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Showing metabocard for 2-carboxy-L-threo-pentonate (HMDB0304062)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:49:56 UTC
Update Date2021-09-24 06:49:56 UTC
HMDB IDHMDB0304062
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-carboxy-L-threo-pentonate
Description2-carboxy-l-threo-pentonate, also known as 2-carboxy-L-xylonate or 2-hydroxy-2-(1,2,3-trihydroxypropyl)propanedioate, is a member of the class of compounds known as hydroxy fatty acids. Hydroxy fatty acids are fatty acids in which the chain bears a hydroxyl group. 2-carboxy-l-threo-pentonate is soluble (in water) and a moderately acidic compound (based on its pKa). 2-carboxy-l-threo-pentonate can be found in a number of food items such as star anise, chinese chestnut, passion fruit, and persimmon, which makes 2-carboxy-l-threo-pentonate a potential biomarker for the consumption of these food products.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304062 (2-carboxy-L-threo-pentonate)


  Mrv1533007131514082D          

 14 13  0  0  0  0            999 V2000
    2.9684    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -1.0164    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1270    1.1270    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
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  8  2  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  2  0  0  0  0
 11  4  1  0  0  0  0
 12  5  2  0  0  0  0
 13  5  1  0  0  0  0
 14  6  1  0  0  0  0
M  CHG  2  11  -1  13  -1
M  END
Download

3D MOL for HMDB0304062 (2-carboxy-L-threo-pentonate)

HMDB0304062
     RDKit          3D
2-carboxy-L-threo-pentonate
 22 21  0  0  0  0  0  0  0  0999 V2000
   -2.5035   -2.4509   -0.5688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2476   -1.3973    0.0561 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8849   -1.1800    1.2695 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.2823   -0.4382   -0.5261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8269   -0.9500   -1.7406 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9131    0.8890   -0.7275 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0006    1.4323   -1.8490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4243    1.5494    0.3731 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.1422   -0.3362    0.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4214   -1.5841    0.7136 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9439    0.5824   -0.0078 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4964    0.0578   -1.1902 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0627    0.5199    1.0281 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1654    1.2504    0.6625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4493   -0.5698   -2.4365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5717    0.1029    1.4035 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3021   -1.8211    1.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6068    1.6181   -0.1664 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3110    0.5489   -1.4495 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3808   -0.5615    1.0406 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6233    0.8081    1.9998 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9326    1.9299   -0.0164 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  4  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
  9 16  1  0
 10 17  1  0
 11 18  1  0
 12 19  1  0
 13 20  1  0
 13 21  1  0
 14 22  1  0
M  CHG  2   3  -1   8  -1
M  END
Download

3D SDF for HMDB0304062 (2-carboxy-L-threo-pentonate)


  Mrv1533007131514082D          

 14 13  0  0  0  0            999 V2000
    2.9684    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -1.0164    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1270    1.1270    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
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  8  2  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  2  0  0  0  0
 11  4  1  0  0  0  0
 12  5  2  0  0  0  0
 13  5  1  0  0  0  0
 14  6  1  0  0  0  0
M  CHG  2  11  -1  13  -1
M  END
> <DATABASE_ID>
HMDB0304062

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC(O)C(O)C(O)(C([O-])=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O8/c7-1-2(8)3(9)6(14,4(10)11)5(12)13/h2-3,7-9,14H,1H2,(H,10,11)(H,12,13)/p-2

> <INCHI_KEY>
CQIRJDZGDXTXKF-UHFFFAOYSA-L

> <FORMULA>
C6H8O8

> <MOLECULAR_WEIGHT>
208.123

> <EXACT_MASS>
208.023014377

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
16.248412617615774

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-2-(1,2,3-trihydroxypropyl)propanedioate

> <ALOGPS_LOGP>
-1.69

> <JCHEM_LOGP>
-2.921089693666667

> <ALOGPS_LOGS>
0.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.816959516726109

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.2141399747796084

> <JCHEM_PKA_STRONGEST_BASIC>
-2.975232519414714

> <JCHEM_POLAR_SURFACE_AREA>
161.17999999999998

> <JCHEM_REFRACTIVITY>
60.182199999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.91e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-2-(1,2,3-trihydroxypropyl)propanedioate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304062 (2-carboxy-L-threo-pentonate)

HMDB0304062
     RDKit          3D
2-carboxy-L-threo-pentonate
 22 21  0  0  0  0  0  0  0  0999 V2000
   -2.5035   -2.4509   -0.5688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2476   -1.3973    0.0561 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8849   -1.1800    1.2695 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.2823   -0.4382   -0.5261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8269   -0.9500   -1.7406 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9131    0.8890   -0.7275 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0006    1.4323   -1.8490 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4243    1.5494    0.3731 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.1422   -0.3362    0.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4214   -1.5841    0.7136 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9439    0.5824   -0.0078 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4964    0.0578   -1.1902 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0627    0.5199    1.0281 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1654    1.2504    0.6625 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4493   -0.5698   -2.4365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5717    0.1029    1.4035 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3021   -1.8211    1.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6068    1.6181   -0.1664 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3110    0.5489   -1.4495 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3808   -0.5615    1.0406 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6233    0.8081    1.9998 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9326    1.9299   -0.0164 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  4  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
  9 16  1  0
 10 17  1  0
 11 18  1  0
 12 19  1  0
 13 20  1  0
 13 21  1  0
 14 22  1  0
M  CHG  2   3  -1   8  -1
M  END
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PDB for HMDB0304062 (2-carboxy-L-threo-pentonate)

