Showing metabocard for D-glucaro-1,4-lactone (MMDBc0054432)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:12:02 UTC
Update Date2022-08-12 20:09:00 UTC
Metabolite IDMMDBc0054432
Metabolite Identification
Common NameD-glucaro-1,4-lactone
DescriptionD-Glucaro-1,4-lactone, also known as D-saccharolactone or 1,4-D-glucarolactone, belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. D-Glucaro-1,4-lactone has been detected, but not quantified in, several different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), domestic pigs (Sus scrofa domestica), and milk (cow). This could make D-glucaro-1,4-lactone a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on D-Glucaro-1,4-lactone.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f921bf0a578>


  Mrv1652304032018422D          

 17 17  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1296   -1.5764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6145   -2.2438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3091   -1.6626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0778    1.4392    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1304    1.7177    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6447   -0.9089    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7951   -0.0262    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  1  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  1  7  1  1  0  0  0
  2  8  1  6  0  0  0
  3  9  1  1  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  4  1  0  0  0  0
 13  6  1  0  0  0  0
  1 14  1  6  0  0  0
  2 15  1  1  0  0  0
  3 16  1  1  0  0  0
  4 17  1  6  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f921bf0a578>

HMDB0041862
     RDKit          3D
D-Glucaro-1,4-lactone
 21 21  0  0  0  0  0  0  0  0999 V2000
    2.2136   -1.4309   -0.9449 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3184   -0.4914   -0.1247 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5742    0.0090    0.1852 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0687    0.0406    0.4784 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3289    1.0766    1.3677 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1737    0.4994   -0.6624 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0192   -0.6392   -1.4985 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9210   -1.4539   -0.8095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0641   -2.7012   -0.9806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6917   -0.6278    0.1611 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0636   -0.7849   -0.0061 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2371    0.7513   -0.2048 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3202    1.6604    0.8326 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7518    0.9536    0.4843 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5957   -0.7774    1.0580 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4947    0.7417    2.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6274    1.3359   -1.1859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4345   -0.9339    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2889   -0.8758   -0.9687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8164    1.0825   -1.0770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2904    2.5656    0.4254 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
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12  6  1  0
  3 14  1  0
  4 15  1  1
  5 16  1  0
  6 17  1  6
 10 18  1  1
 11 19  1  0
 12 20  1  6
 13 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f921bf0a578>


  Mrv1652304032018422D          

 17 17  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1296   -1.5764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6145   -2.2438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3091   -1.6626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0778    1.4392    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1304    1.7177    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6447   -0.9089    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7951   -0.0262    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  4  3  1  1  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  1  7  1  1  0  0  0
  2  8  1  6  0  0  0
  3  9  1  1  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  2  0  0  0  0
 13  4  1  0  0  0  0
 13  6  1  0  0  0  0
  1 14  1  6  0  0  0
  2 15  1  1  0  0  0
  3 16  1  1  0  0  0
  4 17  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054432

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(C(O)=O)[C@@]1([H])OC(=O)[C@]([H])(O)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O7/c7-1-2(8)6(12)13-4(1)3(9)5(10)11/h1-4,7-9H,(H,10,11)/t1-,2-,3+,4+/m1/s1

> <INCHI_KEY>
XECPAIJNBXCOBO-MMPJQOAZSA-N

> <FORMULA>
C6H8O7

> <MOLECULAR_WEIGHT>
192.1235

> <EXACT_MASS>
192.02700261

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
15.621192243530285

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-[(2S,3R,4R)-3,4-dihydroxy-5-oxooxolan-2-yl]-2-hydroxyacetic acid

> <ALOGPS_LOGP>
-1.89

> <JCHEM_LOGP>
-2.4249986480000003

> <ALOGPS_LOGS>
-0.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.622577499257503

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.0635792127453407

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7457384752052727

> <JCHEM_POLAR_SURFACE_AREA>
124.29

> <JCHEM_REFRACTIVITY>
34.6462

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.59e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-[(2S,3R,4R)-3,4-dihydroxy-5-oxooxolan-2-yl](hydroxy)acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f921bf0a578>

HMDB0041862
     RDKit          3D
D-Glucaro-1,4-lactone
 21 21  0  0  0  0  0  0  0  0999 V2000
    2.2136   -1.4309   -0.9449 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3184   -0.4914   -0.1247 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5742    0.0090    0.1852 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0687    0.0406    0.4784 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3289    1.0766    1.3677 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1737    0.4994   -0.6624 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0192   -0.6392   -1.4985 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9210   -1.4539   -0.8095 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0641   -2.7012   -0.9806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6917   -0.6278    0.1611 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0636   -0.7849   -0.0061 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2371    0.7513   -0.2048 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3202    1.6604    0.8326 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7518    0.9536    0.4843 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5957   -0.7774    1.0580 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4947    0.7417    2.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6274    1.3359   -1.1859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4345   -0.9339    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2889   -0.8758   -0.9687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8164    1.0825   -1.0770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2904    2.5656    0.4254 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
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12  6  1  0
  3 14  1  0
  4 15  1  1
  5 16  1  0
  6 17  1  6
 10 18  1  1
 11 19  1  0
 12 20  1  6
 13 21  1  0
M  END
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PDB for #<Metabolite:0x00007f921bf0a578>

