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Showing metabocard for Phosphoglycolic acid (HMDB0000816)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:12 UTC
HMDB IDHMDB0000816
Secondary Accession Numbers
  • HMDB0060148
  • HMDB00816
  • HMDB60148
Metabolite Identification
Common NamePhosphoglycolic acid
DescriptionPhosphoglycolic acid, also known as phosphoglycolate or glycolate-2-p, belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain. Phosphoglycolic acid is a moderately acidic compound (based on its pKa). Phosphoglycolic acid exists in all living species, ranging from bacteria to humans. Outside of the human body, Phosphoglycolic acid has been detected, but not quantified in, several different foods, such as pomegranates, atlantic herrings, peachs, common verbena, and redcurrants. This could make phosphoglycolic acid a potential biomarker for the consumption of these foods. The O-phospho derivative of glycolic acid.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000816 (Phosphoglycolic acid)

  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 HMDB0000816 (Phosphoglycolic acid)

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 HMDB0000816 (Phosphoglycolic acid)

  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>
HMDB0000816

> <DATABASE_NAME>
hmdb

> <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 HMDB0000816 (Phosphoglycolic acid)

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 HMDB0000816 (Phosphoglycolic acid)

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 HMDB0000816 (Phosphoglycolic acid)

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 HMDB0000816 (Phosphoglycolic acid)

OC(=O)COP(O)(O)=O
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INCHI for HMDB0000816 (Phosphoglycolic acid)

InChI=1S/C2H5O6P/c3-2(4)1-8-9(5,6)7/h1H2,(H,3,4)(H2,5,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
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
Chemical FormulaC2H5O6P
Average Molecular Weight156.0313
Monoisotopic Molecular Weight155.982374404
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
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic phosphoric acids and derivatives
Sub ClassPhosphate esters
Direct ParentMonoalkyl phosphates
Alternative Parents
Substituents
  • Monoalkyl phosphate
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen LocationsNot Available
Tissue Locations
  • Bladder
  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Neuron
  • Pancreas
  • Placenta
  • Platelet
  • Prostate
  • Skeletal Muscle
  • Spleen
  • Testis
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02726
Phenol Explorer Compound IDNot Available
FooDB IDFDB030360
KNApSAcK IDC00007561
Chemspider ID514
KEGG Compound IDC00988
BioCyc IDCPD-67
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound529
PDB IDNot Available
ChEBI ID17150
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceCourtois, Jean. Action of periodic acid on hexosediphosphoric acid. Compt. rend. (1941), 212 1172-4. CAN 38:22678 AN 1944:22678
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Triosephosphate isomerase
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
TPI1
Uniprot ID:
P60174
Molecular weight:
26669.33
Enzyme Details
2. Phosphoglycolate phosphatase
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
PGP
Uniprot ID:
A6NDG6
Molecular weight:
34005.69
Reactions
Phosphoglycolic acid + Water → Glycolic acid + Phosphatedetails
Enzyme Details
3. Triosephosphate isomerase
General function:
Involved in catalytic activity
Specific function:
D-glyceraldehyde 3-phosphate = glycerone phosphate
Gene Name:
Not Available
Uniprot ID:
Q2QD09
Molecular weight:
26942.6