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Showing metabocard for DL-Threonine methyl ester (HMDB0341314)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:21:28 UTC
Update Date2022-09-22 18:34:47 UTC
HMDB IDHMDB0341314
Secondary Accession NumbersNone
Metabolite Identification
Common NameDL-Threonine methyl ester
DescriptionMethyl 2-amino-3-hydroxybutanoate belongs to the class of organic compounds known as alpha amino acid esters. These are ester derivatives of alpha amino acids. Methyl 2-amino-3-hydroxybutanoate is a very strong basic compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341314 (DL-Threonine methyl ester)


  Mrv1533004241514272D          

  9  8  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
M  END
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3D MOL for HMDB0341314 (DL-Threonine methyl ester)

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3D SDF for HMDB0341314 (DL-Threonine methyl ester)

  Mrv1533004241514272D          

  9  8  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341314

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)C(N)C(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO3/c1-3(7)4(6)5(8)9-2/h3-4,7H,6H2,1-2H3

> <INCHI_KEY>
TVHCXXXXQNWQLP-UHFFFAOYSA-N

> <FORMULA>
C5H11NO3

> <MOLECULAR_WEIGHT>
133.147

> <EXACT_MASS>
133.073893218

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.314381512967685

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 2-amino-3-hydroxybutanoate

> <ALOGPS_LOGP>
-1.30

> <JCHEM_LOGP>
-1.0631522006666665

> <ALOGPS_LOGS>
0.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.668839648609524

> <JCHEM_PKA_STRONGEST_BASIC>
6.894207106795362

> <JCHEM_POLAR_SURFACE_AREA>
72.55

> <JCHEM_REFRACTIVITY>
31.2289

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.04e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
DL-threonine, O-methyl-

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341314 (DL-Threonine methyl ester)
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PDB for HMDB0341314 (DL-Threonine methyl ester)
HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.976   2.104   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.310  -0.206   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.311   2.104   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for HMDB0341314 (DL-Threonine methyl ester)
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SMILES for HMDB0341314 (DL-Threonine methyl ester)
COC(=O)C(N)C(C)O
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INCHI for HMDB0341314 (DL-Threonine methyl ester)
InChI=1S/C5H11NO3/c1-3(7)4(6)5(8)9-2/h3-4,7H,6H2,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Methyl 2-amino-3-hydroxybutanoic acidGenerator
Chemical FormulaC5H11NO3
Average Molecular Weight133.147
Monoisotopic Molecular Weight133.073893218
IUPAC Namemethyl 2-amino-3-hydroxybutanoate
Traditional NameDL-threonine, O-methyl-
CAS Registry NumberNot Available
SMILES
COC(=O)C(N)C(C)O
InChI Identifier
InChI=1S/C5H11NO3/c1-3(7)4(6)5(8)9-2/h3-4,7H,6H2,1-2H3
InChI KeyTVHCXXXXQNWQLP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acid esters. These are ester derivatives of alpha amino acids.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acid esters  
Alternative Parents
Substituents
  • Alpha-amino acid ester
    • 

  • Beta-hydroxy acid
    • 

  • Fatty acid ester
    • 

  • Hydroxy acid
    • 

  • Fatty acyl
    • 

  • Methyl ester
    • 

  • Carboxylic acid ester
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary amine
    • 

  • Primary aliphatic amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Organic nitrogen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-1.3ALOGPS
logP-1.1ChemAxon
logS0.58ALOGPS
pKa (Strongest Acidic)14.67ChemAxon
pKa (Strongest Basic)6.89ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area72.55 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity31.23 m³·mol⁻¹ChemAxon
Polarizability13.31 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Retention Times 
Not Available
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 Compound324007  
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  ]