HEADER    PROTEIN                                 03-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-APR-20         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.109  -2.943   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.267  -1.375   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       3.014  -4.188   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.577  -3.104   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.290  -0.290   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       2.012   2.687   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       2.110   3.206   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       1.203  -1.697   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       3.351  -0.049   0.000  0.00  0.00           H+0
CONECT    1    2    4    7   14                                             
CONECT    2    1    6    8   15                                             
CONECT    3    4    5    9   16                                             
CONECT    4    1    3   13   17                                             
CONECT    5    3   10   11                                                  
CONECT    6    2   12   13                                                  
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    3                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    4    6                                                       
CONECT   14    1                                                            
CONECT   15    2                                                            
CONECT   16    3                                                            
CONECT   17    4                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END
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3D PDB for #<Metabolite:0x00007f921bf0a578>

COMPND    HMDB0041862
HETATM    1  O1  UNL     1       2.214  -1.431  -0.945  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.318  -0.491  -0.125  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.574   0.009   0.185  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.069   0.041   0.478  1.00  0.00           C  
HETATM    5  O3  UNL     1       1.329   1.077   1.368  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.174   0.499  -0.662  1.00  0.00           C  
HETATM    7  O4  UNL     1      -0.019  -0.639  -1.498  1.00  0.00           O  
HETATM    8  C4  UNL     1      -0.921  -1.454  -0.809  1.00  0.00           C  
HETATM    9  O5  UNL     1      -1.064  -2.701  -0.981  1.00  0.00           O  
HETATM   10  C5  UNL     1      -1.692  -0.628   0.161  1.00  0.00           C  
HETATM   11  O6  UNL     1      -3.064  -0.785  -0.006  1.00  0.00           O  
HETATM   12  C6  UNL     1      -1.237   0.751  -0.205  1.00  0.00           C  
HETATM   13  O7  UNL     1      -1.320   1.660   0.833  1.00  0.00           O  
HETATM   14  H1  UNL     1       3.752   0.954   0.484  1.00  0.00           H  
HETATM   15  H2  UNL     1       0.596  -0.777   1.058  1.00  0.00           H  
HETATM   16  H3  UNL     1       1.495   0.742   2.291  1.00  0.00           H  
HETATM   17  H4  UNL     1       0.627   1.336  -1.186  1.00  0.00           H  
HETATM   18  H5  UNL     1      -1.434  -0.934   1.179  1.00  0.00           H  
HETATM   19  H6  UNL     1      -3.289  -0.876  -0.969  1.00  0.00           H  
HETATM   20  H7  UNL     1      -1.816   1.082  -1.077  1.00  0.00           H  
HETATM   21  H8  UNL     1      -1.290   2.566   0.425  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   12   17
CONECT    7    8
CONECT    8    9    9   10
CONECT   10   11   12   18
CONECT   11   19
CONECT   12   13   20
CONECT   13   21
END
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SMILES for #<Metabolite:0x00007f921bf0a578>

[H][C@@](O)(C(O)=O)[C@@]1([H])OC(=O)[C@]([H])(O)[C@@]1([H])O
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INCHI for #<Metabolite:0x00007f921bf0a578>

InChI=1S/C6H8O7/c7-1-2(8)6(12)13-4(1)3(9)5(10)11/h1-4,7-9H,(H,10,11)/t1-,2-,3+,4+/m1/s1
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Synonyms
ValueSource
1,4-D-GlucarolactoneChEBI
1,4-GlucarolactoneChEBI
D-SaccharolactoneChEBI
SaccharolactoneChEBI
Saccharolactone, monocalcium salt, (D)-isomerHMDB
Saccharolactone, (D)-isomerHMDB
Saccharolactone, monosodium salt, (D)-isomerHMDB
Glucarate-1,4-lactoneHMDB
Molecular FormulaC6H8O7
Average Mass192.1235
Monoisotopic Mass192.02700261
IUPAC Name(2S)-2-[(2S,3R,4R)-3,4-dihydroxy-5-oxooxolan-2-yl]-2-hydroxyacetic acid
Traditional Name(S)-[(2S,3R,4R)-3,4-dihydroxy-5-oxooxolan-2-yl](hydroxy)acetic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(C(O)=O)[C@@]1([H])OC(=O)[C@]([H])(O)[C@@]1([H])O
InChI Identifier
InChI=1S/C6H8O7/c7-1-2(8)6(12)13-4(1)3(9)5(10)11/h1-4,7-9H,(H,10,11)/t1-,2-,3+,4+/m1/s1
InChI KeyXECPAIJNBXCOBO-MMPJQOAZSA-N