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       5.541   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.207   3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.207   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.644  -0.564   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.541   5.390   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.874   3.850   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       5.541   0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       5.184  -0.564   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       2.874  -1.897   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.206   0.770   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       2.104   2.104   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3    8                                                  
CONECT    3    2    6    9                                                  
CONECT    4    6   10   11                                                  
CONECT    5    6   12   13                                                  
CONECT    6    3    4    5   14                                             
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    3                                                            
CONECT   10    4                                                            
CONECT   11    4                                                            
CONECT   12    5                                                            
CONECT   13    5                                                            
CONECT   14    6                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for HMDB0304062 (2-carboxy-L-threo-pentonate)

COMPND    HMDB0304062
HETATM    1  O1  UNL     1      -2.504  -2.451  -0.569  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.248  -1.397   0.056  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.885  -1.180   1.269  1.00  0.00           O1-
HETATM    4  C2  UNL     1      -1.282  -0.438  -0.526  1.00  0.00           C  
HETATM    5  O3  UNL     1      -0.827  -0.950  -1.741  1.00  0.00           O  
HETATM    6  C3  UNL     1      -1.913   0.889  -0.727  1.00  0.00           C  
HETATM    7  O4  UNL     1      -2.001   1.432  -1.849  1.00  0.00           O  
HETATM    8  O5  UNL     1      -2.424   1.549   0.373  1.00  0.00           O1-
HETATM    9  C4  UNL     1      -0.142  -0.336   0.473  1.00  0.00           C  
HETATM   10  O6  UNL     1       0.421  -1.584   0.714  1.00  0.00           O  
HETATM   11  C5  UNL     1       0.944   0.582  -0.008  1.00  0.00           C  
HETATM   12  O7  UNL     1       1.496   0.058  -1.190  1.00  0.00           O  
HETATM   13  C6  UNL     1       2.063   0.520   1.028  1.00  0.00           C  
HETATM   14  O8  UNL     1       3.165   1.250   0.662  1.00  0.00           O  
HETATM   15  H1  UNL     1      -1.449  -0.570  -2.436  1.00  0.00           H  
HETATM   16  H2  UNL     1      -0.572   0.103   1.403  1.00  0.00           H  
HETATM   17  H3  UNL     1       0.302  -1.821   1.660  1.00  0.00           H  
HETATM   18  H4  UNL     1       0.607   1.618  -0.166  1.00  0.00           H  
HETATM   19  H5  UNL     1       2.311   0.549  -1.449  1.00  0.00           H  
HETATM   20  H6  UNL     1       2.381  -0.562   1.041  1.00  0.00           H  
HETATM   21  H7  UNL     1       1.623   0.808   2.000  1.00  0.00           H  
HETATM   22  H8  UNL     1       2.933   1.930  -0.016  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    6    9
CONECT    5   15
CONECT    6    7    7    8
CONECT    9   10   11   16
CONECT   10   17
CONECT   11   12   13   18
CONECT   12   19
CONECT   13   14   20   21
CONECT   14   22
END
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SMILES for HMDB0304062 (2-carboxy-L-threo-pentonate)

OCC(O)C(O)C(O)(C([O-])=O)C([O-])=O
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INCHI for HMDB0304062 (2-carboxy-L-threo-pentonate)

InChI=1S/C6H10O8/c7-1-2(8)3(9)6(14,4(10)11)5(12)13/h2-3,7-9,14H,1H2,(H,10,11)(H,12,13)/p-2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Hydroxy-2-(1,2,3-trihydroxypropyl)propanedioic acidGenerator
2-Carboxy-L-xylonateMetaCyc
2-Carboxy-L-xylonic acidGenerator
2-Carboxy-L-threo-pentonic acidGenerator
Chemical FormulaC6H8O8
Average Molecular Weight208.123
Monoisotopic Molecular Weight208.023014377
IUPAC Name2-hydroxy-2-(1,2,3-trihydroxypropyl)propanedioate
Traditional Name2-hydroxy-2-(1,2,3-trihydroxypropyl)propanedioate
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)C(O)(C([O-])=O)C([O-])=O
InChI Identifier
InChI=1S/C6H10O8/c7-1-2(8)3(9)6(14,4(10)11)5(12)13/h2-3,7-9,14H,1H2,(H,10,11)(H,12,13)/p-2
InChI KeyCQIRJDZGDXTXKF-UHFFFAOYSA-L
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Beta-hydroxy acid
  • Branched fatty acid
  • Hydroxy fatty acid
  • Short-chain hydroxy acid
  • Dicarboxylic acid or derivatives
  • Hydroxy acid
  • Monosaccharide
  • Tertiary alcohol
  • Secondary alcohol
  • Polyol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Primary alcohol
  • Organooxygen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Alcohol
  • Carbonyl group
  • Organic oxide
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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-1.7ALOGPS
logP-2.9ChemAxon
logS0.45ALOGPS
pKa (Strongest Acidic)2.21ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area161.18 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity60.18 m³·mol⁻¹ChemAxon
Polarizability16.25 ųChemAxon
Number of Rings0ChemAxon
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]+141.84532859911
AllCCS[M+H-H2O]+138.12332859911
AllCCS[M+Na]+146.332859911
AllCCS[M+NH4]+145.30432859911
AllCCS[M-H]-126.79132859911
AllCCS[M+Na-2H]-127.21732859911
AllCCS[M+HCOO]-127.75732859911
DeepCCS[M+H]+132.92330932474
DeepCCS[M-H]-129.70930932474
DeepCCS[M-2H]-165.64230932474
DeepCCS[M+Na]+141.39530932474

Predicted Kovats Retention Indices

Not Available
Spectra
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 IDFDB030326
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound90657336
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