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Showing NP-Card for (-)-Methyl (S)-glycerate (NP0072233)

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Record Information
Version2.0
Created at2022-04-28 17:35:56 UTC
Updated at2022-04-28 17:35:56 UTC
NP-MRD IDNP0072233
Secondary Accession NumbersNone
Natural Product Identification
Common Name(-)-Methyl (S)-glycerate
Description60456-21-5 Belongs to the class of organic compounds known as ketals. These are acetals derived from ketones by replacement of the oxo group by two hydrocarbyloxy groups R2C(OR)2 ( R not Hydrogen ). This term, once abandoned, has been reinstated as a subclass of acetals. (-)-Methyl (S)-glycerate is found in Begonia nantoensis. Based on a literature review very few articles have been published on 60456-21-5.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0072233 ((-)-Methyl (S)-glycerate)


  Mrv1652304282219352D          

 11 11  0  0  1  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4790   -2.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9728    1.8330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1628    1.8330    0.0000 C   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
  1  5  1  0  0  0  0
  4  6  1  1  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1 10  1  0  0  0  0
  1 11  1  0  0  0  0
M  END
Download

3D MOL for NP0072233 ((-)-Methyl (S)-glycerate)

     RDKit          3D

 23 23  0  0  0  0  0  0  0  0999 V2000
    3.3084    1.0741   -0.8151 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1569    0.4906   -0.2657 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5657   -0.6596   -0.7060 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0821   -1.2612   -1.6853 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3448   -1.2655   -0.1127 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8254   -1.2713   -1.0402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8965   -1.0475   -0.1447 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3710   -0.1001    0.7183 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5350    1.2502    0.0648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0787   -0.0603    2.0445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0438   -0.4326    0.9472 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4285    0.8875   -1.9012 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1894    0.5927   -0.3278 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3877    2.1480   -0.6534 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5524   -2.2972    0.2356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9823   -2.3028   -1.4310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7859   -0.5154   -1.8285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9696    1.3543   -0.8679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2814    2.0885    0.7585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6132    1.3529   -0.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1439   -0.3316    1.9865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5178   -0.6874    2.7789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9712    0.9938    2.4319 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
  6  7  1  0
  7  8  1  0
  8  9  1  6
  8 10  1  0
  8 11  1  0
 11  5  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  5 15  1  1
  6 16  1  0
  6 17  1  0
  9 18  1  0
  9 19  1  0
  9 20  1  0
 10 21  1  0
 10 22  1  0
 10 23  1  0
M  END
Download

3D SDF for NP0072233 ((-)-Methyl (S)-glycerate)


  Mrv1652304282219352D          

 11 11  0  0  1  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4790   -2.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9728    1.8330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1628    1.8330    0.0000 C   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
  1  5  1  0  0  0  0
  4  6  1  1  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1 10  1  0  0  0  0
  1 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0072233

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)[C@@H]1COC(C)(C)O1

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O4/c1-7(2)10-4-5(11-7)6(8)9-3/h5H,4H2,1-3H3/t5-/m0/s1

> <INCHI_KEY>
DOWWCCDWPKGNGX-YFKPBYRVSA-N

> <FORMULA>
C7H12O4

> <MOLECULAR_WEIGHT>
160.169

> <EXACT_MASS>
160.073558866

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.013579958660216

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (4S)-2,2-dimethyl-1,3-dioxolane-4-carboxylate

> <ALOGPS_LOGP>
0.43

> <JCHEM_LOGP>
0.3295791869999997

> <ALOGPS_LOGS>
0.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.093546711215856

> <JCHEM_POLAR_SURFACE_AREA>
44.760000000000005

> <JCHEM_REFRACTIVITY>
37.3596

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.30e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (4S)-2,2-dimethyl-1,3-dioxolane-4-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0072233 ((-)-Methyl (S)-glycerate)

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PDB for NP0072233 ((-)-Methyl (S)-glycerate)
HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.306   1.175   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.147  -1.375   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.011  -2.943   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.894  -4.188   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.816   3.422   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.304   3.422   0.000  0.00  0.00           C+0
CONECT    1    2    5   10   11                                             
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4    1                                                       
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8                                                            
CONECT   10    1                                                            
CONECT   11    1                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0072233 ((-)-Methyl (S)-glycerate)
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SMILES for NP0072233 ((-)-Methyl (S)-glycerate)
COC(=O)[C@@H]1COC(C)(C)O1
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INCHI for NP0072233 ((-)-Methyl (S)-glycerate)
InChI=1S/C7H12O4/c1-7(2)10-4-5(11-7)6(8)9-3/h5H,4H2,1-3H3/t5-/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC7H12O4
Average Mass160.1690 Da
Monoisotopic Mass160.07356 Da
IUPAC Namemethyl (4S)-2,2-dimethyl-1,3-dioxolane-4-carboxylate
Traditional Namemethyl (4S)-2,2-dimethyl-1,3-dioxolane-4-carboxylate
CAS Registry NumberNot Available
SMILES
COC(=O)[C@@H]1COC(C)(C)O1
InChI Identifier
InChI=1S/C7H12O4/c1-7(2)10-4-5(11-7)6(8)9-3/h5H,4H2,1-3H3/t5-/m0/s1
InChI KeyDOWWCCDWPKGNGX-YFKPBYRVSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Begonia nantoensisPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as ketals. These are acetals derived from ketones by replacement of the oxo group by two hydrocarbyloxy groups R2C(OR)2 ( R not Hydrogen ). This term, once abandoned, has been reinstated as a subclass of acetals.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassEthers  
Direct ParentKetals  
Alternative Parents
Substituents
  • Ketal
    • 

  • Methyl ester
    • 

  • Meta-dioxolane
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Carbonyl group
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP0.43ALOGPS
logP0.33ChemAxon
logS0.16ALOGPS
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area44.76 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity37.36 m³·mol⁻¹ChemAxon
Polarizability16.01 ųChemAxon
Number of Rings1ChemAxon
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 IDC00032010  
Chemspider ID745591  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound853165  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available