Showing metabocard for L-2-Hydroxyglutaric acid (MMDBc0029505)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:25:02 UTC
Update Date2022-08-31 13:37:07 UTC
Metabolite IDMMDBc0029505
Metabolite Identification
Common NameL-2-Hydroxyglutaric acid
DescriptionL-2-hydroxyglutaric acid is a member of the chemical class known as Short-chain Hydroxy Acids and Derivatives. These are hydroxy acids with an alkyl chain the contains less than 6 carbon atoms. L-2-Hydroxyglutaric acid (2-hydroxyglutaric acid) is an alpha hydroxy acid. In bacteria it is formed by a 2-hydroxyglutarate synthase (EC 2.3.3.11) and oxidized by 2-hydroxyglutarate oxidase. (Wikipedia , PMID 14491016 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fe272bf1cb8>


  Mrv1652305271900172D          

 10  9  0  0  0  0            999 V2000
 9998.6124 9997.7078    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9997.8979 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1831 9997.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4684 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.7534 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4684 9998.9448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3301 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0437 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3301 9998.9448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6124 9996.8823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 10  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fe272bf1cb8>

HMDB0000694
     RDKit          3D
L-2-Hydroxyglutaric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
    1.9977   -0.2899   -1.4646 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1686    0.1066   -0.3001 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4952    0.0307    0.1750 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1853    0.6390    0.6379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2303    0.6592    0.2044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8392   -0.6798   -0.0787 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2355   -1.4124   -1.0744 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3010   -0.5240   -0.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7416   -1.0283   -1.4581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0707    0.1863    0.4926 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6610   -0.4993    1.0067 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2910    0.0467    1.6018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5412    1.6852    0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4219    1.3837   -0.6309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8187    1.1009    1.0675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8160   -1.3288    0.8399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6126   -1.2382   -1.9753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2525    1.1624    0.4668 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
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  1
  7 17  1  0
 10 18  1  0
M  END
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3D SDF for #<Metabolite:0x00007fe272bf1cb8>


  Mrv1652305271900172D          

 10  9  0  0  0  0            999 V2000
 9998.6124 9997.7078    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9997.8979 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1831 9997.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4684 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.7534 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4684 9998.9448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3301 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0437 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3301 9998.9448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6124 9996.8823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 10  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029505

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m0/s1

> <INCHI_KEY>
HWXBTNAVRSUOJR-VKHMYHEASA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173366

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.9730498807228

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-hydroxypentanedioic acid

> <ALOGPS_LOGP>
-1.04

> <JCHEM_LOGP>
-0.824980223

> <ALOGPS_LOGS>
0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.159324461588801

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.276485914460605

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8068384384876675

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
29.6302

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.57e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-2-hydroxyglutaric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fe272bf1cb8>

HMDB0000694
     RDKit          3D
L-2-Hydroxyglutaric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
    1.9977   -0.2899   -1.4646 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1686    0.1066   -0.3001 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4952    0.0307    0.1750 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1853    0.6390    0.6379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2303    0.6592    0.2044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8392   -0.6798   -0.0787 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2355   -1.4124   -1.0744 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3010   -0.5240   -0.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7416   -1.0283   -1.4581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0707    0.1863    0.4926 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6610   -0.4993    1.0067 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2910    0.0467    1.6018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5412    1.6852    0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4219    1.3837   -0.6309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8187    1.1009    1.0675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8160   -1.3288    0.8399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6126   -1.2382   -1.9753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2525    1.1624    0.4668 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
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  1
  7 17  1  0
 10 18  1  0
M  END
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PDB for #<Metabolite:0x00007fe272bf1cb8>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0    8664.0768662.388   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8662.7438663.157   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8661.4088662.388   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8660.0748663.157   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8658.7408662.388   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8660.0748664.697   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8665.4168663.157   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8666.7488662.388   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8665.4168664.697   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8664.0768660.847   0.000  0.00  0.00           O+0
CONECT    1    2    7   10                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    1                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00007fe272bf1cb8>

COMPND    HMDB0000694
HETATM    1  O1  UNL     1       1.998  -0.290  -1.465  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.169   0.107  -0.300  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.495   0.031   0.175  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.185   0.639   0.638  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.230   0.659   0.204  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.839  -0.680  -0.079  1.00  0.00           C  
HETATM    7  O3  UNL     1      -0.235  -1.412  -1.074  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.301  -0.524  -0.411  1.00  0.00           C  
HETATM    9  O4  UNL     1      -2.742  -1.028  -1.458  1.00  0.00           O  
HETATM   10  O5  UNL     1      -3.071   0.186   0.493  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.661  -0.499   1.007  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.291   0.047   1.602  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.541   1.685   0.901  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.422   1.384  -0.631  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.819   1.101   1.067  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.816  -1.329   0.840  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.613  -1.238  -1.975  1.00  0.00           H  
HETATM   18  H8  UNL     1      -3.253   1.162   0.467  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5   12   13
CONECT    5    6   14   15
CONECT    6    7    8   16
CONECT    7   17
CONECT    8    9    9   10
CONECT   10   18
END
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SMILES for #<Metabolite:0x00007fe272bf1cb8>

O[C@@H](CCC(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007fe272bf1cb8>

InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m0/s1
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Synonyms
ValueSource
(S)-2-HydroxyglutarateChEBI
(S)-2-Hydroxyglutaric acidGenerator
L-2-HydroxyglutarateGenerator
(S)-Α-hydroxyglutarateHMDB
(S)-Α-hydroxyglutaric acidHMDB
(S)-alpha-HydroxyglutarateHMDB
(S)-alpha-Hydroxyglutaric acidHMDB
2-Hydroxy-(S)-pentanedioateHMDB
2-Hydroxy-(S)-pentanedioic acidHMDB
2-Hydroxy-L-glutarateHMDB
2-Hydroxy-L-glutaric acidHMDB
L-Α-hydroxyglutarateHMDB
L-Α-hydroxyglutaric acidHMDB
L-alpha-HydroxyglutarateHMDB
L-alpha-Hydroxyglutaric acidHMDB
L-2-Hydroxyglutaric acidHMDB
Molecular FormulaC5H8O5
Average Mass148.114
Monoisotopic Mass148.037173366
IUPAC Name(2S)-2-hydroxypentanedioic acid
Traditional NameL-2-hydroxyglutaric acid
CAS Registry Number13095-48-2
SMILES
O[C@@H](CCC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m0/s1
InChI KeyHWXBTNAVRSUOJR-VKHMYHEASA-N