Showing metabocard for 2-dehydro-3-deoxy-L-arabinonate (MMDBc0055215)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-17 19:46:33 UTC
Update Date2025-10-07 16:09:01 UTC
Metabolite IDMMDBc0055215
Metabolite Identification
Common Name2-dehydro-3-deoxy-L-arabinonate
Description2-dehydro-3-deoxy-L-arabinonate is a carbohydrate derivative belonging to the class of organic compounds known as sugar acids. Its chemical structure features a dehydro and deoxy modification of the L-arabinose sugar backbone, which plays a role in various metabolic pathways. Specifically, 2-dehydro-3-deoxy-L-arabinonate is produced through the enzymatic action of L-arabinonate dehydratase, which catalyzes the conversion of L-arabinonate, a precursor in the pentose phosphate pathway, to this metabolite (PMID:28574691 ). Additionally, it is involved in the broader context of carbohydrate metabolism, where D-xylonate dehydratase catalyzes the dehydration of D-xylonate to yield 2-dehydro-3-deoxy-D-xylonate, highlighting its role in the interconversion of sugar acids (PMID:27487924 ). These transformations indicate its significance in the metabolic pathways that process pentose sugars, which are crucial for various biological processes, including nucleotide synthesis and energy production.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007f9ad35baa98>


  Mrv1652306172221462D          

 11 10  0  0  1  0            999 V2000
    3.9039    1.4289    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  2  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
    1.7605    1.8414    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
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  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
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  4  1  0  0  0  0
  6  2  1  0  0  0  0
  3  7  1  1  0  0  0
  8  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  5  2  0  0  0  0
  3 11  1  1  0  0  0
M  CHG  1   9  -1
M  END
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3D MOL for #<Metabolite:0x00007f9ad35baa98>

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3D SDF for #<Metabolite:0x00007f9ad35baa98>

  Mrv1652306172221462D          

 11 10  0  0  1  0            999 V2000
    3.9039    1.4289    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  2  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
    1.7605    1.8414    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
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  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
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  4  1  0  0  0  0
  6  2  1  0  0  0  0
  3  7  1  1  0  0  0
  8  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  5  2  0  0  0  0
  3 11  1  1  0  0  0
M  CHG  1   9  -1
M  END
> <DATABASE_ID>
MMDBc0055215

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c6-2-3(7)1-4(8)5(9)10/h3,6-7H,1-2H2,(H,9,10)/p-1/t3-/m1/s1

> <INCHI_KEY>
UQIGQRSJIKIPKZ-GSVOUGTGSA-M

> <FORMULA>
C5H7O5

> <MOLECULAR_WEIGHT>
147.107

> <EXACT_MASS>
147.029896905

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
12.42321818762325

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R)-4,5-dihydroxy-2-oxopentanoate

> <JCHEM_LOGP>
-1.1446962983333338

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.12213716943176

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9063050280407245

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9433681969036742

> <JCHEM_POLAR_SURFACE_AREA>
97.66

> <JCHEM_REFRACTIVITY>
41.1909

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2-dehydro-3-deoxy-L-pentonate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007f9ad35baa98>
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PDB for #<Metabolite:0x00007f9ad35baa98>
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       7.287   2.667   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       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       5.954   1.897   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    3    6                                                       
CONECT    3    1    2    7   11                                             
CONECT    4    1    5    8                                                  
CONECT    5    4    9   10                                                  
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    5                                                            
CONECT   11    3                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for #<Metabolite:0x00007f9ad35baa98>
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SMILES for #<Metabolite:0x00007f9ad35baa98>
[H][C@](O)(CO)CC(=O)C([O-])=O
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INCHI for #<Metabolite:0x00007f9ad35baa98>
InChI=1S/C5H8O5/c6-2-3(7)1-4(8)5(9)10/h3,6-7H,1-2H2,(H,9,10)/p-1/t3-/m1/s1
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Synonyms
ValueSource
2-Dehydro-3-deoxy-L-arabinonic acidGenerator
Molecular FormulaC5H7O5
Average Mass147.107
Monoisotopic Mass147.029896905
IUPAC Name(4R)-4,5-dihydroxy-2-oxopentanoate
Traditional Name2-dehydro-3-deoxy-L-pentonate
CAS Registry NumberNot Available
SMILES
[H][C@](O)(CO)CC(=O)C([O-])=O
InChI Identifier
InChI=1S/C5H8O5/c6-2-3(7)1-4(8)5(9)10/h3,6-7H,1-2H2,(H,9,10)/p-1/t3-/m1/s1
InChI KeyUQIGQRSJIKIPKZ-GSVOUGTGSA-M