Showing metabocard for Glyceric acid (MMDBc0000041)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:28:13 UTC
Update Date2022-08-30 23:13:59 UTC
Metabolite IDMMDBc0000041
Metabolite Identification
Common NameGlyceric acid
DescriptionGlyceric acid is a colourless syrupy acid, obtained from oxidation of glycerol. It is a compound that is secreted excessively in the urine by patients suffering from D-glyceric aciduria, an inborn error of metabolism, and D-glycerate anemia. Deficiency of human glycerate kinase leads to D-glycerate acidemia/D-glyceric aciduria. Symptoms of the disease include progressive neurological impairment, hypotonia, seizures, failure to thrive, and metabolic acidosis. At sufficiently high levels, glyceric acid can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Glyceric acid is an organic acid. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart abnormalities, seizures, coma, and possibly death. These are also the characteristic symptoms of untreated glyceric aciduria. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures. Elevated values may also be due to microbial sources such as yeast (Aspergillus, Penicillium, probably Candida) or due to dietary sources containing glycerol (glycerine). Glyceric acid is isolated from various plants (e.g. brassicas, pulses, and Vicia faba).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be26cd150>

      
  Mrv1652309032023542D          

  7  6  0  0  0  0            999 V2000
10000.0234 9999.7990    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.308710000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5939 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.308710001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.738110000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4559 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.0234 9998.9737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  1  1  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000560be26cd150>

HMDB0000139
     RDKit          3D
Glyceric acid
 13 12  0  0  0  0  0  0  0  0999 V2000
    0.7473    0.4350    2.2873 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9500    0.2125    1.0629 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0845   -0.4463    0.6526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0365    0.6630    0.0767 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1107    1.3055    0.6709 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4693   -0.5298   -0.7473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1232   -1.4505    0.0629 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5674   -0.2581   -0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4397    1.3811   -0.6113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5616    1.8640   -0.0319 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4443   -1.0275   -1.1260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1498   -0.2275   -1.5701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7820   -1.9214   -0.5067 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  1  0
  3  8  1  0
  4  9  1  6
  5 10  1  0
  6 11  1  0
  6 12  1  0
  7 13  1  0
M  END
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3D SDF for #<Metabolite:0x0000560be26cd150>

      
  Mrv1652309032023542D          

  7  6  0  0  0  0            999 V2000
10000.0234 9999.7990    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.308710000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5939 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.308710001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.738110000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4559 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.0234 9998.9737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  1  1  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000041

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)/t2-/m1/s1

> <INCHI_KEY>
RBNPOMFGQQGHHO-UWTATZPHSA-N

> <FORMULA>
C3H6O4

> <MOLECULAR_WEIGHT>
106.0773

> <EXACT_MASS>
106.02660868

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
8.95589682155052

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2,3-dihydroxypropanoic acid

> <ALOGPS_LOGP>
-1.72

> <JCHEM_LOGP>
-1.5187394846666669

> <ALOGPS_LOGS>
0.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.495349861440904

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4186061267841343

> <JCHEM_PKA_STRONGEST_BASIC>
-3.042760876836586

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
20.383499999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.39e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycerate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000560be26cd150>

HMDB0000139
     RDKit          3D
Glyceric acid
 13 12  0  0  0  0  0  0  0  0999 V2000
    0.7473    0.4350    2.2873 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9500    0.2125    1.0629 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0845   -0.4463    0.6526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0365    0.6630    0.0767 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1107    1.3055    0.6709 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4693   -0.5298   -0.7473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1232   -1.4505    0.0629 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5674   -0.2581   -0.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4397    1.3811   -0.6113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5616    1.8640   -0.0319 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4443   -1.0275   -1.1260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1498   -0.2275   -1.5701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7820   -1.9214   -0.5067 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  1  0
  3  8  1  0
  4  9  1  6
  5 10  1  0
  6 11  1  0
  6 12  1  0
  7 13  1  0
M  END
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PDB for #<Metabolite:0x0000560be26cd150>

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0    8666.7108666.291   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8665.3768667.061   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8664.0428666.291   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8665.3768668.601   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8668.0448667.061   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8669.3848666.291   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8666.7108664.751   0.000  0.00  0.00           O+0
CONECT    1    2    5    7                                                  
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6                                                       
CONECT    6    5                                                            
CONECT    7    1                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for #<Metabolite:0x0000560be26cd150>

COMPND    HMDB0000139
HETATM    1  O1  UNL     1       0.747   0.435   2.287  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.950   0.213   1.063  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.084  -0.446   0.653  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.036   0.663   0.077  1.00  0.00           C  
HETATM    5  O3  UNL     1      -1.111   1.306   0.671  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.469  -0.530  -0.747  1.00  0.00           C  
HETATM    7  O4  UNL     1      -1.123  -1.451   0.063  1.00  0.00           O  
HETATM    8  H1  UNL     1       2.567  -0.258  -0.220  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.440   1.381  -0.611  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.562   1.864  -0.032  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.444  -1.028  -1.126  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.150  -0.228  -1.570  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.782  -1.921  -0.507  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    8
CONECT    4    5    6    9
CONECT    5   10
CONECT    6    7   11   12
CONECT    7   13
END
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SMILES for #<Metabolite:0x0000560be26cd150>

OC[C@@H](O)C(O)=O
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INCHI for #<Metabolite:0x0000560be26cd150>

InChI=1S/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)/t2-/m1/s1
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Synonyms
ValueSource
alpha,beta-Hydroxypropionic acidChEBI
D-GroAChEBI
R-Glyceric acidChEBI
GlycerateKegg
(R)-GlycerateKegg
a,b-HydroxypropionateGenerator
a,b-Hydroxypropionic acidGenerator
alpha,beta-HydroxypropionateGenerator
R-GlycerateGenerator
(R)-Glyceric acidGenerator
D-GlycerateHMDB
D-Glyceric acidHMDB
(2R)-2,3-Dihydroxypropanoic acidHMDB
(R)-2,3-Dihydroxypropanoic acidHMDB
D-2,3-Dihydroxypropanoic acidHMDB
Molecular FormulaC3H6O4
Average Mass106.0773
Monoisotopic Mass106.02660868
IUPAC Name(2R)-2,3-dihydroxypropanoic acid
Traditional Nameglycerate
CAS Registry Number473-81-4
SMILES
OC[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C3H6O4/c4-1-2(5)3(6)7/h2,4-5H,1H2,(H,6,7)/t2-/m1/s1
InChI KeyRBNPOMFGQQGHHO-UWTATZPHSA-N