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Showing metabocard for cyclo(pro-thr) (HMDB0341303)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:17:14 UTC
Update Date2022-09-22 18:34:46 UTC
HMDB IDHMDB0341303
Secondary Accession NumbersNone
Metabolite Identification
Common Namecyclo(pro-thr)
Descriptioncyclo(pro-thr) 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. Based on a literature review very few articles have been published on cyclo(pro-thr).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341303 (cyclo(pro-thr))

  Mrv1652309092222552D          

 14 15  0  0  0  0            999 V2000
    3.4990    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -0.1271    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  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  3 13  1  0  0  0  0
  2 14  1  0  0  0  0
M  END
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3D MOL for HMDB0341303 (cyclo(pro-thr))

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3D SDF for HMDB0341303 (cyclo(pro-thr))
  Mrv1652309092222552D          

 14 15  0  0  0  0            999 V2000
    3.4990    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    3.1729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -0.1271    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  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  3 13  1  0  0  0  0
  2 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341303

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)C1NC(=O)C2CCCN2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N2O3/c1-5(12)7-9(14)11-4-2-3-6(11)8(13)10-7/h5-7,12H,2-4H2,1H3,(H,10,13)

> <INCHI_KEY>
UBLWFFBGMBRBMC-UHFFFAOYSA-N

> <FORMULA>
C9H14N2O3

> <MOLECULAR_WEIGHT>
198.222

> <EXACT_MASS>
198.100442319

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
19.821109767478042

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(1-hydroxyethyl)-octahydropyrrolo[1,2-a]pyrazine-1,4-dione

> <JCHEM_LOGP>
-1.4307073590000003

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.478697189096202

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.808272773784386

> <JCHEM_PKA_STRONGEST_BASIC>
-2.937307156038881

> <JCHEM_POLAR_SURFACE_AREA>
69.64

> <JCHEM_REFRACTIVITY>
48.2464

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-(1-hydroxyethyl)-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341303 (cyclo(pro-thr))
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PDB for HMDB0341303 (cyclo(pro-thr))
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       6.531   2.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.198   1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.530  -0.237   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       1.197   2.073   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -0.268   1.597   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.268   4.089   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.530   5.923   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       3.864   3.613   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       5.198  -0.237   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4   13                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6   11                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    3                                                       
CONECT   14    2                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

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3D PDB for HMDB0341303 (cyclo(pro-thr))
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SMILES for HMDB0341303 (cyclo(pro-thr))
CC(O)C1NC(=O)C2CCCN2C1=O
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INCHI for HMDB0341303 (cyclo(pro-thr))
InChI=1S/C9H14N2O3/c1-5(12)7-9(14)11-4-2-3-6(11)8(13)10-7/h5-7,12H,2-4H2,1H3,(H,10,13)
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC9H14N2O3
Average Molecular Weight198.222
Monoisotopic Molecular Weight198.100442319
IUPAC Name3-(1-hydroxyethyl)-octahydropyrrolo[1,2-a]pyrazine-1,4-dione
Traditional Name3-(1-hydroxyethyl)-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
CAS Registry NumberNot Available
SMILES
CC(O)C1NC(=O)C2CCCN2C1=O
InChI Identifier
InChI=1S/C9H14N2O3/c1-5(12)7-9(14)11-4-2-3-6(11)8(13)10-7/h5-7,12H,2-4H2,1H3,(H,10,13)
InChI KeyUBLWFFBGMBRBMC-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
    • 

  • N-alkylpiperazine
    • 

  • 1,4-diazinane
    • 

  • Piperazine
    • 

  • Pyrrolidine
    • 

  • Tertiary carboxylic acid amide
    • 

  • Carboxamide group
    • 

  • Lactam
    • 

  • Secondary alcohol
    • 

  • Secondary carboxylic acid amide
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic 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-1.4ChemAxon
pKa (Strongest Acidic)10.81ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area69.64 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity48.25 m³·mol⁻¹ChemAxon
Polarizability19.82 ųChemAxon
Number of Rings2ChemAxon
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 Compound73146465  
PDB IDNot Available
ChEBI ID181655  
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  ]