Showing metabocard for 3-Dehydro-L-gulonate (MMDBc0029825)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:43:16 UTC
Update Date2022-08-31 17:18:54 UTC
Metabolite IDMMDBc0029825
Metabolite Identification
Common Name3-Dehydro-L-gulonate
Description3-Dehydro-L-gulonate is an intermediate in ascorbic acid degradation. It is a substrate for the enzyme 2,3-diketo-L-gulonate reductase. This enzyme catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH, to form 3-keto-L-gulonate. It participates in the reaction: 3-dehydro-L-gulonate + NAD(P)+ = (4R,5S)-4,5,6-trihydroxy-2,3-dioxohexanoate + NAD(P)H. Several pathways for the irreversible catabolism of ascorbate have been described. Facultatively aerobic bacteria such as Escherichia coli degrade L-ascorbate by different pathways under aerobic and anaerobic conditions. The anaerobic pathway begins with phosphorylation of ascorbate (mediated by a PTS-type transporter), while the aerobic pathway proceeds via 2,3-dioxo-L-gulonate. Both pathways produce D-xylulose 5-phosphate, a centeral metabolite that is fed into the pentose phosphate pathway.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9253df7108>


  Mrv0541 02231220382D          

 13 12  0  0  1  0            999 V2000
   17.1753   -5.2526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4608   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0318   -4.0151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6043   -5.2526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8898   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0332   -4.4276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3188   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1753   -4.4276    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4608   -4.0151    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.8898   -4.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7464   -4.4276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6043   -4.4276    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.3188   -4.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  6  0  0  0
  3 11  1  0  0  0  0
 12  4  1  1  0  0  0
  5 10  2  0  0  0  0
  6 13  1  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
 12 13  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f9253df7108>

HMDB0006334
     RDKit          3D
3-Dehydro-L-gulonate
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.5727   -0.6625    1.6324 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8696    0.2206    1.0928 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9096    1.5226    1.5479 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9977   -0.1587   -0.0392 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1186   -1.4918   -0.3175 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6057    0.2508    0.2947 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4585    1.4298    0.5484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5396   -0.6577    0.3300 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1336   -1.9866    0.0903 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5250   -0.2423   -0.7717 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5775   -1.1842   -0.6442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0932    1.1220   -0.5645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6525    1.3039    0.6836 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2919    2.2995    1.0426 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2998    0.4888   -0.9120 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0939   -1.7156   -0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1066   -0.5959    1.2786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7148   -2.3815   -0.6256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0505   -0.3655   -1.7601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3771   -0.8852   -1.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9181    1.2322   -1.3373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3501    1.9203   -0.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1793    0.5368    1.0047 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  2  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
  3 14  1  0
  4 15  1  6
  5 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  6
 11 20  1  0
 12 21  1  0
 12 22  1  0
 13 23  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f9253df7108>


  Mrv0541 02231220382D          

 13 12  0  0  1  0            999 V2000
   17.1753   -5.2526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4608   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0318   -4.0151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6043   -5.2526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8898   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0332   -4.4276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3188   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1753   -4.4276    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4608   -4.0151    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.8898   -4.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7464   -4.4276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6043   -4.4276    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.3188   -4.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  6  0  0  0
  3 11  1  0  0  0  0
 12  4  1  1  0  0  0
  5 10  2  0  0  0  0
  6 13  1  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
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029825

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H](O)[C@@H](O)C(=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/h2-3,5,7-9,11H,1H2,(H,12,13)/t2-,3+,5-/m0/s1

> <INCHI_KEY>
WTAHRPBPWHCMHW-LWKDLAHASA-N

> <FORMULA>
C6H10O7

> <MOLECULAR_WEIGHT>
194.1394

> <EXACT_MASS>
194.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
16.2999332828514

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.56

> <JCHEM_LOGP>
-2.642378918666667

> <ALOGPS_LOGS>
-0.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.43781434344056

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.161083010088812

> <JCHEM_PKA_STRONGEST_BASIC>
-2.979764264053207

> <JCHEM_POLAR_SURFACE_AREA>
135.29000000000002

> <JCHEM_REFRACTIVITY>
37.5794

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-dehydro-L-gulonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f9253df7108>

