Showing metabocard for D-Galacturonate (MMDBc0049945)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:46:48 UTC
Update Date2022-12-15 22:52:19 UTC
Metabolite IDMMDBc0049945
Metabolite Identification
Common NameD-Galacturonate
DescriptionGalacturonic acid, also known as D-galacturonate or sodium pectate, belongs to the class of organic compounds known as glucuronic acid derivatives. Glucuronic acid derivatives are compounds containing a glucuronic acid moiety (or a derivative), which consists of a glucose moiety with the C6 carbon oxidized to a carboxylic acid. Galacturonic acid exists in all living species, ranging from bacteria to plants to humans. Galacturonic acid is found, on average, in the highest concentration within flaxseeds (Linum usitatissimum) and grape wine. Galacturonic acid has also been detected, but not quantified in, several different foods, such as olives (Olea europaea), milk (cow), domestic pigs (Sus scrofa domestica), german camomiles (Matricaria recutita), and figs (Ficus carica). This could make galacturonic acid a potential biomarker for the consumption of these foods. Galacturonic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Galacturonic acid.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f5a8905c720>


  Mrv1652303202019002D          

 13 12  0  0  1  0            999 V2000
   12.6753   -4.4406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3898   -2.3781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9609   -2.3781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1043   -4.4406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5319   -3.2031    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2464   -4.4406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8188   -2.3781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6753   -3.6156    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.3898   -3.2031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.9609   -3.2031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.1043   -3.6156    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.2464   -3.6156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8188   -3.2031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  1  0  0  0
  9  2  1  6  0  0  0
 10  3  1  1  0  0  0
 11  4  1  6  0  0  0
  5 12  1  0  0  0  0
  6 12  2  0  0  0  0
  7 13  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f5a8905c720>

HMDB0002545
     RDKit          3D
Galacturonic acid
 23 22  0  0  0  0  0  0  0  0999 V2000
   -3.6497    0.2405   -0.8210 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0668    0.8402    0.0557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6779    0.4964    0.4937 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2842    1.3304    1.4854 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7739    0.3107   -0.6767 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4382    1.4382   -1.3912 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2422   -0.7541   -0.6003 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4233   -1.2615   -1.9522 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6462   -0.4032   -0.2150 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3268   -1.6726   -0.3204 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9073    0.0837    1.1274 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6454    1.2553    1.4667 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4658   -0.7065    2.1385 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5755    1.6575    0.5392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7841   -0.5358    0.9557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9964    0.8892    2.3217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5574   -0.1700   -1.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1324    1.1412   -2.2885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1655   -1.6217   -0.0549 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9847   -0.5704   -2.4287 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1317    0.2025   -1.0139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2862   -1.5190   -0.4325 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0424   -0.6711    3.0627 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
  2 14  1  0
  3 15  1  1
  4 16  1  0
  5 17  1  6
  6 18  1  0
  7 19  1  1
  8 20  1  0
  9 21  1  6
 10 22  1  0
 13 23  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f5a8905c720>


  Mrv1652303202019002D          

 13 12  0  0  1  0            999 V2000
   12.6753   -4.4406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3898   -2.3781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9609   -2.3781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1043   -4.4406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5319   -3.2031    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2464   -4.4406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8188   -2.3781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6753   -3.6156    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.3898   -3.2031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.9609   -3.2031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.1043   -3.6156    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.2464   -3.6156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8188   -3.2031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  1  0  0  0
  9  2  1  6  0  0  0
 10  3  1  1  0  0  0
 11  4  1  6  0  0  0
  5 12  1  0  0  0  0
  6 12  2  0  0  0  0
  7 13  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049945

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h1-5,8-11H,(H,12,13)/t2-,3+,4+,5-/m0/s1

> <INCHI_KEY>
IAJILQKETJEXLJ-RSJOWCBRSA-N

> <FORMULA>
C6H10O7

> <MOLECULAR_WEIGHT>
194.1394

> <EXACT_MASS>
194.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.23442601587284

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.32

> <JCHEM_LOGP>
-3.248086025

> <ALOGPS_LOGS>
-0.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.262057101736255

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2378873610898107

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6897568428527263

> <JCHEM_POLAR_SURFACE_AREA>
135.29

> <JCHEM_REFRACTIVITY>
37.213

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.00e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
aldehydo-D-galacturonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f5a8905c720>

HMDB0002545
     RDKit          3D
Galacturonic acid
 23 22  0  0  0  0  0  0  0  0999 V2000
   -3.6497    0.2405   -0.8210 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0668    0.8402    0.0557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6779    0.4964    0.4937 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2842    1.3304    1.4854 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7739    0.3107   -0.6767 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4382    1.4382   -1.3912 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2422   -0.7541   -0.6003 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4233   -1.2615   -1.9522 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6462   -0.4032   -0.2150 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3268   -1.6726   -0.3204 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9073    0.0837    1.1274 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6454    1.2553    1.4667 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4658   -0.7065    2.1385 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5755    1.6575    0.5392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7841   -0.5358    0.9557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9964    0.8892    2.3217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5574   -0.1700   -1.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1324    1.1412   -2.2885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1655   -1.6217   -0.0549 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9847   -0.5704   -2.4287 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1317    0.2025   -1.0139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2862   -1.5190   -0.4325 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0424   -0.6711    3.0627 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
  2 14  1  0
  3 15  1  1
  4 16  1  0
  5 17  1  6
  6 18  1  0
  7 19  1  1
  8 20  1  0
  9 21  1  6
 10 22  1  0
 13 23  1  0
M  END
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PDB for #<Metabolite:0x00007f5a8905c720>

