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Showing NP-Card for methyl (2s)-2,3-dihydroxypropanoate (NP0157534)

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Record Information
Version2.0
Created at2022-09-02 14:56:32 UTC
Updated at2022-09-02 14:56:32 UTC
NP-MRD IDNP0157534
Secondary Accession NumbersNone
Natural Product Identification
Common Namemethyl (2s)-2,3-dihydroxypropanoate
Description(S)-Methyl 2,3-dihydroxypropanoate belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. methyl (2s)-2,3-dihydroxypropanoate is found in Begonia nantoensis. Based on a literature review very few articles have been published on (S)-Methyl 2,3-dihydroxypropanoate.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0157534 (methyl (2s)-2,3-dihydroxypropanoate)


  Mrv1652309022216562D          

  8  7  0  0  1  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  1  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   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 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  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
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3D MOL for NP0157534 (methyl (2s)-2,3-dihydroxypropanoate)

     RDKit          3D

 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.7760   -0.5725   -0.3609 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3963   -0.3304   -0.5642 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6429    0.5271    0.2158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2486    1.1141    1.1569 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8100    0.7355   -0.0555 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3332    1.6292    0.8529 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5384   -0.6031    0.0362 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8833   -0.3345   -0.2510 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3725    0.3550   -0.3025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1225   -1.1160   -1.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9797   -1.2526    0.4796 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9671    1.1612   -1.0773 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1277    2.0568    0.4241 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0863   -1.2798   -0.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4113   -0.9329    1.0972 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3812   -1.1574   -0.0830 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  5 12  1  6
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
M  END
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3D SDF for NP0157534 (methyl (2s)-2,3-dihydroxypropanoate)


  Mrv1652309022216562D          

  8  7  0  0  1  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  1  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   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 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  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0157534

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O4/c1-8-4(7)3(6)2-5/h3,5-6H,2H2,1H3/t3-/m0/s1

> <INCHI_KEY>
COFCNNXZXGCREM-VKHMYHEASA-N

> <FORMULA>
C4H8O4

> <MOLECULAR_WEIGHT>
120.104

> <EXACT_MASS>
120.042258738

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
11.057140939909583

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (2S)-2,3-dihydroxypropanoate

> <ALOGPS_LOGP>
-1.38

> <JCHEM_LOGP>
-1.3728454286666667

> <ALOGPS_LOGS>
0.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.347398776152492

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.94608618769761

> <JCHEM_PKA_STRONGEST_BASIC>
-3.042918728207269

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
25.152599999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.70e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2S)-2,3-dihydroxypropanoate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0157534 (methyl (2s)-2,3-dihydroxypropanoate)

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PDB for NP0157534 (methyl (2s)-2,3-dihydroxypropanoate)
HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         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  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.311   2.104   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                                                       
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0157534 (methyl (2s)-2,3-dihydroxypropanoate)
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SMILES for NP0157534 (methyl (2s)-2,3-dihydroxypropanoate)
COC(=O)[C@@H](O)CO
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INCHI for NP0157534 (methyl (2s)-2,3-dihydroxypropanoate)
InChI=1S/C4H8O4/c1-8-4(7)3(6)2-5/h3,5-6H,2H2,1H3/t3-/m0/s1
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View in JSmol
Synonyms
ValueSource
(S)-Methyl 2,3-dihydroxypropanoic acidGenerator
Chemical FormulaC4H8O4
Average Mass120.1040 Da
Monoisotopic Mass120.04226 Da
IUPAC Namemethyl (2S)-2,3-dihydroxypropanoate
Traditional Namemethyl (2S)-2,3-dihydroxypropanoate
CAS Registry NumberNot Available
SMILES
COC(=O)[C@@H](O)CO
InChI Identifier
InChI=1S/C4H8O4/c1-8-4(7)3(6)2-5/h3,5-6H,2H2,1H3/t3-/m0/s1
InChI KeyCOFCNNXZXGCREM-VKHMYHEASA-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
Begonia nantoensisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentSugar acids and derivatives  
Alternative Parents
Substituents
  • Beta-hydroxy acid
    • 

  • Sugar acid
    • 

  • Glyceric_acid
    • 

  • Monosaccharide
    • 

  • Hydroxy acid
    • 

  • Methyl ester
    • 

  • 1,2-diol
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Carboxylic acid derivative
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • 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-1.4ALOGPS
logP-1.4ChemAxon
logS0.86ALOGPS
pKa (Strongest Acidic)11.95ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.76 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity25.15 m³·mol⁻¹ChemAxon
Polarizability11.06 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 ID9259026  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11083880  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]