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Showing metabocard for 2-Amino-2-deoxy-D-gluconic acid (HMDB0250755)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:51:39 UTC
Update Date2021-09-26 23:02:23 UTC
HMDB IDHMDB0250755
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Amino-2-deoxy-D-gluconic acid
Description2-Amino-2-deoxy-D-gluconic acid belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Based on a literature review a small amount of articles have been published on 2-Amino-2-deoxy-D-gluconic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-amino-2-deoxy-d-gluconic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Amino-2-deoxy-D-gluconic acid is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0250755 (2-Amino-2-deoxy-D-gluconic acid)

  Mrv1652309112109512D          

 13 12  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  5  9  1  0  0  0  0
  4 10  1  0  0  0  0
  3 11  1  0  0  0  0
  2 12  1  0  0  0  0
  1 13  1  0  0  0  0
M  END
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3D MOL for HMDB0250755 (2-Amino-2-deoxy-D-gluconic acid)

HMDB0250755
     RDKit          3D
2-Amino-2-deoxy-D-gluconic acid
 26 25  0  0  0  0  0  0  0  0999 V2000
    0.5122    1.7786   -0.6359 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3731    0.6394   -0.5678 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5388    0.9792    0.3164 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6061    2.1178    0.8380 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5500    0.0574    0.5717 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6692   -0.5554   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6606   -1.6002    0.0268 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4031   -1.1527   -0.8847 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7879   -2.3413   -0.1881 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6643   -0.3695   -1.0173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5937    0.8123   -1.6957 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3797   -0.2467    0.3167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7822    0.6345    1.1861 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8959    2.5480   -1.2291 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4191    2.1610    0.3483 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8590    0.4262   -1.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2130   -0.1701   -0.1614 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3114   -0.4060    0.9967 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2251   -2.4820   -0.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0264   -1.4928   -1.8611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6407   -2.2495    0.7749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3581   -1.0244   -1.6312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1878    1.5224   -1.3317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4349    0.1196    0.1649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4145   -1.2500    0.7803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1603    1.5443    1.0782 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  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
  1 14  1  0
  1 15  1  0
  2 16  1  0
  5 17  1  0
  6 18  1  0
  7 19  1  0
  8 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  0
 12 24  1  0
 12 25  1  0
 13 26  1  0
M  END
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3D SDF for HMDB0250755 (2-Amino-2-deoxy-D-gluconic acid)

  Mrv1652309112109512D          

 13 12  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  5  9  1  0  0  0  0
  4 10  1  0  0  0  0
  3 11  1  0  0  0  0
  2 12  1  0  0  0  0
  1 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250755

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO6/c7-3(6(12)13)5(11)4(10)2(9)1-8/h2-5,8-11H,1,7H2,(H,12,13)

> <INCHI_KEY>
UFYKDFXCZBTLOO-UHFFFAOYSA-N

> <FORMULA>
C6H13NO6

> <MOLECULAR_WEIGHT>
195.171

> <EXACT_MASS>
195.074287143

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
17.733410457899154

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-3,4,5,6-tetrahydroxyhexanoic acid

> <ALOGPS_LOGP>
-3.24

> <JCHEM_LOGP>
-5.777403946832564

> <ALOGPS_LOGS>
-0.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.827339282682512

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8132118690847614

> <JCHEM_PKA_STRONGEST_BASIC>
8.311694397405732

> <JCHEM_POLAR_SURFACE_AREA>
144.24

> <JCHEM_REFRACTIVITY>
39.92849999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.48e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glucosaminic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0250755 (2-Amino-2-deoxy-D-gluconic acid)

HMDB0250755
     RDKit          3D
2-Amino-2-deoxy-D-gluconic acid
 26 25  0  0  0  0  0  0  0  0999 V2000
    0.5122    1.7786   -0.6359 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3731    0.6394   -0.5678 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5388    0.9792    0.3164 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6061    2.1178    0.8380 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5500    0.0574    0.5717 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6692   -0.5554   -0.0275 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6606   -1.6002    0.0268 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4031   -1.1527   -0.8847 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7879   -2.3413   -0.1881 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6643   -0.3695   -1.0173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5937    0.8123   -1.6957 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3797   -0.2467    0.3167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7822    0.6345    1.1861 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8959    2.5480   -1.2291 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4191    2.1610    0.3483 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8590    0.4262   -1.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2130   -0.1701   -0.1614 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3114   -0.4060    0.9967 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2251   -2.4820   -0.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0264   -1.4928   -1.8611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6407   -2.2495    0.7749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3581   -1.0244   -1.6312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1878    1.5224   -1.3317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4349    0.1196    0.1649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4145   -1.2500    0.7803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1603    1.5443    1.0782 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  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
  1 14  1  0
  1 15  1  0
  2 16  1  0
  5 17  1  0
  6 18  1  0
  7 19  1  0
  8 20  1  0
  9 21  1  0
 10 22  1  0
 11 23  1  0
 12 24  1  0
 12 25  1  0
 13 26  1  0
M  END
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PDB for HMDB0250755 (2-Amino-2-deoxy-D-gluconic acid)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       8.621   4.977   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.953   2.667   0.000  0.00  0.00           O+0
CONECT    1    2   13                                                       
CONECT    2    1    3   12                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    9                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    5                                                            
CONECT   10    4                                                            
CONECT   11    3                                                            
CONECT   12    2                                                            
CONECT   13    1                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for HMDB0250755 (2-Amino-2-deoxy-D-gluconic acid)