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  O   UNK     0      23.661  -8.289   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      24.994  -4.439   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      22.327  -4.439   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      26.328  -8.289   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      19.660  -5.979   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      20.993  -8.289   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      27.662  -4.439   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      23.661  -6.749   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      24.994  -5.979   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      22.327  -5.979   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      26.328  -6.749   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      20.993  -6.749   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      27.662  -5.979   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   11                                                            
CONECT    5   12                                                            
CONECT    6   12                                                            
CONECT    7   13                                                            
CONECT    8    1    9   10                                                  
CONECT    9    2    8   11                                                  
CONECT   10    3    8   12                                                  
CONECT   11    4    9   13                                                  
CONECT   12    5    6   10                                                  
CONECT   13    7   11                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for #<Metabolite:0x00007f5a8905c720>

COMPND    HMDB0002545
HETATM    1  O1  UNL     1      -3.650   0.241  -0.821  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.067   0.840   0.056  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.678   0.496   0.494  1.00  0.00           C  
HETATM    4  O2  UNL     1      -1.284   1.330   1.485  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.774   0.311  -0.677  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.438   1.438  -1.391  1.00  0.00           O  
HETATM    7  C4  UNL     1       0.242  -0.754  -0.600  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.423  -1.262  -1.952  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.646  -0.403  -0.215  1.00  0.00           C  
HETATM   10  O5  UNL     1       2.327  -1.673  -0.320  1.00  0.00           O  
HETATM   11  C6  UNL     1       1.907   0.084   1.127  1.00  0.00           C  
HETATM   12  O6  UNL     1       1.645   1.255   1.467  1.00  0.00           O  
HETATM   13  O7  UNL     1       2.466  -0.706   2.138  1.00  0.00           O  
HETATM   14  H1  UNL     1      -3.575   1.657   0.539  1.00  0.00           H  
HETATM   15  H2  UNL     1      -1.784  -0.536   0.956  1.00  0.00           H  
HETATM   16  H3  UNL     1      -0.996   0.889   2.322  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.557  -0.170  -1.452  1.00  0.00           H  
HETATM   18  H5  UNL     1      -0.132   1.141  -2.288  1.00  0.00           H  
HETATM   19  H6  UNL     1      -0.165  -1.622  -0.055  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.985  -0.570  -2.429  1.00  0.00           H  
HETATM   21  H8  UNL     1       2.132   0.203  -1.014  1.00  0.00           H  
HETATM   22  H9  UNL     1       3.286  -1.519  -0.432  1.00  0.00           H  
HETATM   23  H10 UNL     1       2.042  -0.671   3.063  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   14
CONECT    3    4    5   15
CONECT    4   16
CONECT    5    6    7   17
CONECT    6   18
CONECT    7    8    9   19
CONECT    8   20
CONECT    9   10   11   21
CONECT   10   22
CONECT   11   12   12   13
CONECT   13   23
END
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SMILES for #<Metabolite:0x00007f5a8905c720>

O[C@@H](C=O)[C@@H](O)[C@@H](O)[C@H](O)C(O)=O
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INCHI for #<Metabolite:0x00007f5a8905c720>

InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h1-5,8-11H,(H,12,13)/t2-,3+,4+,5-/m0/s1
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Synonyms
ValueSource
(2S,3R,4S,5R)-2,3,4,5-Tetrahydroxy-6-oxohexanoic acidChEBI
D-Galacturonic acidChEBI
(2S,3R,4S,5R)-2,3,4,5-Tetrahydroxy-6-oxohexanoateGenerator
D-GalacturonateGenerator
GalacturonateGenerator
DL-Galacturonic acidHMDB
D-Galactopyranuronic acidHMDB
Galacturonic acid, (D)-isomerHMDB
Galacturonic acid, (alpha-D)-isomerHMDB
Galacturonic acid, calcium, sodium salt, (D)-isomerHMDB
Galacturonic acid, monosodium salt, (D)-isomerHMDB
Aldehydo-D-galacturonateHMDB
Polygalacturonic acid, aluminum saltHMDB
Sodium pectateHMDB
GalacturonanHMDB
HomogalacturonanHMDB
Pectic acidHMDB
Polygalacturonic acid homopolymerHMDB
Polygalacturonic acid, sulfatedHMDB
Calcium polygalacturonateHMDB
PectateHMDB
Polygalacturonic acidHMDB
Polygalacturonic acid, calcium saltHMDB
Polygalacturonic acid, homopolymer sodium saltHMDB
Sodium polygalacturonateHMDB
Anhydrogalacturonic acidHMDB
Calcium pectateHMDB
Polygalacturonic acid, homopolymer (D)-isomerHMDB
Aldehydo-D-galacturonic acidHMDB
(DL)-Galacturonic acidHMDB
(D)-Galacturonic acidHMDB
Galacturonic acidMeSH
Molecular FormulaC6H10O7
Average Mass194.1394
Monoisotopic Mass194.042652674
IUPAC Name(2S,3R,4S,5R)-2,3,4,5-tetrahydroxy-6-oxohexanoic acid
Traditional Namealdehydo-D-galacturonic acid
CAS Registry Number14982-50-4
SMILES
O[C@@H](C=O)[C@@H](O)[C@@H](O)[C@H](O)C(O)=O
InChI Identifier
InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h1-5,8-11H,(H,12,13)/t2-,3+,4+,5-/m0/s1
InChI KeyIAJILQKETJEXLJ-RSJOWCBRSA-N