Showing metabocard for Hydroxypropanedioic acid (MMDBc0000807)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 22:03:28 UTC
Update Date2024-04-30 19:33:44 UTC
Metabolite IDMMDBc0000807
Metabolite Identification
Common NameHydroxypropanedioic acid
DescriptionHydroxypropanedioic acid is found in potato. Tartronic acid or 2-hydroxymalonic acid is a dicarboxylic acid with the structural formula of HOOCCH(OH)COOH. (Wikipedia ). Hydroxypropanedioic acid has been identified in the human placenta (PMID: 32033212 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9250a1c0b8>


  Mrv1652305062021452D          

  8  7  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   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  1  1  0  0  0  0
  5  2  2  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9250a1c0b8>

HMDB0035227
     RDKit          3D
Hydroxypropanedioic acid
 12 11  0  0  0  0  0  0  0  0999 V2000
    1.8053   -0.8106   -0.9713 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3142   -0.0805   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0341    0.1683    1.0514 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0246    0.5093   -0.2781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4041    1.2989    0.8166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9829   -0.6119   -0.4509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8025   -1.4286   -1.3876 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0458   -0.7350    0.4143 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4773   -0.5666    1.6150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0853    1.1198   -1.2253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3432    2.2609    0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9424   -1.1240    0.0956 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  2  0
  6  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  8 12  1  0
M  END
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3D SDF for #<Metabolite:0x00007f9250a1c0b8>


  Mrv1652305062021452D          

  8  7  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   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  1  1  0  0  0  0
  5  2  2  0  0  0  0
  6  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  3  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000807

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H4O5/c4-1(2(5)6)3(7)8/h1,4H,(H,5,6)(H,7,8)

> <INCHI_KEY>
ROBFUDYVXSDBQM-UHFFFAOYSA-N

> <FORMULA>
C3H4O5

> <MOLECULAR_WEIGHT>
120.0609

> <EXACT_MASS>
120.005873238

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.960469502826717

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxypropanedioic acid

> <ALOGPS_LOGP>
-1.01

> <JCHEM_LOGP>
-1.0462757289999998

> <ALOGPS_LOGS>
0.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.791393825073156

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.156503841175261

> <JCHEM_PKA_STRONGEST_BASIC>
-4.856106978575348

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
20.326

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.82e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tartronic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9250a1c0b8>

HMDB0035227
     RDKit          3D
Hydroxypropanedioic acid
 12 11  0  0  0  0  0  0  0  0999 V2000
    1.8053   -0.8106   -0.9713 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3142   -0.0805   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0341    0.1683    1.0514 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0246    0.5093   -0.2781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4041    1.2989    0.8166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9829   -0.6119   -0.4509 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8025   -1.4286   -1.3876 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0458   -0.7350    0.4143 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4773   -0.5666    1.6150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0853    1.1198   -1.2253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3432    2.2609    0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9424   -1.1240    0.0956 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  2  0
  6  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  8 12  1  0
M  END
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PDB for #<Metabolite:0x00007f9250a1c0b8>

HEADER    PROTEIN                                 06-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-20         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.000   2.667   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.310  -1.334   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
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1                                                            
CONECT    5    2                                                            
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    3                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00007f9250a1c0b8>

COMPND    HMDB0035227
HETATM    1  O1  UNL     1       1.805  -0.811  -0.971  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.314  -0.080  -0.092  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.034   0.168   1.051  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.025   0.509  -0.278  1.00  0.00           C  
HETATM    5  O3  UNL     1      -0.404   1.299   0.817  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.983  -0.612  -0.451  1.00  0.00           C  
HETATM    7  O4  UNL     1      -0.803  -1.429  -1.388  1.00  0.00           O  
HETATM    8  O5  UNL     1      -2.046  -0.735   0.414  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.477  -0.567   1.615  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.085   1.120  -1.225  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.343   2.261   0.630  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.942  -1.124   0.096  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    6   10
CONECT    5   11
CONECT    6    7    7    8
CONECT    8   12
END
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SMILES for #<Metabolite:0x00007f9250a1c0b8>

OC(C(O)=O)C(O)=O
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INCHI for #<Metabolite:0x00007f9250a1c0b8>

InChI=1S/C3H4O5/c4-1(2(5)6)3(7)8/h1,4H,(H,5,6)(H,7,8)
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Synonyms
ValueSource
2-HydroxymalonateChEBI
2-Hydroxymalonic acidChEBI
2-Hydroxypropanedioic acidChEBI
2-Tartronic acidChEBI
Tartronic acidChEBI
Hydroxymalonic acidKegg
2-HydroxypropanedioateGenerator
2-TartronateGenerator
TartronateGenerator
HydroxymalonateGenerator
HydroxypropanedioateGenerator
Hydroxy-malonic acidHMDB
Propanedioic acid, hydroxy- (9ci)HMDB
Tartronic acid, 8ciHMDB
Molecular FormulaC3H4O5
Average Mass120.0609
Monoisotopic Mass120.005873238
IUPAC Name2-hydroxypropanedioic acid
Traditional Nametartronic acid
CAS Registry NumberNot Available
SMILES
OC(C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C3H4O5/c4-1(2(5)6)3(7)8/h1,4H,(H,5,6)(H,7,8)
InChI KeyROBFUDYVXSDBQM-UHFFFAOYSA-N