLAR_SURFACE_AREA>
121.52

> <JCHEM_REFRACTIVITY>
62.69740000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-amino-2-[(5-oxopyrrolidin-2-yl)formamido]hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for HMDB0341383 (pyroglutamyllysine)
Download
PDB for HMDB0341383 (pyroglutamyllysine)
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       1.169   0.914   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.139   2.058   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.909   3.392   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.282   4.799   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       2.415   3.072   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       2.576   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.910   0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.910  -0.770   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       5.243   1.540   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       6.577   0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.911   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.245   0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.578   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.912   0.770   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      13.246   1.540   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       6.577  -0.770   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       7.911  -1.540   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       5.243  -1.540   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   10   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Download
3D PDB for HMDB0341383 (pyroglutamyllysine)
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SMILES for HMDB0341383 (pyroglutamyllysine)
NCCCCC(NC(=O)C1CCC(=O)N1)C(O)=O
Download
INCHI for HMDB0341383 (pyroglutamyllysine)
InChI=1S/C11H19N3O4/c12-6-2-1-3-8(11(17)18)14-10(16)7-4-5-9(15)13-7/h7-8H,1-6,12H2,(H,13,15)(H,14,16)(H,17,18)
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC11H19N3O4
Average Molecular Weight257.29
Monoisotopic Molecular Weight257.137556104
IUPAC Name6-amino-2-[(5-oxopyrrolidin-2-yl)formamido]hexanoic acid
Traditional Name6-amino-2-[(5-oxopyrrolidin-2-yl)formamido]hexanoic acid
CAS Registry NumberNot Available
SMILES
NCCCCC(NC(=O)C1CCC(=O)N1)C(O)=O
InChI Identifier
InChI=1S/C11H19N3O4/c12-6-2-1-3-8(11(17)18)14-10(16)7-4-5-9(15)13-7/h7-8H,1-6,12H2,(H,13,15)(H,14,16)(H,17,18)
InChI KeyNJNKDMFTMAKPIE-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
    • 

  • N-acyl-alpha-amino acid
    • 

  • N-acyl-alpha amino acid or derivatives
    • 

  • Proline or derivatives
    • 

  • Alpha-amino acid amide
    • 

  • Alpha-amino acid or derivatives
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • Pyrrolidine-2-carboxamide
    • 

  • Medium-chain fatty acid
    • 

  • Amino fatty acid
    • 

  • Heterocyclic fatty acid
    • 

  • 2-pyrrolidone
    • 

  • Pyrrolidone
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Pyrrolidine
    • 

  • Secondary carboxylic acid amide
    • 

  • Amino acid
    • 

  • Amino acid or derivatives
    • 

  • Carboxamide group
    • 

  • Lactam
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Hydrocarbon derivative
    • 

  • Primary aliphatic amine
    • 

  • Organopnictogen compound
    • 

  • Organic nitrogen compound
    • 

  • Organic oxide
    • 

  • Organonitrogen compound
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Amine
    • 

  • Organic oxygen compound
    • 

  • Primary amine
    • 

  • 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-3.8ChemAxon
pKa (Strongest Acidic)3.65ChemAxon
pKa (Strongest Basic)10.17ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area121.52 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity62.7 m³·mol⁻¹ChemAxon
Polarizability26.5 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound85107445  
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  ]