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Showing NP-Card for 2-Phosphoglycolate (NP0055014)

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Record Information
Version2.0
Created at2022-04-28 01:11:15 UTC
Updated at2022-04-28 01:11:15 UTC
NP-MRD IDNP0055014
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Phosphoglycolate
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. 2-Phosphoglycolate is found in Mus musculus and Rhodobacter capsulatus. The O-phospho derivative of glycolic acid.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0055014 (2-Phosphoglycolate)


  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 NP0055014 (2-Phosphoglycolate)

     RDKit          3D

 14 13  0  0  0  0  0  0  0  0999 V2000
   -2.6978   -1.2924    1.7692 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1971   -0.7209    0.7769 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0198   -0.2987   -0.2461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7328   -0.5163    0.7341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3801    0.1298   -0.4397 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2511    0.4143   -0.5977 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.4677    1.8220   -1.1137 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8458   -0.6160   -1.8296 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1067    0.1611    0.8453 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8506   -0.4554   -1.2254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4667    0.1842    1.5684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2328   -1.4741    0.8935 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8359   -0.5864   -1.7435 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0705    0.1810    0.6083 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  8  1  0
  6  9  1  0
  6  7  2  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 NP0055014 (2-Phosphoglycolate)


  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>
NP0055014

> <DATABASE_NAME>
NP-MRD

> <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 NP0055014 (2-Phosphoglycolate)

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PDB for NP0055014 (2-Phosphoglycolate)
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 NP0055014 (2-Phosphoglycolate)
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SMILES for NP0055014 (2-Phosphoglycolate)
OC(=O)COP(O)(O)=O
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INCHI for NP0055014 (2-Phosphoglycolate)
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 JSmol
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 Mass156.0313 Da
Monoisotopic Mass155.98237 Da
IUPAC Name2-(phosphonooxy)acetic acid
Traditional Namephosphoglycolate
CAS Registry NumberNot Available
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
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Mus musculusLOTUS Database
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Rhodobacter capsulatus--
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.3ALOGPS
logP-1.2ChemAxon
logS-0.93ALOGPS
pKa (Strongest Acidic)1.14ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area104.06 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity25.22 m³·mol⁻¹ChemAxon
Polarizability10.67 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0060148  
DrugBank IDDB02726  
Phenol Explorer Compound IDNot Available
FoodDB 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  
Good Scents IDNot Available
References
General ReferencesNot Available