HMDB0006334
     RDKit          3D
3-Dehydro-L-gulonate
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.5727   -0.6625    1.6324 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8696    0.2206    1.0928 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9096    1.5226    1.5479 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9977   -0.1587   -0.0392 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1186   -1.4918   -0.3175 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6057    0.2508    0.2947 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4585    1.4298    0.5484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5396   -0.6577    0.3300 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1336   -1.9866    0.0903 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5250   -0.2423   -0.7717 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5775   -1.1842   -0.6442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0932    1.1220   -0.5645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6525    1.3039    0.6836 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2919    2.2995    1.0426 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2998    0.4888   -0.9120 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0939   -1.7156   -0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1066   -0.5959    1.2786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7148   -2.3815   -0.6256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0505   -0.3655   -1.7601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3771   -0.8852   -1.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9181    1.2322   -1.3373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3501    1.9203   -0.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1793    0.5368    1.0047 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  2  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
  3 14  1  0
  4 15  1  6
  5 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  6
 11 20  1  0
 12 21  1  0
 12 22  1  0
 13 23  1  0
M  END
Download

PDB for #<Metabolite:0x00007f9253df7108>

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      32.061  -9.805   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      30.727  -5.955   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      28.059  -7.495   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      34.728  -9.805   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      33.394  -5.955   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      37.395  -8.265   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      36.062  -5.955   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      32.061  -8.265   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.727  -7.495   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      33.394  -7.495   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.393  -8.265   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      34.728  -8.265   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      36.062  -7.495   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3   11                                                            
CONECT    4   12                                                            
CONECT    5   10                                                            
CONECT    6   13                                                            
CONECT    7   13                                                            
CONECT    8    1    9   10                                                  
CONECT    9    2    8   11                                                  
CONECT   10    5    8   12                                                  
CONECT   11    3    9                                                       
CONECT   12    4   10   13                                                  
CONECT   13    6    7   12                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for #<Metabolite:0x00007f9253df7108>

COMPND    HMDB0006334
HETATM    1  O1  UNL     1       3.573  -0.663   1.632  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.870   0.221   1.093  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.910   1.523   1.548  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.998  -0.159  -0.039  1.00  0.00           C  
HETATM    5  O3  UNL     1       2.119  -1.492  -0.318  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.606   0.251   0.295  1.00  0.00           C  
HETATM    7  O4  UNL     1       0.459   1.430   0.548  1.00  0.00           O  
HETATM    8  C4  UNL     1      -0.540  -0.658   0.330  1.00  0.00           C  
HETATM    9  O5  UNL     1      -0.134  -1.987   0.090  1.00  0.00           O  
HETATM   10  C5  UNL     1      -1.525  -0.242  -0.772  1.00  0.00           C  
HETATM   11  O6  UNL     1      -2.578  -1.184  -0.644  1.00  0.00           O  
HETATM   12  C6  UNL     1      -2.093   1.122  -0.565  1.00  0.00           C  
HETATM   13  O7  UNL     1      -2.653   1.304   0.684  1.00  0.00           O  
HETATM   14  H1  UNL     1       3.292   2.299   1.043  1.00  0.00           H  
HETATM   15  H2  UNL     1       2.300   0.489  -0.912  1.00  0.00           H  
HETATM   16  H3  UNL     1       3.094  -1.716  -0.290  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.107  -0.596   1.279  1.00  0.00           H  
HETATM   18  H5  UNL     1      -0.715  -2.382  -0.626  1.00  0.00           H  
HETATM   19  H6  UNL     1      -1.050  -0.365  -1.760  1.00  0.00           H  
HETATM   20  H7  UNL     1      -3.377  -0.885  -1.165  1.00  0.00           H  
HETATM   21  H8  UNL     1      -2.918   1.232  -1.337  1.00  0.00           H  
HETATM   22  H9  UNL     1      -1.350   1.920  -0.730  1.00  0.00           H  
HETATM   23  H10 UNL     1      -3.179   0.537   1.005  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    7    8
CONECT    8    9   10   17
CONECT    9   18
CONECT   10   11   12   19
CONECT   11   20
CONECT   12   13   21   22
CONECT   13   23
END
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SMILES for #<Metabolite:0x00007f9253df7108>

OC[C@H](O)[C@@H](O)C(=O)[C@H](O)C(O)=O
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INCHI for #<Metabolite:0x00007f9253df7108>

InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-3,5,7-9,11H,1H2,(H,12,13)/t2-,3+,5-/m0/s1
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Synonyms
ValueSource
3-Dehydro-L-gulonic acidGenerator
L-Xylo-hex-3-ulosonic acidHMDB
Molecular FormulaC6H10O7
Average Mass194.1394
Monoisotopic Mass194.042652674
IUPAC Name(2S,4R,5S)-2,4,5,6-tetrahydroxy-3-oxohexanoic acid
Traditional Name3-dehydro-L-gulonic acid
CAS Registry NumberNot Available
SMILES
OC[C@H](O)[C@@H](O)C(=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/h2-3,5,7-9,11H,1H2,(H,12,13)/t2-,3+,5-/m0/s1
InChI KeyWTAHRPBPWHCMHW-LWKDLAHASA-N