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Showing metabocard for 2-Carboxyarabinitol (HMDB0303760)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 04:25:30 UTC
Update Date2021-09-24 04:25:30 UTC
HMDB IDHMDB0303760
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Carboxyarabinitol
Description2-carboxyarabinitol 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-carboxyarabinitol is soluble (in water) and a weakly acidic compound (based on its pKa). 2-carboxyarabinitol can be found in a number of food items such as tarragon, dandelion, ginkgo nuts, and spinach, which makes 2-carboxyarabinitol a potential biomarker for the consumption of these food products.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303760 (2-Carboxyarabinitol)

  Mrv0541 02241215192D          

 13 12  0  0  0  0            999 V2000
    0.7424   -1.8156    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004   -1.4031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5773   -1.8985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4031   -0.9898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8254   -0.4951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004   -0.5773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8254   -0.5773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6603    0.7424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004    0.2477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603    0.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4031    0.4121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603    1.4853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004    1.8985    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
  2  6  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
Download

3D MOL for HMDB0303760 (2-Carboxyarabinitol)

HMDB0303760
     RDKit          3D
2-Carboxyarabinitol
 25 24  0  0  0  0  0  0  0  0999 V2000
   -1.3105   -1.0958    1.8165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5573   -1.1657    0.5942 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3178   -2.2696    0.1990 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0937   -0.1746   -0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7188   -0.5270   -1.6365 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6864    1.1897   -0.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2845    1.7593    1.0708 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3661   -0.0839   -0.6138 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8613   -1.3318   -1.0796 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2070    0.3377    0.5443 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1506   -0.6330    1.5379 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6766    0.4198    0.1330 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8838    1.3555   -0.8588 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3917   -3.1160    0.7371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6520   -0.7567   -1.3652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7998    1.0173   -0.0208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5185    1.8426   -0.9880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9204    2.4077    1.4138 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5899    0.5944   -1.5094 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2445   -1.6288   -1.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9275    1.3202    0.9576 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3581   -1.5125    1.1075 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2230    0.7463    1.0473 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0452   -0.5674   -0.1630 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7178    1.8725   -0.6734 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  1  0
  4  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
M  END
Download

3D SDF for HMDB0303760 (2-Carboxyarabinitol)

  Mrv0541 02241215192D          

 13 12  0  0  0  0            999 V2000
    0.7424   -1.8156    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004   -1.4031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5773   -1.8985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4031   -0.9898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8254   -0.4951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004   -0.5773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8254   -0.5773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6603    0.7424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004    0.2477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603    0.6603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4031    0.4121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6603    1.4853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0004    1.8985    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
  2  6  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  9  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0303760

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC(O)C(O)C(O)(CO)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O7/c7-1-3(9)4(10)6(13,2-8)5(11)12/h3-4,7-10,13H,1-2H2,(H,11,12)

> <INCHI_KEY>
XONDRGRALZTVKD-UHFFFAOYSA-N

> <FORMULA>
C6H12O7

> <MOLECULAR_WEIGHT>
196.1553

> <EXACT_MASS>
196.058302738

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.054962098445248

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanoic acid

> <ALOGPS_LOGP>
-2.44

> <JCHEM_LOGP>
-3.3935534493333335

> <ALOGPS_LOGS>
0.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.082634557256219

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.304239008548323

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9748649602552684

> <JCHEM_POLAR_SURFACE_AREA>
138.45000000000002

> <JCHEM_REFRACTIVITY>
38.5655

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.57e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0303760 (2-Carboxyarabinitol)

HMDB0303760
     RDKit          3D
2-Carboxyarabinitol
 25 24  0  0  0  0  0  0  0  0999 V2000
   -1.3105   -1.0958    1.8165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5573   -1.1657    0.5942 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3178   -2.2696    0.1990 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0937   -0.1746   -0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7188   -0.5270   -1.6365 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6864    1.1897   -0.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2845    1.7593    1.0708 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3661   -0.0839   -0.6138 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8613   -1.3318   -1.0796 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2070    0.3377    0.5443 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1506   -0.6330    1.5379 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6766    0.4198    0.1330 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8838    1.3555   -0.8588 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3917   -3.1160    0.7371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6520   -0.7567   -1.3652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7998    1.0173   -0.0208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5185    1.8426   -0.9880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9204    2.4077    1.4138 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5899    0.5944   -1.5094 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2445   -1.6288   -1.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9275    1.3202    0.9576 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3581   -1.5125    1.1075 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2230    0.7463    1.0473 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0452   -0.5674   -0.1630 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7178    1.8725   -0.6734 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  1  0
  4  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
M  END
Download

