Showing metabocard for Galactonic acid (MMDBc0000354)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:35:59 UTC
Update Date2022-08-31 06:02:31 UTC
Metabolite IDMMDBc0000354
Metabolite Identification
Common NameGalactonic acid
DescriptionGalactonic acid is a sugar acid that is a metabolic breakdown product of galactose. Galactose dehydrogenase is responsible for converting galactose to galactonolactone, which then spontaneously or enzymatically converts to galactonic acid. Once formed, galactonic acid may enter the pentose phosphate pathway. Galactonic acid is increased in red blood cells of galactosemic patients, due to a galactose-1-phosphate uridyltransferase (GALT) deficiency (PMID: 14680973 , OMMBID: The Online Metabolic and Molecular Bases of Inherited Disease, Ch.72). When present in sufficiently high levels, galactonic acid can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of galactonic acid are associated with at least two inborn errors of metabolism, including galactosemia and galactosemia type II. Galactonic acid is an organic acid. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart abnormalities, liver abnormalities (jaundice), kidney abnormalities, seizures, coma, and possibly death. These are also the characteristic symptoms of untreated galactosemia. Many affected children with organic acidemias experience intellectual disability or delayed development. High levels of galactonic acid in infants are specifically associated with hepatomegaly (an enlarged liver), cirrhosis, renal failure, cataracts, vomiting, seizure, hypoglycemia, lethargy, brain damage, and ovarian failure.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f12407349f8>


  Mrv1652305271900132D          

 13 12  0  0  0  0            999 V2000
 9991.8108 9991.2533    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9991.0969 9991.6652    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9990.3821 9991.2533    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9989.6675 9991.6652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9988.9529 9991.2533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.3821 9990.4280    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9991.0969 9992.4899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5263 9991.6652    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9993.2417 9991.2533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9993.9551 9991.6652    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.2417 9990.4280    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5263 9992.4899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9991.8108 9990.4280    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  1 13  1  1  0  0  0
  2  3  1  0  0  0  0
  2  7  1  6  0  0  0
  3  4  1  0  0  0  0
  3  6  1  6  0  0  0
  4  5  1  0  0  0  0
  8  9  1  0  0  0  0
  8 12  1  1  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f12407349f8>

HMDB0000565
     RDKit          3D
Galactonic acid
 25 24  0  0  0  0  0  0  0  0999 V2000
   -3.3767    1.0005    1.0256 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1738    0.9302    0.6415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2542    1.7582    1.2550 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8295   -0.0170   -0.4234 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9667   -0.7057   -0.8826 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8477   -1.0886   -0.0001 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6004   -1.8568   -1.1353 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3915   -0.5559    0.6227 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1911   -1.6563    0.9844 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2286    0.2780   -0.3143 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6078   -0.4182   -1.4477 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4903    0.7690    0.3584 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2237    1.4865    1.5162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5507    2.6821    1.5473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4118    0.5191   -1.3009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5252   -1.0193   -0.1337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3791   -1.7497    0.7146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7726   -1.3570   -1.9698 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1893   -0.0242    1.5652 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6113   -2.4340    1.1917 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6613    1.1754   -0.6212 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0587   -1.2637   -1.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1402   -0.0975    0.6498 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0279    1.4228   -0.3577 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8667    2.2219    1.6815 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
  6  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
  4 15  1  6
  5 16  1  0
  6 17  1  1
  7 18  1  0
  8 19  1  1
  9 20  1  0
 10 21  1  6
 11 22  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f12407349f8>


  Mrv1652305271900132D          

 13 12  0  0  0  0            999 V2000
 9991.8108 9991.2533    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9991.0969 9991.6652    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9990.3821 9991.2533    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9989.6675 9991.6652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9988.9529 9991.2533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9990.3821 9990.4280    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9991.0969 9992.4899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5263 9991.6652    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9993.2417 9991.2533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9993.9551 9991.6652    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9993.2417 9990.4280    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9992.5263 9992.4899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9991.8108 9990.4280    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  1 13  1  1  0  0  0
  2  3  1  0  0  0  0
  2  7  1  6  0  0  0
  3  4  1  0  0  0  0
  3  6  1  6  0  0  0
  4  5  1  0  0  0  0
  8  9  1  0  0  0  0
  8 12  1  1  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000354

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)/t2-,3+,4+,5-/m1/s1

> <INCHI_KEY>
RGHNJXZEOKUKBD-MGCNEYSASA-N

> <FORMULA>
C6H12O7

> <MOLECULAR_WEIGHT>
196.1553

> <EXACT_MASS>
196.058302738

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
17.069696029240205

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5R)-2,3,4,5,6-pentahydroxyhexanoic acid

> <ALOGPS_LOGP>
-2.57

> <JCHEM_LOGP>
-3.4097443106666665

> <ALOGPS_LOGS>
-0.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.593710458724516

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.388205574321856

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974220927705365

> <JCHEM_POLAR_SURFACE_AREA>
138.45

> <JCHEM_REFRACTIVITY>
38.271

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.59e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
galactonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f12407349f8>

