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Showing NP-Card for methylserine (NP0166856)

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Record Information
Version2.0
Created at2022-09-03 02:18:08 UTC
Updated at2022-09-03 02:18:08 UTC
NP-MRD IDNP0166856
Secondary Accession NumbersNone
Natural Product Identification
Common Namemethylserine
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. methylserine is found in Dichapetalum cymosum. 3-Hydroxy-2-(methylamino)propanoic acid is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0166856 (methylserine)


  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
Download

3D MOL for NP0166856 (methylserine)

     RDKit          3D

 17 16  0  0  0  0  0  0  0  0999 V2000
    2.0777   -0.6375   -0.3169 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7635   -0.6755   -0.8304 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1979    0.2341   -0.3582 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5265   -0.5607   -0.2806 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5451    0.2571    0.2565 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0997    0.8448    0.9217 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8418    0.3713    1.7811 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4898    2.0877    1.2420 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3576    0.3212    0.1092 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8496   -0.8367   -1.1094 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2224   -1.4822    0.4075 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5024   -1.4398   -1.4308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3956    1.0424   -1.1379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4659   -1.4746    0.3154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8264   -0.8344   -1.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8283   -0.0968    1.1638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4392    2.8795    0.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  8  1  0
  6  7  2  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  6
  4 14  1  0
  4 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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3D SDF for NP0166856 (methylserine)


  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>
NP0166856

> <DATABASE_NAME>
NP-MRD

> <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 NP0166856 (methylserine)

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PDB for NP0166856 (methylserine)
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 NP0166856 (methylserine)
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SMILES for NP0166856 (methylserine)
CNC(CO)C(O)=O
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INCHI for NP0166856 (methylserine)
InChI=1S/C4H9NO3/c1-5-3(2-6)4(7)8/h3,5-6H,2H2,1H3,(H,7,8)
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Synonyms
ValueSource
3-Hydroxy-2-(methylamino)propanoateGenerator
Chemical FormulaC4H9NO3
Average Mass119.1200 Da
Monoisotopic Mass119.05824 Da
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
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Dichapetalum cymosumLOTUS Database
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
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-3.7ChemAxon
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
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 Compound554048  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]