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Showing metabocard for N-Methyl-L-serine (HMDB0341356)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:38:26 UTC
Update Date2022-09-22 18:34:50 UTC
HMDB IDHMDB0341356
Secondary Accession NumbersNone
Metabolite Identification
Common NameN-Methyl-L-serine
Description3-hydroxy-2-(methylamino)propanoic acid belongs to the class of organic compounds known as serine and derivatives. Serine and derivatives are compounds containing serine or a derivative thereof resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 3-hydroxy-2-(methylamino)propanoic acid is a very strong basic compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341356 (N-Methyl-L-serine)


  Mrv1533004241501142D          

  8  7  0  0  0  0            999 V2000
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 N   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
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  3  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
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3D MOL for HMDB0341356 (N-Methyl-L-serine)

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3D SDF for HMDB0341356 (N-Methyl-L-serine)

  Mrv1533004241501142D          

  8  7  0  0  0  0            999 V2000
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 N   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
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  3  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341356

> <DATABASE_NAME>
hmdb

> <SMILES>
CNC(CO)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO3/c1-5-3(2-6)4(7)8/h3,5-6H,2H2,1H3,(H,7,8)

> <INCHI_KEY>
PSFABYLDRXJYID-UHFFFAOYSA-N

> <FORMULA>
C4H9NO3

> <MOLECULAR_WEIGHT>
119.12

> <EXACT_MASS>
119.058243154

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.365721597458911

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-2-(methylamino)propanoic acid

> <ALOGPS_LOGP>
-3.10

> <JCHEM_LOGP>
-3.664328678310794

> <ALOGPS_LOGS>
0.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.158421872594399

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7578363998686726

> <JCHEM_PKA_STRONGEST_BASIC>
9.817695674004764

> <JCHEM_POLAR_SURFACE_AREA>
69.56

> <JCHEM_REFRACTIVITY>
26.8156

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.08e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-2-(methylamino)propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341356 (N-Methyl-L-serine)
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PDB for HMDB0341356 (N-Methyl-L-serine)
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       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.540  -2.667   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.620   0.000   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.310   1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for HMDB0341356 (N-Methyl-L-serine)
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SMILES for HMDB0341356 (N-Methyl-L-serine)
CNC(CO)C(O)=O
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INCHI for HMDB0341356 (N-Methyl-L-serine)
InChI=1S/C4H9NO3/c1-5-3(2-6)4(7)8/h3,5-6H,2H2,1H3,(H,7,8)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-Hydroxy-2-(methylamino)propanoateGenerator
Chemical FormulaC4H9NO3
Average Molecular Weight119.12
Monoisotopic Molecular Weight119.058243154
IUPAC Name3-hydroxy-2-(methylamino)propanoic acid
Traditional Name3-hydroxy-2-(methylamino)propanoic acid
CAS Registry NumberNot Available
SMILES
CNC(CO)C(O)=O
InChI Identifier
InChI=1S/C4H9NO3/c1-5-3(2-6)4(7)8/h3,5-6H,2H2,1H3,(H,7,8)
InChI KeyPSFABYLDRXJYID-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as serine and derivatives. Serine and derivatives are compounds containing serine or a derivative thereof resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentSerine and derivatives  
Alternative Parents
Substituents
  • Serine or derivatives
    • 

  • Alpha-amino acid
    • 

  • Beta-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Secondary amine
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary alcohol
    • 

  • 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-3.1ALOGPS
logP-3.7ChemAxon
logS0.53ALOGPS
pKa (Strongest Acidic)1.76ChemAxon
pKa (Strongest Basic)9.82ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity26.82 m³·mol⁻¹ChemAxon
Polarizability11.37 ųChemAxon
Number of Rings0ChemAxon
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 Compound554048  
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  ]