COMPND    HMDB0250755
HETATM    1  N1  UNL     1       0.512   1.779  -0.636  1.00  0.00           N  
HETATM    2  C1  UNL     1       1.373   0.639  -0.568  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.539   0.979   0.316  1.00  0.00           C  
HETATM    4  O1  UNL     1       2.606   2.118   0.838  1.00  0.00           O  
HETATM    5  O2  UNL     1       3.550   0.057   0.572  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.669  -0.555  -0.027  1.00  0.00           C  
HETATM    7  O3  UNL     1       1.661  -1.600   0.027  1.00  0.00           O  
HETATM    8  C4  UNL     1      -0.403  -1.153  -0.885  1.00  0.00           C  
HETATM    9  O4  UNL     1      -0.788  -2.341  -0.188  1.00  0.00           O  
HETATM   10  C5  UNL     1      -1.664  -0.369  -1.017  1.00  0.00           C  
HETATM   11  O5  UNL     1      -1.594   0.812  -1.696  1.00  0.00           O  
HETATM   12  C6  UNL     1      -2.380  -0.247   0.317  1.00  0.00           C  
HETATM   13  O6  UNL     1      -1.782   0.634   1.186  1.00  0.00           O  
HETATM   14  H1  UNL     1       0.896   2.548  -1.229  1.00  0.00           H  
HETATM   15  H2  UNL     1       0.419   2.161   0.348  1.00  0.00           H  
HETATM   16  H3  UNL     1       1.859   0.426  -1.570  1.00  0.00           H  
HETATM   17  H4  UNL     1       4.213  -0.170  -0.161  1.00  0.00           H  
HETATM   18  H5  UNL     1       0.311  -0.406   0.997  1.00  0.00           H  
HETATM   19  H6  UNL     1       1.225  -2.482  -0.006  1.00  0.00           H  
HETATM   20  H7  UNL     1      -0.026  -1.493  -1.861  1.00  0.00           H  
HETATM   21  H8  UNL     1      -0.641  -2.250   0.775  1.00  0.00           H  
HETATM   22  H9  UNL     1      -2.358  -1.024  -1.631  1.00  0.00           H  
HETATM   23  H10 UNL     1      -2.188   1.522  -1.332  1.00  0.00           H  
HETATM   24  H11 UNL     1      -3.435   0.120   0.165  1.00  0.00           H  
HETATM   25  H12 UNL     1      -2.414  -1.250   0.780  1.00  0.00           H  
HETATM   26  H13 UNL     1      -2.160   1.544   1.078  1.00  0.00           H  
CONECT    1    2   14   15
CONECT    2    3    6   16
CONECT    3    4    4    5
CONECT    5   17
CONECT    6    7    8   18
CONECT    7   19
CONECT    8    9   10   20
CONECT    9   21
CONECT   10   11   12   22
CONECT   11   23
CONECT   12   13   24   25
CONECT   13   26
END
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SMILES for HMDB0250755 (2-Amino-2-deoxy-D-gluconic acid)

NC(C(O)C(O)C(O)CO)C(O)=O
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INCHI for HMDB0250755 (2-Amino-2-deoxy-D-gluconic acid)

InChI=1S/C6H13NO6/c7-3(6(12)13)5(11)4(10)2(9)1-8/h2-5,8-11H,1,7H2,(H,12,13)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Amino-2-deoxy-D-gluconateGenerator
Chemical FormulaC6H13NO6
Average Molecular Weight195.171
Monoisotopic Molecular Weight195.074287143
IUPAC Name2-amino-3,4,5,6-tetrahydroxyhexanoic acid
Traditional Nameglucosaminic acid
CAS Registry NumberNot Available
SMILES
NC(C(O)C(O)C(O)CO)C(O)=O
InChI Identifier
InChI=1S/C6H13NO6/c7-3(6(12)13)5(11)4(10)2(9)1-8/h2-5,8-11H,1,7H2,(H,12,13)
InChI KeyUFYKDFXCZBTLOO-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • Medium-chain hydroxy acid
  • Medium-chain fatty acid
  • Hydroxy fatty acid
  • Amino fatty acid
  • Amino saccharide
  • Beta-hydroxy acid
  • Fatty acid
  • Hydroxy acid
  • Monosaccharide
  • Fatty acyl
  • 1,3-aminoalcohol
  • Secondary alcohol
  • Amino acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Polyol
  • Organic nitrogen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organooxygen compound
  • Primary alcohol
  • Primary amine
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Organopnictogen compound
  • Amine
  • Organic oxygen compound
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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 Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID205865
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound235915
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 References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]