Showing metabocard for Phosphoglycolic acid (MMDBc0029801)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:42:12 UTC
Update Date2022-08-31 17:18:19 UTC
Metabolite IDMMDBc0029801
Metabolite Identification
Common NamePhosphoglycolic acid
Description2-Phosphoglycolic acid is a substrate for 2-phosphoglycolate phosphatase from Escherichia coli, which is encoded by the gph gene. It is converted to glycolic acid which is involved in general two-carbon metabolism. This housekeeping enzyme is involved in the dissimilation of the intracellular 2-phosphoglycolate formed in the DNA repair of 3'-phosphoglycolate ends.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f5a63469230>


  Mrv1652305231920412D          

  9  8  0  0  0  0            999 V2000
   -0.1914   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f5a63469230>

HMDB0000816
     RDKit          3D
Phosphoglycolic acid
 14 13  0  0  0  0  0  0  0  0999 V2000
    2.9883   -1.4421    0.7451 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1890   -0.6289    0.2095 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7618    0.3608   -0.5835 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7190   -0.7271    0.4171 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1181    0.2872   -0.2875 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5616    0.2855   -0.1326 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.0860   -0.9021   -0.9042 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9688    0.0838    1.5192 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2380    1.7345   -0.6261 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0528    1.2425   -0.1664 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4862   -0.7092    1.5047 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943   -1.7444    0.0694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9697    0.0967    1.5297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8853    2.0628   -1.4891 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  2  0
  6  8  1  0
  6  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  8 13  1  0
  9 14  1  0
M  END
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3D SDF for #<Metabolite:0x00007f5a63469230>


  Mrv1652305231920412D          

  9  8  0  0  0  0            999 V2000
   -0.1914   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029801

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C2H5O6P/c3-2(4)1-8-9(5,6)7/h1H2,(H,3,4)(H2,5,6,7)

> <INCHI_KEY>
ASCFNMCAHFUBCO-UHFFFAOYSA-N

> <FORMULA>
C2H5O6P

> <MOLECULAR_WEIGHT>
156.0313

> <EXACT_MASS>
155.982374404

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.672348907073108

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(phosphonooxy)acetic acid

> <ALOGPS_LOGP>
-2.26

> <JCHEM_LOGP>
-1.1641597916666666

> <ALOGPS_LOGS>
-0.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.599355522037208

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.143159703328946

> <JCHEM_POLAR_SURFACE_AREA>
104.06

> <JCHEM_REFRACTIVITY>
25.218799999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.84e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
phosphoglycolate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f5a63469230>

HMDB0000816
     RDKit          3D
Phosphoglycolic acid
 14 13  0  0  0  0  0  0  0  0999 V2000
    2.9883   -1.4421    0.7451 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1890   -0.6289    0.2095 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7618    0.3608   -0.5835 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7190   -0.7271    0.4171 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1181    0.2872   -0.2875 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5616    0.2855   -0.1326 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.0860   -0.9021   -0.9042 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9688    0.0838    1.5192 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2380    1.7345   -0.6261 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0528    1.2425   -0.1664 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4862   -0.7092    1.5047 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3943   -1.7444    0.0694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9697    0.0967    1.5297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8853    2.0628   -1.4891 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  2  0
  6  8  1  0
  6  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  8 13  1  0
  9 14  1  0
M  END
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PDB for #<Metabolite:0x00007f5a63469230>

HEADER    PROTEIN                                 23-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAY-19         0                                  
HETATM    1  O   UNK     0      -0.357  -1.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.976  -2.104   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.976  -3.644   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.644  -2.104   0.000  0.00  0.00           O+0
HETATM    6  P   UNK     0       4.977  -1.334   0.000  0.00  0.00           P+0
HETATM    7  O   UNK     0       6.311  -0.564   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.747  -2.667   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.207   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x00007f5a63469230>

COMPND    HMDB0000816
HETATM    1  O1  UNL     1       2.988  -1.442   0.745  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.189  -0.629   0.209  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.762   0.361  -0.583  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.719  -0.727   0.417  1.00  0.00           C  
HETATM    5  O3  UNL     1       0.118   0.287  -0.288  1.00  0.00           O  
HETATM    6  P1  UNL     1      -1.562   0.285  -0.133  1.00  0.00           P  
HETATM    7  O4  UNL     1      -2.086  -0.902  -0.904  1.00  0.00           O  
HETATM    8  O5  UNL     1      -1.969   0.084   1.519  1.00  0.00           O  
HETATM    9  O6  UNL     1      -2.238   1.735  -0.626  1.00  0.00           O  
HETATM   10  H1  UNL     1       3.053   1.243  -0.166  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.486  -0.709   1.505  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.394  -1.744   0.069  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.970   0.097   1.530  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.885   2.063  -1.489  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5   11   12
CONECT    5    6
CONECT    6    7    7    8    9
CONECT    8   13
CONECT    9   14
END
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SMILES for #<Metabolite:0x00007f5a63469230>

OC(=O)COP(O)(O)=O
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INCHI for #<Metabolite:0x00007f5a63469230>

InChI=1S/C2H5O6P/c3-2(4)1-8-9(5,6)7/h1H2,(H,3,4)(H2,5,6,7)
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Synonyms
ValueSource
2-PhosphoglycolateChEBI
2-Phosphoglycolic acidGenerator
PhosphoglycolateGenerator
2-PhosphoglicolateMeSH
Glycolate-2-pMeSH
(Phosphonooxy)-acetateHMDB
(Phosphonooxy)-acetic acidHMDB
(Phosphonooxy)acetateHMDB
(Phosphonooxy)acetic acidHMDB
2-PhosphonatoglycolateHMDB
Glycolic acid di-H phosphateHMDB
Glycolic acid dihydrogen phosphateHMDB
Glycolic acid phosphateHMDB
GlycophosphorateHMDB
Glycophosphoric acidHMDB
Molecular FormulaC2H5O6P
Average Mass156.0313
Monoisotopic Mass155.982374404
IUPAC Name2-(phosphonooxy)acetic acid
Traditional Namephosphoglycolate
CAS Registry Number13147-57-4
SMILES
OC(=O)COP(O)(O)=O
InChI Identifier
InChI=1S/C2H5O6P/c3-2(4)1-8-9(5,6)7/h1H2,(H,3,4)(H2,5,6,7)
InChI KeyASCFNMCAHFUBCO-UHFFFAOYSA-N