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Showing NP-Card for l-glycerate (NP0156922)

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Record Information
Version2.0
Created at2022-09-02 14:12:11 UTC
Updated at2022-09-02 14:12:12 UTC
NP-MRD IDNP0156922
Secondary Accession NumbersNone
Natural Product Identification
Common Namel-glycerate
DescriptionL-Glyceric acid, also known as (S)-glycerate, 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. L-Glyceric acid is an extremely weak basic (essentially neutral) compound (based on its pKa). An optically active form of glyceric acid having L-configuration. l-glycerate is found in Lotus corniculatus and Trypanosoma brucei. L-Glyceric acid, with regard to humans, has been linked to several inborn metabolic disorders including glutaric acidemia type 2 and glycolic aciduria.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0156922 (l-glycerate)


  Mrv0541 02231220382D          

  7  6  0  0  1  0            999 V2000
   17.5327   -4.9870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.1038   -4.1620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9616   -4.1620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2472   -2.9245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5327   -4.1620    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.8183   -3.7495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2472   -3.7495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  1  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  7  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
M  END
Download

3D MOL for NP0156922 (l-glycerate)

     RDKit          3D

 13 12  0  0  0  0  0  0  0  0999 V2000
    1.1021    1.9389   -0.1971 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0317    0.6866   -0.2970 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8327    0.0352   -1.2204 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1066   -0.0721    0.5605 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5933    0.7747    1.4056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9043   -0.7935   -0.3217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6479    0.0972   -1.0821 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4904   -0.6842   -0.9520 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6356   -0.8528    1.1338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2565    0.7505    2.3130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3540   -1.4448   -1.0545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5879   -1.3743    0.3126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8553    0.9386   -0.6007 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  4  1  0
  4  5  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  7 13  1  0
  6 11  1  0
  6 12  1  0
  4  9  1  1
  5 10  1  0
  3  8  1  0
M  END
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3D SDF for NP0156922 (l-glycerate)


  Mrv0541 02231220382D          

  7  6  0  0  1  0            999 V2000
   17.5327   -4.9870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.1038   -4.1620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9616   -4.1620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2472   -2.9245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5327   -4.1620    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.8183   -3.7495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2472   -3.7495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  1  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  7  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0156922

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)/t2-/m0/s1

> <INCHI_KEY>
RBNPOMFGQQGHHO-REOHCLBHSA-N

> <FORMULA>
C3H6O4

> <MOLECULAR_WEIGHT>
106.0773

> <EXACT_MASS>
106.02660868

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
8.939794088251016

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2,3-dihydroxypropanoic acid

> <ALOGPS_LOGP>
-1.72

> <JCHEM_LOGP>
-1.5187394846666669

> <ALOGPS_LOGS>
0.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.495349861440904

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4186061267841343

> <JCHEM_PKA_STRONGEST_BASIC>
-3.042760876836586

> <JCHEM_POLAR_SURFACE_AREA>
77.75999999999999

> <JCHEM_REFRACTIVITY>
20.383499999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-glycerate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0156922 (l-glycerate)

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PDB for NP0156922 (l-glycerate)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      32.728  -9.309   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      30.060  -7.769   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      35.395  -7.769   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      34.061  -5.459   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      32.728  -7.769   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      31.394  -6.999   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      34.061  -6.999   0.000  0.00  0.00           C+0
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    7                                                            
CONECT    4    7                                                            
CONECT    5    1    6    7                                                  
CONECT    6    2    5                                                       
CONECT    7    3    4    5                                                  
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END

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3D PDB for NP0156922 (l-glycerate)
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SMILES for NP0156922 (l-glycerate)
OC[C@H](O)C(O)=O
Download
INCHI for NP0156922 (l-glycerate)
InChI=1S/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)/t2-/m0/s1
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View in JSmol
Synonyms
ValueSource
(S)-Glyceric acidChEBI
(S)-GlycerateGenerator
L-GlycerateGenerator
(2S)-2,3-Dihydroxy-propanoateHMDB
(2S)-2,3-Dihydroxy-propanoic acidHMDB
(S)-2,3-Dihydroxy-propanoateHMDB
(S)-2,3-Dihydroxy-propanoic acidHMDB
(S)-2,3-DihydroxypropanoateHMDB
(S)-2,3-Dihydroxypropanoic acidHMDB
Chemical FormulaC3H6O4
Average Mass106.0773 Da
Monoisotopic Mass106.02661 Da
IUPAC Name(2S)-2,3-dihydroxypropanoic acid
Traditional NameL-glycerate
CAS Registry NumberNot Available
SMILES
OC[C@H](O)C(O)=O
InChI Identifier
InChI=1S/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)/t2-/m0/s1
InChI KeyRBNPOMFGQQGHHO-REOHCLBHSA-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
Lotus corniculatusLOTUS Database
Trypanosoma bruceiLOTUS 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
    • 

  • Glyceric_acid
    • 

  • Sugar acid
    • 

  • Alpha-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Monosaccharide
    • 

  • 1,2-diol
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Primary alcohol
    • 

  • Hydrocarbon derivative
    • 

  • 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-1.7ALOGPS
logP-1.5ChemAxon
logS0.78ALOGPS
pKa (Strongest Acidic)3.42ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity20.38 m³·mol⁻¹ChemAxon
Polarizability8.94 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0006372  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023907  
KNApSAcK IDNot Available
Chemspider ID4885497  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG ID2226325  
Wikipedia LinkGlyceric acid  
METLIN IDNot Available
PubChem Compound6326776  
PDB IDNot Available
ChEBI ID74324  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]