Showing metabocard for 3-Dehydro-2-deoxy-D-gluconate (MMDBc0029768)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:40:47 UTC
Update Date2024-04-30 19:41:51 UTC
Metabolite IDMMDBc0029768
Metabolite Identification
Common Name3-Dehydro-2-deoxy-D-gluconate
Description3-Dehydro-2-deoxy-D-gluconate is an intermediate in pectin degradation and is involved in carbohydrate metabolism as well as pentose and glucuronate interconversions. It is a substrate for the enzyme 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase. This enzyme catalyzes the reduction of 2,5-diketo-3-deoxygluconate (DKII or 4,6-dihydroxy-2,5-dioxohexanoate) into 2-keto-3-deoxygluconate (KDG or 2-dehydro-3-deoxygluconate) with a concomitant oxidation of NADH
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007f9231959640>

Structure #1
  Mrv0541 02241206302D          

 12 11  0  0  0  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  0  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  0  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  0  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
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  2  4  1  0  0  0  0
  2  7  1  0  0  0  0
  3  6  1  0  0  0  0
  3  8  2  0  0  0  0
  4  6  1  0  0  0  0
  4  9  1  0  0  0  0
  5 10  2  0  0  0  0
  5 11  1  0  0  0  0
  6 12  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9231959640>

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3D SDF for #<Metabolite:0x00007f9231959640>
Structure #1
  Mrv0541 02241206302D          

 12 11  0  0  0  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  0  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  0  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  0  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
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  2  4  1  0  0  0  0
  2  7  1  0  0  0  0
  3  6  1  0  0  0  0
  3  8  2  0  0  0  0
  4  6  1  0  0  0  0
  4  9  1  0  0  0  0
  5 10  2  0  0  0  0
  5 11  1  0  0  0  0
  6 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029768

> <DATABASE_NAME>
MIME

> <SMILES>
OCC(O)C(O)C(=O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h4,6-7,9,12H,1-2H2,(H,10,11)

> <INCHI_KEY>
CNLFCQPCBQQMHK-UHFFFAOYSA-N

> <FORMULA>
C6H10O6

> <MOLECULAR_WEIGHT>
178.14

> <EXACT_MASS>
178.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
15.50700924919401

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5,6-trihydroxy-3-oxohexanoic acid

> <ALOGPS_LOGP>
-2.01

> <JCHEM_LOGP>
-1.9272204580000003

> <ALOGPS_LOGS>
0.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.018411911399458

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7494938686116095

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9796952799010628

> <JCHEM_POLAR_SURFACE_AREA>
115.06

> <JCHEM_REFRACTIVITY>
36.2412

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.09e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5,6-trihydroxy-3-oxohexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007f9231959640>
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PDB for #<Metabolite:0x00007f9231959640>
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         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+0
HETATM   12  O   UNK     0       2.874   2.310   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    7                                                       
CONECT    3    1    6    8                                                  
CONECT    4    2    6    9                                                  
CONECT    5    1   10   11                                                  
CONECT    6    3    4   12                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for #<Metabolite:0x00007f9231959640>
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SMILES for #<Metabolite:0x00007f9231959640>
OCC(O)C(O)C(=O)CC(O)=O
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INCHI for #<Metabolite:0x00007f9231959640>
InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h4,6-7,9,12H,1-2H2,(H,10,11)
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Synonyms
ValueSource
3-Dehydro-2-deoxy-D-gluconic acidGenerator
Molecular FormulaC6H10O6
Average Mass178.14
Monoisotopic Mass178.047738052
IUPAC Name4,5,6-trihydroxy-3-oxohexanoic acid
Traditional Name4,5,6-trihydroxy-3-oxohexanoic acid
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)C(=O)CC(O)=O
InChI Identifier
InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h4,6-7,9,12H,1-2H2,(H,10,11)
InChI KeyCNLFCQPCBQQMHK-UHFFFAOYSA-N