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Showing NP-Card for O-Methylserine (NP0333452)

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Record Information
Version2.0
Created at2024-06-21 18:45:11 UTC
Updated at2024-09-03 04:22:33 UTC
NP-MRD IDNP0333452
Natural Product DOIhttps://doi.org/10.57994/2897
Secondary Accession NumbersNone
Natural Product Identification
Common NameO-Methylserine
DescriptionO-methylserine, also known as O-methyl-L-ser, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. O-methylserine is a very strong basic compound (based on its pKa). O-Methylserine was first documented in 1974 (PMID: 4854587). A serine derivative that is L-serine with a methyl group replacing the hydrogen on the hydroxy side chain.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0333452 (O-Methylserine)


  Mrv1572004251600472D          

  9  8  0  0  1  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  1  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
    1.2375    1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  3  5  1  1  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  8  1  1  0  0  0  0
  8  2  1  0  0  0  0
  3  9  1  1  0  0  0
M  END
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3D MOL for NP0333452 (O-Methylserine)

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3D SDF for NP0333452 (O-Methylserine)

  Mrv1572004251600472D          

  9  8  0  0  1  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  1  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
    1.2375    1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  3  5  1  1  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  8  1  1  0  0  0  0
  8  2  1  0  0  0  0
  3  9  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0333452

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@](N)(COC)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO3/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m0/s1

> <INCHI_KEY>
KNTFCRCCPLEUQZ-VKHMYHEASA-N

> <FORMULA>
C4H9NO3

> <MOLECULAR_WEIGHT>
119.12

> <EXACT_MASS>
119.058243154

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.454902641531781

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-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>
2.205292421586123

> <JCHEM_PKA_STRONGEST_BASIC>
8.823345028612785

> <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>
(2S)-2-amino-3-methoxypropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0333452 (O-Methylserine)
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PDB for NP0333452 (O-Methylserine)
HEADER    PROTEIN                                 25-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-16         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
HETATM    9  H   UNK     0       2.310   2.874   0.000  0.00  0.00           H+0
CONECT    1    8                                                            
CONECT    2    3    8                                                       
CONECT    3    2    4    5    9                                             
CONECT    4    3    6    7                                                  
CONECT    5    3                                                            
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    1    2                                                       
CONECT    9    3                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0333452 (O-Methylserine)
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SMILES for NP0333452 (O-Methylserine)
[H][C@](N)(COC)C(O)=O
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INCHI for NP0333452 (O-Methylserine)
InChI=1S/C4H9NO3/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m0/s1
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Synonyms
ValueSource
O-Methyl-L-serChEBI
(2S)-2-amino-3-MethoxypropanoateGenerator
O-Methylserine, (DL)-isomerMeSH
O-Methylserine, (L)-isomerMeSH
O-Methylserine, (D)-isomerMeSH
O-MethylserineMeSH
Chemical FormulaC4H9NO3
Average Mass119.1200 Da
Monoisotopic Mass119.05824 Da
IUPAC Name(2S)-2-amino-3-methoxypropanoic acid
Traditional Name(2S)-2-amino-3-methoxypropanoic acid
CAS Registry NumberNot Available
SMILES
[H][C@](N)(COC)C(O)=O
InChI Identifier
InChI=1S/C4H9NO3/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m0/s1
InChI KeyKNTFCRCCPLEUQZ-VKHMYHEASA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-21View Spectrum
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-21View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-21View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-21View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-21View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600, CD3OD, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-21View Spectrum
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentL-alpha-amino acids  
Alternative Parents
Substituents
  • L-alpha-amino acid
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Dialkyl ether
    • 

  • Ether
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic nitrogen compound
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted 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
Polarizability11.45 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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 Compound88250  
PDB IDNot Available
ChEBI ID74798  
Good Scents IDNot Available
References
General References
  1. Hodges RS, Merrifield RB: Synthesis of O-methyl-L-serine and Nalpha-tert-butyloxycarbonyl-O-methyl-L-serine. J Org Chem. 1974 Jun 28;39(13):1870-2. doi: 10.1021/jo00927a018. [PubMed:4854587  ]