HMDB0000565
     RDKit          3D
Galactonic acid
 25 24  0  0  0  0  0  0  0  0999 V2000
   -3.3767    1.0005    1.0256 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1738    0.9302    0.6415 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2542    1.7582    1.2550 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8295   -0.0170   -0.4234 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9667   -0.7057   -0.8826 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8477   -1.0886   -0.0001 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6004   -1.8568   -1.1353 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3915   -0.5559    0.6227 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1911   -1.6563    0.9844 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2286    0.2780   -0.3143 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6078   -0.4182   -1.4477 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4903    0.7690    0.3584 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2237    1.4865    1.5162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5507    2.6821    1.5473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4118    0.5191   -1.3009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5252   -1.0193   -0.1337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3791   -1.7497    0.7146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7726   -1.3570   -1.9698 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1893   -0.0242    1.5652 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6113   -2.4340    1.1917 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6613    1.1754   -0.6212 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0587   -1.2637   -1.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1402   -0.0975    0.6498 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0279    1.4228   -0.3577 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8667    2.2219    1.6815 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
  6  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
  4 15  1  6
  5 16  1  0
  6 17  1  1
  7 18  1  0
  8 19  1  1
  9 20  1  0
 10 21  1  6
 11 22  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
M  END
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PDB for #<Metabolite:0x00007f12407349f8>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0    8651.3808650.339   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8650.0488651.108   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8648.7138650.339   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8647.3798651.108   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8646.0458650.339   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8648.7138648.799   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8650.0488652.648   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8652.7168651.108   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8654.0518650.339   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0    8655.3838651.108   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8654.0518648.799   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8652.7168652.648   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0    8651.3808648.799   0.000  0.00  0.00           O+0
CONECT    1    2    8   13                                                  
CONECT    2    1    3    7                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3                                                            
CONECT    7    2                                                            
CONECT    8    1    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8                                                            
CONECT   13    1                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for #<Metabolite:0x00007f12407349f8>

COMPND    HMDB0000565
HETATM    1  O1  UNL     1      -3.377   1.000   1.026  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.174   0.930   0.641  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.254   1.758   1.255  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.830  -0.017  -0.423  1.00  0.00           C  
HETATM    5  O3  UNL     1      -2.967  -0.706  -0.883  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.848  -1.089  -0.000  1.00  0.00           C  
HETATM    7  O4  UNL     1      -0.600  -1.857  -1.135  1.00  0.00           O  
HETATM    8  C4  UNL     1       0.392  -0.556   0.623  1.00  0.00           C  
HETATM    9  O5  UNL     1       1.191  -1.656   0.984  1.00  0.00           O  
HETATM   10  C5  UNL     1       1.229   0.278  -0.314  1.00  0.00           C  
HETATM   11  O6  UNL     1       1.608  -0.418  -1.448  1.00  0.00           O  
HETATM   12  C6  UNL     1       2.490   0.769   0.358  1.00  0.00           C  
HETATM   13  O7  UNL     1       2.224   1.487   1.516  1.00  0.00           O  
HETATM   14  H1  UNL     1      -1.551   2.682   1.547  1.00  0.00           H  
HETATM   15  H2  UNL     1      -1.412   0.519  -1.301  1.00  0.00           H  
HETATM   16  H3  UNL     1      -3.525  -1.019  -0.134  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.379  -1.750   0.715  1.00  0.00           H  
HETATM   18  H5  UNL     1      -0.773  -1.357  -1.970  1.00  0.00           H  
HETATM   19  H6  UNL     1       0.189  -0.024   1.565  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.611  -2.434   1.192  1.00  0.00           H  
HETATM   21  H8  UNL     1       0.661   1.175  -0.621  1.00  0.00           H  
HETATM   22  H9  UNL     1       2.059  -1.264  -1.187  1.00  0.00           H  
HETATM   23  H10 UNL     1       3.140  -0.097   0.650  1.00  0.00           H  
HETATM   24  H11 UNL     1       3.028   1.423  -0.358  1.00  0.00           H  
HETATM   25  H12 UNL     1       2.867   2.222   1.681  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5    6   15
CONECT    5   16
CONECT    6    7    8   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 #<Metabolite:0x00007f12407349f8>

OC[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(O)=O
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INCHI for #<Metabolite:0x00007f12407349f8>

InChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)/t2-,3+,4+,5-/m1/s1
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Synonyms
ValueSource
D-Galactonic acidKegg
D-GalactonateGenerator
GalactonateGenerator
Galactonic acid, (D)-isomerHMDB
Galactonic acid, monopotassium saltHMDB
Galactonic acid, (L)-isomerHMDB
Molecular FormulaC6H12O7
Average Mass196.1553
Monoisotopic Mass196.058302738
IUPAC Name(2R,3S,4S,5R)-2,3,4,5,6-pentahydroxyhexanoic acid
Traditional Namegalactonic acid
CAS Registry NumberNot Available
SMILES
OC[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)/t2-,3+,4+,5-/m1/s1
InChI KeyRGHNJXZEOKUKBD-MGCNEYSASA-N