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Showing NP-Card for (2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid (NP0202414)

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Record Information
Version2.0
Created at2022-09-04 21:37:22 UTC
Updated at2022-09-04 21:37:22 UTC
NP-MRD IDNP0202414
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid
Description(2R,3R)-2-Hydroxycitric acid 5,2-lactone belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. (2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid is found in Garcinia gummi-gutta. Based on a literature review very few articles have been published on (2R,3R)-2-Hydroxycitric acid 5,2-lactone.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0202414 ((2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid)


  Mrv1652309042223372D          

 13 13  0  0  1  0            999 V2000
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2707    2.5120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7912    1.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1913    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  6  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  9 13  1  0  0  0  0
  2 13  1  0  0  0  0
M  END
Download

3D MOL for NP0202414 ((2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid)

     RDKit          3D

 19 19  0  0  0  0  0  0  0  0999 V2000
   -0.6278   -3.0208   -1.5593 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3317   -1.8689   -1.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3077   -0.8857   -0.5619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4891    0.0526    0.3002 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9353   -0.0136    1.6389 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5913    1.4190   -0.1841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2445    1.6906   -1.3513 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0627    2.4453    0.6034 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8688   -0.5518    0.2430 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9791    0.3607    0.4233 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0835    1.0528    1.4538 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9444    0.4762   -0.5527 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9071   -1.2575   -0.9829 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7266   -0.3526   -1.4589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1128   -1.3844    0.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7172   -0.5960    1.6851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9420    2.4006    1.1010 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9356   -1.3421    1.0453 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3703    1.3757   -0.7722 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 10  1  0
 10 11  2  0
 10  9  1  0
  9 13  1  0
 13  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  1
  4  6  1  0
  6  8  1  0
  6  7  2  0
  4  9  1  0
 12 19  1  0
  9 18  1  1
  3 14  1  0
  3 15  1  0
  5 16  1  0
  8 17  1  0
M  END
Download

3D SDF for NP0202414 ((2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid)


  Mrv1652309042223372D          

 13 13  0  0  1  0            999 V2000
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1198    1.7274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0157    1.7274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2707    2.5120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7912    1.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1913    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  6  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  9 13  1  0  0  0  0
  2 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0202414

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H6O7/c7-2-1-6(12,5(10)11)3(13-2)4(8)9/h3,12H,1H2,(H,8,9)(H,10,11)/t3-,6+/m0/s1

> <INCHI_KEY>
PFHZIWAVXDSFTB-BBIVZNJYSA-N

> <FORMULA>
C6H6O7

> <MOLECULAR_WEIGHT>
190.107

> <EXACT_MASS>
190.011352533

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.652724972306311

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid

> <JCHEM_LOGP>
-1.373374788

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.375401359367241

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2478625334621753

> <JCHEM_PKA_STRONGEST_BASIC>
-4.5893693563786355

> <JCHEM_POLAR_SURFACE_AREA>
121.13

> <JCHEM_REFRACTIVITY>
33.46990000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0202414 ((2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid)

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PDB for NP0202414 ((2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid)
HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.090   3.224   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.029   3.224   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.505   4.689   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.477   2.904   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.770   1.651   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.915   0.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.091   3.157   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6    9                                             
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    4   10   13                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    9    2                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

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3D PDB for NP0202414 ((2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid)
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SMILES for NP0202414 ((2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid)
OC(=O)[C@@H]1OC(=O)C[C@]1(O)C(O)=O
Download
INCHI for NP0202414 ((2r,3r)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid)
InChI=1S/C6H6O7/c7-2-1-6(12,5(10)11)3(13-2)4(8)9/h3,12H,1H2,(H,8,9)(H,10,11)/t3-,6+/m0/s1
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View in JSmol
Synonyms
ValueSource
(2R,3R)-2-Hydroxycitrate 5,2-lactoneGenerator
Chemical FormulaC6H6O7
Average Mass190.1070 Da
Monoisotopic Mass190.01135 Da
IUPAC Name(2R,3R)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid
Traditional Name(2R,3R)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid
CAS Registry NumberNot Available
SMILES
OC(=O)[C@@H]1OC(=O)C[C@]1(O)C(O)=O
InChI Identifier
InChI=1S/C6H6O7/c7-2-1-6(12,5(10)11)3(13-2)4(8)9/h3,12H,1H2,(H,8,9)(H,10,11)/t3-,6+/m0/s1
InChI KeyPFHZIWAVXDSFTB-BBIVZNJYSA-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
Garcinia gummi-guttaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassTricarboxylic acids and derivatives  
Direct ParentTricarboxylic acids and derivatives  
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
    • 

  • Alpha-hydroxy acid
    • 

  • Gamma butyrolactone
    • 

  • Hydroxy acid
    • 

  • Tertiary alcohol
    • 

  • Oxolane
    • 

  • Carboxylic acid ester
    • 

  • Lactone
    • 

  • Carboxylic acid
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Hydrocarbon derivative
    • 

  • Alcohol
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • 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
logP-1.4ChemAxon
pKa (Strongest Acidic)3.25ChemAxon
pKa (Strongest Basic)-4.6ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area121.13 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity33.47 m³·mol⁻¹ChemAxon
Polarizability14.65 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 IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound101406944  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]