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Showing metabocard for cyclic- 3,4-O-oxalyl-L-threonate (HMDB0304308)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 08:47:43 UTC
Update Date2021-09-24 08:47:44 UTC
HMDB IDHMDB0304308
Secondary Accession NumbersNone
Metabolite Identification
Common Namecyclic- 3,4-O-oxalyl-L-threonate
DescriptionCyclic- 3,4-o-oxalyl-l-threonate, also known as 3,4-cyclic oxalyl theronolactone, belongs to tricarboxylic acids and derivatives class of compounds. Those are carboxylic acids containing exactly three carboxyl groups. Cyclic- 3,4-o-oxalyl-l-threonate is soluble (in water) and a moderately acidic compound (based on its pKa). Cyclic- 3,4-o-oxalyl-l-threonate can be found in a number of food items such as pot marjoram, arrowhead, naranjilla, and corn salad, which makes cyclic- 3,4-o-oxalyl-l-threonate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304308 (cyclic- 3,4-O-oxalyl-L-threonate)


  Mrv1533007131514152D          

 13 13  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 11  6  2  0  0  0  0
 12  1  1  0  0  0  0
 12  5  1  0  0  0  0
 13  2  1  0  0  0  0
 13  6  1  0  0  0  0
M  CHG  1   9  -1
M  END
Download

3D MOL for HMDB0304308 (cyclic- 3,4-O-oxalyl-L-threonate)

HMDB0304308
     RDKit          3D
cyclic- 3,4-O-oxalyl-L-threonate
 18 18  0  0  0  0  0  0  0  0999 V2000
    3.4673    0.7058    1.0378 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3526    0.3706    0.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4210    1.3453    0.1973 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5478    1.0601   -0.8892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1515   -0.2862   -0.6684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2711   -0.0129    0.2996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0606    1.0075   -0.2762 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1495   -1.1496    0.5379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1557   -2.1907   -0.1582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0374   -1.0864    1.5979 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.7287   -1.2798   -0.2456 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9764   -1.0168    0.3033 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7964   -1.9172    0.6042 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1103    1.0042   -1.8211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2140    1.8618   -0.9203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5994   -0.6048   -1.6240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8141    0.3591    1.2426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9472    1.8302    0.2407 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  5 11  1  0
 11 12  1  0
 12 13  2  0
 12  2  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
M  CHG  1  10  -1
M  END
Download

3D SDF for HMDB0304308 (cyclic- 3,4-O-oxalyl-L-threonate)


  Mrv1533007131514152D          

 13 13  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 11  6  2  0  0  0  0
 12  1  1  0  0  0  0
 12  5  1  0  0  0  0
 13  2  1  0  0  0  0
 13  6  1  0  0  0  0
M  CHG  1   9  -1
M  END
> <DATABASE_ID>
HMDB0304308

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(C1COC(=O)C(=O)O1)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H6O7/c7-3(4(8)9)2-1-12-5(10)6(11)13-2/h2-3,7H,1H2,(H,8,9)/p-1

> <INCHI_KEY>
FTDFTFXOJYXVTH-UHFFFAOYSA-M

> <FORMULA>
C6H5O7

> <MOLECULAR_WEIGHT>
189.1

> <EXACT_MASS>
189.004076081

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.143258686482916

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(5,6-dioxo-1,4-dioxan-2-yl)-2-hydroxyacetate

> <ALOGPS_LOGP>
-1.10

> <JCHEM_LOGP>
-0.6172170800000003

> <ALOGPS_LOGS>
-0.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.203013622169003

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9149608117022026

> <JCHEM_PKA_STRONGEST_BASIC>
-4.2633475669799425

> <JCHEM_POLAR_SURFACE_AREA>
112.96000000000001

> <JCHEM_REFRACTIVITY>
44.6373

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.97e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(5,6-dioxo-1,4-dioxan-2-yl)-2-hydroxyacetate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304308 (cyclic- 3,4-O-oxalyl-L-threonate)

HMDB0304308
     RDKit          3D
cyclic- 3,4-O-oxalyl-L-threonate
 18 18  0  0  0  0  0  0  0  0999 V2000
    3.4673    0.7058    1.0378 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3526    0.3706    0.5418 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4210    1.3453    0.1973 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5478    1.0601   -0.8892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1515   -0.2862   -0.6684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2711   -0.0129    0.2996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0606    1.0075   -0.2762 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1495   -1.1496    0.5379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1557   -2.1907   -0.1582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0374   -1.0864    1.5979 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.7287   -1.2798   -0.2456 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9764   -1.0168    0.3033 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7964   -1.9172    0.6042 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1103    1.0042   -1.8211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2140    1.8618   -0.9203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5994   -0.6048   -1.6240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8141    0.3591    1.2426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9472    1.8302    0.2407 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  5 11  1  0
 11 12  1  0
 12 13  2  0
 12  2  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
M  CHG  1  10  -1
M  END
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PDB for HMDB0304308 (cyclic- 3,4-O-oxalyl-L-threonate)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   6.160   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
CONECT    1    2   12                                                       
CONECT    2    1    3   13                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    8    9                                                  
CONECT    5    6   10   12                                                  
CONECT    6    5   11   13                                                  
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    1    5                                                       
CONECT   13    2    6                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0304308 (cyclic- 3,4-O-oxalyl-L-threonate)

