Showing metabocard for Glyoxylic acid (MMDBc0000031)

Plant
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:27:51 UTC
Update Date2022-08-30 23:10:58 UTC
Metabolite IDMMDBc0000031
Metabolite Identification
Common NameGlyoxylic acid
DescriptionGlyoxylic acid or oxoacetic acid is an organic compound that is both an aldehyde and a carboxylic acid. Glyoxylic acid is a liquid with a melting point of -93°C and a boiling point of 111°C. It is an intermediate of the glyoxylate cycle, which enables certain organisms to convert fatty acids into carbohydrates. The conjugate base of glyoxylic acid is known as glyoxylate (PMID: 16396466 ). In humans, glyoxylate is produced via two pathways: (1) through the oxidation of glycolate in peroxisomes and (2) through the catabolism of hydroxyproline in mitochondria. In the peroxisomes, glyoxylate is converted into glycine by glyoxylate aminotransferase (AGT1) or into oxalate by glycolate oxidase. In the mitochondria, glyoxylate is converted into glycine by mitochondrial glyoxylate aminotransferase AGT2 or into glycolate by glycolate reductase. A small amount of glyoxylate is converted into oxalate by cytoplasmic lactate dehydrogenase. Glyoxylic acid is found to be associated with primary hyperoxaluria I, which is an inborn error of metabolism. Under certain circumstances, glyoxylate can be a nephrotoxin and a metabotoxin. A nephrotoxin is a compound that causes damage to the kidney and kidney tissues. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. High levels of glyoxylate are involved in the development of hyperoxaluria, a key cause of nephrolithiasis (commonly known as kidney stones). Glyoxylate is both a substrate and inductor of sulfate anion transporter-1 (SAT-1), a gene responsible for oxalate transportation, allowing it to increase SAT-1 mRNA expression, and as a result oxalate efflux from the cell. The increased oxalate release allows the buildup of calcium oxalate in the urine, and thus the eventual formation of kidney stones. As an aldehyde, glyoxylate is also highly reactive and will modify proteins to form advanced glycation products (AGEs).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be20f2c58>


  Mrv1652309032023522D          

  5  4  0  0  0  0            999 V2000
   -0.6695    0.1223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3841   -0.2901    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6695    0.9474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0450   -0.2901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7595    0.1223    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  4  5  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000560be20f2c58>

HMDB0000119
     RDKit          3D
Glyoxylic acid
  7  6  0  0  0  0  0  0  0  0999 V2000
    1.4768   -0.7904   -0.6827 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0212    0.1407    0.0153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4045    0.3577    0.1124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8334    1.2923    0.8145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3383   -0.4315   -0.5449 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6984    0.7792    0.5432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6202   -1.3481   -0.2578 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  5  7  1  0
M  END
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3D SDF for #<Metabolite:0x0000560be20f2c58>


  Mrv1652309032023522D          

  5  4  0  0  0  0            999 V2000
   -0.6695    0.1223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3841   -0.2901    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6695    0.9474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0450   -0.2901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7595    0.1223    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  4  5  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000031

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C2H2O3/c3-1-2(4)5/h1H,(H,4,5)

> <INCHI_KEY>
HHLFWLYXYJOTON-UHFFFAOYSA-N

> <FORMULA>
C2H2O3

> <MOLECULAR_WEIGHT>
74.0355

> <EXACT_MASS>
74.00039393

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
5.350371249097624

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-oxoacetic acid

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
-0.13367503833333333

> <ALOGPS_LOGS>
0.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.605312628420254

> <JCHEM_PKA_STRONGEST_BASIC>
-9.240766856996258

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
13.5

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.24e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glyoxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000560be20f2c58>

HMDB0000119
     RDKit          3D
Glyoxylic acid
  7  6  0  0  0  0  0  0  0  0999 V2000
    1.4768   -0.7904   -0.6827 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0212    0.1407    0.0153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4045    0.3577    0.1124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8334    1.2923    0.8145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3383   -0.4315   -0.5449 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6984    0.7792    0.5432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6202   -1.3481   -0.2578 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  5  7  1  0
M  END
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PDB for #<Metabolite:0x0000560be20f2c58>

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0      -1.250   0.228   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -2.584  -0.542   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -1.250   1.768   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.084  -0.542   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.418   0.228   0.000  0.00  0.00           O+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5                                                       
CONECT    5    4                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for #<Metabolite:0x0000560be20f2c58>

COMPND    HMDB0000119
HETATM    1  O1  UNL     1       1.477  -0.790  -0.683  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.021   0.141   0.015  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.404   0.358   0.112  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.833   1.292   0.815  1.00  0.00           O  
HETATM    5  O3  UNL     1      -1.338  -0.431  -0.545  1.00  0.00           O  
HETATM    6  H1  UNL     1       1.698   0.779   0.543  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.620  -1.348  -0.258  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    6
CONECT    3    4    4    5
CONECT    5    7
END
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SMILES for #<Metabolite:0x0000560be20f2c58>

OC(=O)C=O
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INCHI for #<Metabolite:0x0000560be20f2c58>

InChI=1S/C2H2O3/c3-1-2(4)5/h1H,(H,4,5)
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Synonyms
ValueSource
alpha-Ketoacetic acidChEBI
Formylformic acidChEBI
GlyoxalateChEBI
GlyoxalsaeureChEBI
GlyoxylateChEBI
GlyoxylsaeureChEBI
Oxalaldehydic acidChEBI
Oxoethanoic acidChEBI
a-KetoacetateGenerator
a-Ketoacetic acidGenerator
alpha-KetoacetateGenerator
Α-ketoacetateGenerator
Α-ketoacetic acidGenerator
FormylformateGenerator
Glyoxalic acidGenerator
OxalaldehydateGenerator
OxoethanoateGenerator
OxoacetateHMDB
Oxoacetic acidHMDB
Glyoxylic acid, 2-(14)C-labeledHMDB
Glyoxylic acid, sodium saltHMDB
Glyoxylic acid, sodium salt, 2-(14)C-labeledHMDB
Glyoxylic acid, 14c2-labeledHMDB
Glyoxylic acid, calcium saltHMDB
Glyoxylic acid, sodium salt, 14C-labeledHMDB
Molecular FormulaC2H2O3
Average Mass74.0355
Monoisotopic Mass74.00039393
IUPAC Name2-oxoacetic acid
Traditional Nameglyoxylic acid
CAS Registry Number298-12-4
SMILES
OC(=O)C=O
InChI Identifier
InChI=1S/C2H2O3/c3-1-2(4)5/h1H,(H,4,5)
InChI KeyHHLFWLYXYJOTON-UHFFFAOYSA-N