Showing metabocard for D-4-Hydroxy-2-oxoglutarate (MMDBc0030053)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:52:09 UTC
Update Date2024-04-30 19:44:26 UTC
Metabolite IDMMDBc0030053
Metabolite Identification
Common NameD-4-Hydroxy-2-oxoglutarate
DescriptionD-4-hydroxy-2-oxoglutarate is a member of the chemical class known as Gamma Keto-Acids and Derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the C4 carbon atom.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645c6ccc3d0>


  Mrv0541 08131209292D          

 12 11  0  0  0  0            999 V2000
    3.9039    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
    2.4750    1.4289    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
    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
    1.7605    1.8414    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
    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
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  2  6  1  1  0  0  0
  7  3  2  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  5  2  0  0  0  0
  2 12  1  1  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00005645c6ccc3d0>

HMDB0060466
     RDKit          3D
D-4-Hydroxy-2-oxoglutarate
 17 16  0  0  0  0  0  0  0  0999 V2000
    1.8865   -1.2576   -1.2563 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3271   -0.5827   -0.2940 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6567   -0.2117   -0.2173 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4139   -0.1884    0.7552 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8507    0.4828    1.7197 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0025   -0.5702    0.6862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8725    0.5829    0.1818 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4798    0.9717   -1.0799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2498    0.0745    0.1326 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7979   -0.3347    1.1699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9294    0.0522   -1.0572 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9017    0.7018   -0.5469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3918   -0.9257    1.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1837   -1.4096   -0.0273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7655    1.4684    0.8452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8599    1.8476   -1.2985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5088   -0.7013   -1.3820 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
  9 11  1  0
  3 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  1
  8 16  1  0
 11 17  1  0
M  END
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3D SDF for #<Metabolite:0x00005645c6ccc3d0>


  Mrv0541 08131209292D          

 12 11  0  0  0  0            999 V2000
    3.9039    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
    2.4750    1.4289    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
    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
    1.7605    1.8414    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
    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
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  2  6  1  1  0  0  0
  7  3  2  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  5  2  0  0  0  0
  2 12  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030053

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O6/c6-2(4(8)9)1-3(7)5(10)11/h2,6H,1H2,(H,8,9)(H,10,11)/t2-/m1/s1

> <INCHI_KEY>
WXSKVKPSMAHCSG-UWTATZPHSA-N

> <FORMULA>
C5H6O6

> <MOLECULAR_WEIGHT>
162.0975

> <EXACT_MASS>
162.016437924

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
12.943136077944253

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxy-4-oxopentanedioic acid

> <ALOGPS_LOGP>
-1.11

> <JCHEM_LOGP>
-0.8244217603333331

> <ALOGPS_LOGS>
-0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.331193900932068

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.449105918946765

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8864249286801433

> <JCHEM_POLAR_SURFACE_AREA>
111.9

> <JCHEM_REFRACTIVITY>
30.221200000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.98e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-4-hydroxy-2-oxoglutaric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00005645c6ccc3d0>

HMDB0060466
     RDKit          3D
D-4-Hydroxy-2-oxoglutarate
 17 16  0  0  0  0  0  0  0  0999 V2000
    1.8865   -1.2576   -1.2563 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3271   -0.5827   -0.2940 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6567   -0.2117   -0.2173 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4139   -0.1884    0.7552 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8507    0.4828    1.7197 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0025   -0.5702    0.6862 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8725    0.5829    0.1818 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4798    0.9717   -1.0799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2498    0.0745    0.1326 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7979   -0.3347    1.1699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9294    0.0522   -1.0572 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9017    0.7018   -0.5469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3918   -0.9257    1.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1837   -1.4096   -0.0273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7655    1.4684    0.8452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8599    1.8476   -1.2985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5088   -0.7013   -1.3820 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
  9 11  1  0
  3 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  1
  8 16  1  0
 11 17  1  0
M  END
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PDB for #<Metabolite:0x00005645c6ccc3d0>

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4    6   12                                             
CONECT    3    1    5    7                                                  
CONECT    4    2    8    9                                                  
CONECT    5    3   10   11                                                  
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for #<Metabolite:0x00005645c6ccc3d0>

COMPND    HMDB0060466
HETATM    1  O1  UNL     1       1.887  -1.258  -1.256  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.327  -0.583  -0.294  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.657  -0.212  -0.217  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.414  -0.188   0.755  1.00  0.00           C  
HETATM    5  O3  UNL     1       1.851   0.483   1.720  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.003  -0.570   0.686  1.00  0.00           C  
HETATM    7  C4  UNL     1      -0.872   0.583   0.182  1.00  0.00           C  
HETATM    8  O4  UNL     1      -0.480   0.972  -1.080  1.00  0.00           O  
HETATM    9  C5  UNL     1      -2.250   0.074   0.133  1.00  0.00           C  
HETATM   10  O5  UNL     1      -2.798  -0.335   1.170  1.00  0.00           O  
HETATM   11  O6  UNL     1      -2.929   0.052  -1.057  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.902   0.702  -0.547  1.00  0.00           H  
HETATM   13  H2  UNL     1      -0.392  -0.926   1.669  1.00  0.00           H  
HETATM   14  H3  UNL     1      -0.184  -1.410  -0.027  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.765   1.468   0.845  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.860   1.848  -1.299  1.00  0.00           H  
HETATM   17  H6  UNL     1      -3.509  -0.701  -1.382  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5    5    6
CONECT    6    7   13   14
CONECT    7    8    9   15
CONECT    8   16
CONECT    9   10   10   11
CONECT   11   17
END
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SMILES for #<Metabolite:0x00005645c6ccc3d0>

[H][C@@](O)(CC(=O)C(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00005645c6ccc3d0>

InChI=1S/C5H6O6/c6-2(4(8)9)1-3(7)5(10)11/h2,6H,1H2,(H,8,9)(H,10,11)/t2-/m1/s1
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Synonyms
ValueSource
(R)-2-Hydroxy-4-ketopentanedioic acidChEBI
(R)-2-Hydroxy-4-oxopentanedioic acidChEBI
D-4-Hydroxy-2-ketoglutaric acidChEBI
(R)-2-Hydroxy-4-oxopentanedioateKegg
(R)-2-Hydroxy-4-ketopentanedioateGenerator
D-4-Hydroxy-2-ketoglutarateGenerator
D-4-Hydroxy-2-oxoglutaric acidGenerator
Molecular FormulaC5H6O6
Average Mass162.0975
Monoisotopic Mass162.016437924
IUPAC Name(2R)-2-hydroxy-4-oxopentanedioic acid
Traditional NameD-4-hydroxy-2-oxoglutaric acid
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(CC(=O)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H6O6/c6-2(4(8)9)1-3(7)5(10)11/h2,6H,1H2,(H,8,9)(H,10,11)/t2-/m1/s1
InChI KeyWXSKVKPSMAHCSG-UWTATZPHSA-N