Hmdb loader
Survey
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.

Showing metabocard for O-Methyl-DL-serine (HMDB0341365)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:42:13 UTC
Update Date2022-09-22 18:34:51 UTC
HMDB IDHMDB0341365
Secondary Accession NumbersNone
Metabolite Identification
Common NameO-Methyl-DL-serine
Description
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for HMDB0341365 (O-Methyl-DL-serine)

Structure #1
  Mrv0541 02241207202D          

  8  7  0  0  0  0            999 V2000
    3.3809    1.1270    0.0000 C   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
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  8  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  2  0  0  0  0
  4  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0341365 (O-Methyl-DL-serine)

Download
3D SDF for HMDB0341365 (O-Methyl-DL-serine)
Structure #1
  Mrv0541 02241207202D          

  8  7  0  0  0  0            999 V2000
    3.3809    1.1270    0.0000 C   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
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  8  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  2  0  0  0  0
  4  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341365

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO3/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)

> <INCHI_KEY>
KNTFCRCCPLEUQZ-UHFFFAOYSA-N

> <FORMULA>
C4H9NO3

> <MOLECULAR_WEIGHT>
119.1192

> <EXACT_MASS>
119.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
11.528290285402363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-3-methoxypropanoic acid

> <ALOGPS_LOGP>
-3.08

> <JCHEM_LOGP>
-3.2440268048037613

> <ALOGPS_LOGS>
0.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.205292421586125

> <JCHEM_PKA_STRONGEST_BASIC>
8.823345028612783

> <JCHEM_POLAR_SURFACE_AREA>
72.55000000000001

> <JCHEM_REFRACTIVITY>
26.7922

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.85e+02 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for HMDB0341365 (O-Methyl-DL-serine)
Download
PDB for HMDB0341365 (O-Methyl-DL-serine)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       6.311   2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.310  -0.206   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.977   1.334   0.000  0.00  0.00           O+0
CONECT    1    8                                                            
CONECT    2    3    8                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3    6    7                                                  
CONECT    5    3                                                            
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    1    2                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

Download
3D PDB for HMDB0341365 (O-Methyl-DL-serine)
Download
SMILES for HMDB0341365 (O-Methyl-DL-serine)
COCC(N)C(O)=O
Download
INCHI for HMDB0341365 (O-Methyl-DL-serine)
InChI=1S/C4H9NO3/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Amino-3-methoxypropanoateGenerator
O-Methylserine, (DL)-isomerMeSH
O-MethylserineMeSH
O-Methylserine, (L)-isomerMeSH
O-Methylserine, (D)-isomerMeSH
Chemical FormulaC4H9NO3
Average Molecular Weight119.1192
Monoisotopic Molecular Weight119.058243159
IUPAC Name2-amino-3-methoxypropanoic acid
Traditional NameDL-serine, O-methyl-
CAS Registry NumberNot Available
SMILES
COCC(N)C(O)=O
InChI Identifier
InChI=1S/C4H9NO3/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)
InChI KeyKNTFCRCCPLEUQZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids  
Alternative Parents
Substituents
  • Alpha-amino acid
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Dialkyl ether
    • 

  • Ether
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Carbonyl group
    • 

  • Primary aliphatic amine
    • 

  • Amine
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen 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-3.2ChemAxon
logS0.69ALOGPS
pKa (Strongest Acidic)2.21ChemAxon
pKa (Strongest Basic)8.82ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area72.55 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity26.79 m³·mol⁻¹ChemAxon
Polarizability11.53 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
MS/MS Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - O-Methyl-DL-serine  10V, Positive-QTOFsplash10-00di-9600000000-6dc89dbe17171805324e2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - O-Methyl-DL-serine  20V, Positive-QTOFsplash10-00dl-9000000000-bd04d07414eb0bf04dde2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - O-Methyl-DL-serine  40V, Positive-QTOFsplash10-0006-9000000000-c5bad810b2ac741a7ad32016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - O-Methyl-DL-serine  10V, Negative-QTOFsplash10-014i-3900000000-8af22682da74387153622016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - O-Methyl-DL-serine  20V, Negative-QTOFsplash10-01bi-9300000000-70ec0fb69595c6d02b392016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - O-Methyl-DL-serine  40V, Negative-QTOFsplash10-00di-9000000000-da8f0c48702153a344ee2016-08-03Wishart LabView Spectrum
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 Compound97963  
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  ]