COMPND    HMDB0304308
HETATM    1  O1  UNL     1       3.467   0.706   1.038  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.353   0.371   0.542  1.00  0.00           C  
HETATM    3  O2  UNL     1       1.421   1.345   0.197  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.548   1.060  -0.889  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.151  -0.286  -0.668  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.271  -0.013   0.300  1.00  0.00           C  
HETATM    7  O3  UNL     1      -2.061   1.008  -0.276  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.149  -1.150   0.538  1.00  0.00           C  
HETATM    9  O4  UNL     1      -2.156  -2.191  -0.158  1.00  0.00           O  
HETATM   10  O5  UNL     1      -3.037  -1.086   1.598  1.00  0.00           O1-
HETATM   11  O6  UNL     1       0.729  -1.280  -0.246  1.00  0.00           O  
HETATM   12  C6  UNL     1       1.976  -1.017   0.303  1.00  0.00           C  
HETATM   13  O7  UNL     1       2.796  -1.917   0.604  1.00  0.00           O  
HETATM   14  H1  UNL     1       1.110   1.004  -1.821  1.00  0.00           H  
HETATM   15  H2  UNL     1      -0.214   1.862  -0.920  1.00  0.00           H  
HETATM   16  H3  UNL     1      -0.599  -0.605  -1.624  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.814   0.359   1.243  1.00  0.00           H  
HETATM   18  H5  UNL     1      -1.947   1.830   0.241  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   12
CONECT    3    4
CONECT    4    5   14   15
CONECT    5    6   11   16
CONECT    6    7    8   17
CONECT    7   18
CONECT    8    9    9   10
CONECT   11   12
CONECT   12   13   13
END
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SMILES for HMDB0304308 (cyclic- 3,4-O-oxalyl-L-threonate)

OC(C1COC(=O)C(=O)O1)C([O-])=O
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INCHI for HMDB0304308 (cyclic- 3,4-O-oxalyl-L-threonate)

InChI=1S/C6H6O7/c7-3(4(8)9)2-1-12-5(10)6(11)13-2/h2-3,7H,1H2,(H,8,9)/p-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-(5,6-Dioxo-1,4-dioxan-2-yl)-2-hydroxyacetic acidGenerator
3,4-Cyclic oxalyl theronolactoneMetaCyc
Cyclic- 3,4-O-oxalyl-L-threonic acidGenerator
Chemical FormulaC6H5O7
Average Molecular Weight189.1
Monoisotopic Molecular Weight189.004076081
IUPAC Name2-(5,6-dioxo-1,4-dioxan-2-yl)-2-hydroxyacetate
Traditional Name2-(5,6-dioxo-1,4-dioxan-2-yl)-2-hydroxyacetate
CAS Registry NumberNot Available
SMILES
OC(C1COC(=O)C(=O)O1)C([O-])=O
InChI Identifier
InChI=1S/C6H6O7/c7-3(4(8)9)2-1-12-5(10)6(11)13-2/h2-3,7H,1H2,(H,8,9)/p-1
InChI KeyFTDFTFXOJYXVTH-UHFFFAOYSA-M
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
  • Para-dioxane
  • Carboxylic acid ester
  • Lactone
  • Secondary alcohol
  • Carboxylic acid
  • Organoheterocyclic compound
  • Oxacycle
  • Organic oxide
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.1ALOGPS
logP-0.62ChemAxon
logS-0.02ALOGPS
pKa (Strongest Acidic)2.91ChemAxon
pKa (Strongest Basic)-4.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area112.96 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity44.64 m³·mol⁻¹ChemAxon
Polarizability14.14 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+140.1332859911
AllCCS[M+H-H2O]+135.94932859911
AllCCS[M+Na]+145.14632859911
AllCCS[M+NH4]+144.02332859911
AllCCS[M-H]-131.53132859911
AllCCS[M+Na-2H]-132.15532859911
AllCCS[M+HCOO]-132.90832859911
DeepCCS[M+H]+133.73130932474
DeepCCS[M-H]-129.91330932474
DeepCCS[M-2H]-166.63330932474
DeepCCS[M+Na]+142.41630932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cyclic- 3,4-O-oxalyl-L-threonate 10V, Negative-QTOFsplash10-00dl-4900000000-c3bc7bcb8b0ebc4cce192019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cyclic- 3,4-O-oxalyl-L-threonate 20V, Negative-QTOFsplash10-00xs-3900000000-ad64e835728ab50541862019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - cyclic- 3,4-O-oxalyl-L-threonate 40V, Negative-QTOFsplash10-05fu-9000000000-68f73fbd48373e6381292019-02-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030761
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound90658084
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available