PDB for HMDB0303760 (2-Carboxyarabinitol)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       1.386  -3.389   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.001  -2.619   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.078  -3.544   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -2.619  -1.848   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.541  -0.924   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.001  -1.078   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.541  -1.078   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.233   1.386   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.001   0.462   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.233   1.233   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.619   0.769   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.233   2.773   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.001   3.544   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2                                                            
CONECT    4    5                                                            
CONECT    5    4    6                                                       
CONECT    6    2    5    7    9                                             
CONECT    7    6                                                            
CONECT    8    9                                                            
CONECT    9    6    8   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for HMDB0303760 (2-Carboxyarabinitol)

COMPND    HMDB0303760
HETATM    1  O1  UNL     1      -1.311  -1.096   1.816  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.557  -1.166   0.594  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.318  -2.270   0.199  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.094  -0.175  -0.373  1.00  0.00           C  
HETATM    5  O3  UNL     1      -1.719  -0.527  -1.637  1.00  0.00           O  
HETATM    6  C3  UNL     1      -1.686   1.190  -0.102  1.00  0.00           C  
HETATM    7  O4  UNL     1      -1.285   1.759   1.071  1.00  0.00           O  
HETATM    8  C4  UNL     1       0.366  -0.084  -0.614  1.00  0.00           C  
HETATM    9  O5  UNL     1       0.861  -1.332  -1.080  1.00  0.00           O  
HETATM   10  C5  UNL     1       1.207   0.338   0.544  1.00  0.00           C  
HETATM   11  O6  UNL     1       1.151  -0.633   1.538  1.00  0.00           O  
HETATM   12  C6  UNL     1       2.677   0.420   0.133  1.00  0.00           C  
HETATM   13  O7  UNL     1       2.884   1.355  -0.859  1.00  0.00           O  
HETATM   14  H1  UNL     1      -2.392  -3.116   0.737  1.00  0.00           H  
HETATM   15  H2  UNL     1      -2.652  -0.757  -1.365  1.00  0.00           H  
HETATM   16  H3  UNL     1      -2.800   1.017  -0.021  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.519   1.843  -0.988  1.00  0.00           H  
HETATM   18  H5  UNL     1      -1.920   2.408   1.414  1.00  0.00           H  
HETATM   19  H6  UNL     1       0.590   0.594  -1.509  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.244  -1.629  -1.775  1.00  0.00           H  
HETATM   21  H8  UNL     1       0.927   1.320   0.958  1.00  0.00           H  
HETATM   22  H9  UNL     1       1.358  -1.513   1.107  1.00  0.00           H  
HETATM   23  H10 UNL     1       3.223   0.746   1.047  1.00  0.00           H  
HETATM   24  H11 UNL     1       3.045  -0.567  -0.163  1.00  0.00           H  
HETATM   25  H12 UNL     1       3.718   1.873  -0.673  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5    6    8
CONECT    5   15
CONECT    6    7   16   17
CONECT    7   18
CONECT    8    9   10   19
CONECT    9   20
CONECT   10   11   12   21
CONECT   11   22
CONECT   12   13   23   24
CONECT   13   25
END
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SMILES for HMDB0303760 (2-Carboxyarabinitol)

OCC(O)C(O)C(O)(CO)C(O)=O
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INCHI for HMDB0303760 (2-Carboxyarabinitol)

InChI=1S/C6H12O7/c7-1-3(9)4(10)6(13,2-8)5(11)12/h3-4,7-10,13H,1-2H2,(H,11,12)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,3,4,5-Tetrahydroxy-2-(hydroxymethyl)pentanoateGenerator
Chemical FormulaC6H12O7
Average Molecular Weight196.1553
Monoisotopic Molecular Weight196.058302738
IUPAC Name2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanoic acid
Traditional Name2,3,4,5-tetrahydroxy-2-(hydroxymethyl)pentanoic acid
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)C(O)(CO)C(O)=O
InChI Identifier
InChI=1S/C6H12O7/c7-1-3(9)4(10)6(13,2-8)5(11)12/h3-4,7-10,13H,1-2H2,(H,11,12)
InChI KeyXONDRGRALZTVKD-UHFFFAOYSA-N
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
  • Short-chain hydroxy acid
  • Hydroxy fatty acid
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Monosaccharide
  • Tertiary alcohol
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Polyol
  • Monocarboxylic acid or derivatives
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Primary alcohol
  • Organic oxygen compound
  • Organic oxide
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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
Predicted Chromatographic Properties
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 IDFDB020764
KNApSAcK IDNot Available
Chemspider ID4338536
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5165850
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