Showing metabocard for 5-dehydro-2-deoxy-D-gluconic acid (MMDBc0055554)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-17 19:58:45 UTC
Update Date2022-08-12 20:09:24 UTC
Metabolite IDMMDBc0055554
Metabolite Identification
Common Name5-dehydro-2-deoxy-D-gluconic acid
Description5-dehydro-2-deoxy-D-gluconate belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain. Based on a literature review very few articles have been published on 5-dehydro-2-deoxy-D-gluconate.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fd5f8eaf300>

  Mrv1652306172221582D          

 14 13  0  0  1  0            999 V2000
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6039   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.5395    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  0  0  0  0
  3  8  1  6  0  0  0
  9  4  2  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
  6 12  1  6  0  0  0
  3 13  1  6  0  0  0
  6 14  1  6  0  0  0
M  CHG  1  11  -1
M  END
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3D MOL for #<Metabolite:0x00007fd5f8eaf300>

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3D SDF for #<Metabolite:0x00007fd5f8eaf300>
  Mrv1652306172221582D          

 14 13  0  0  1  0            999 V2000
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6039   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.5395    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  0  0  0  0
  3  8  1  6  0  0  0
  9  4  2  0  0  0  0
 10  5  2  0  0  0  0
 11  5  1  0  0  0  0
  6 12  1  6  0  0  0
  3 13  1  6  0  0  0
  6 14  1  6  0  0  0
M  CHG  1  11  -1
M  END
> <DATABASE_ID>
MMDBc0055554

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h3,6-8,12H,1-2H2,(H,10,11)/p-1/t3-,6+/m1/s1

> <INCHI_KEY>
UCYNJPYWOSFBAT-CVYQJGLWSA-M

> <FORMULA>
C6H9O6

> <MOLECULAR_WEIGHT>
177.133

> <EXACT_MASS>
177.04046159

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.983760625866406

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S)-3,4,6-trihydroxy-5-oxohexanoate

> <JCHEM_LOGP>
-2.2315988933333335

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.124380169821285

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.821926222658468

> <JCHEM_PKA_STRONGEST_BASIC>
-3.327588544284506

> <JCHEM_POLAR_SURFACE_AREA>
117.89000000000001

> <JCHEM_REFRACTIVITY>
46.9281

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
5-dehydro-2-deoxy-D-gluconate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007fd5f8eaf300>
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PDB for #<Metabolite:0x00007fd5f8eaf300>
HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       5.541   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.875   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.127  -0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.207  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.208   0.770   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.875  -1.540   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       2.874   2.310   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       4.207   1.540   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       2.874  -0.770   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4    7                                                       
CONECT    3    1    6    8   13                                             
CONECT    4    2    6    9                                                  
CONECT    5    1   10   11                                                  
CONECT    6    3    4   12   14                                             
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    3                                                            
CONECT   14    6                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

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3D PDB for #<Metabolite:0x00007fd5f8eaf300>
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SMILES for #<Metabolite:0x00007fd5f8eaf300>
[H][C@@](O)(CC([O-])=O)[C@]([H])(O)C(=O)CO
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INCHI for #<Metabolite:0x00007fd5f8eaf300>
InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h3,6-8,12H,1-2H2,(H,10,11)/p-1/t3-,6+/m1/s1
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Synonyms
ValueSource
5-Dehydro-2-deoxy-D-gluconic acidGenerator
Molecular FormulaC6H9O6
Average Mass177.133
Monoisotopic Mass177.04046159
IUPAC Name(3R,4S)-3,4,6-trihydroxy-5-oxohexanoate
Traditional Name5-dehydro-2-deoxy-D-gluconate
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(CC([O-])=O)[C@]([H])(O)C(=O)CO
InChI Identifier
InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h3,6-8,12H,1-2H2,(H,10,11)/p-1/t3-,6+/m1/s1
InChI KeyUCYNJPYWOSFBAT-CVYQJGLWSA-M