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Showing NP-Card for Glycerol 2-phosphate (NP0054955)

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Record Information
Version2.0
Created at2022-04-28 01:08:58 UTC
Updated at2022-04-28 01:08:58 UTC
NP-MRD IDNP0054955
Secondary Accession NumbersNone
Natural Product Identification
Common NameGlycerol 2-phosphate
DescriptionBeta-Glycerophosphoric acid, also known as β-glycerophosphate or BGA, belongs to the class of organic compounds known as glycerophosphates. Glycerophosphates are compounds containing a glycerol linked to a phosphate group. A glycerol monophosphate having the phosphate group at the 2-position. Beta-Glycerophosphoric acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Beta-Glycerophosphoric acid exists in all living species, ranging from bacteria to humans. Outside of the human body, beta-Glycerophosphoric acid has been detected, but not quantified in, milk (cow). Glycerol 2-phosphate is found in Arabidopsis thaliana, Chlamydomonas reinhardtii, Solanum lycopersicum and Trypanosoma brucei. Glycerol 2-phosphate was first documented in 2009 (PMID: 19429609). This could make beta-glycerophosphoric acid a potential biomarker for the consumption of these foods.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0054955 (Glycerol 2-phosphate)

      
  Mrv1652305101917272D          

 10  9  0  0  0  0            999 V2000
    0.4751    0.1381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1896   -0.2743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9040    0.1381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6185   -0.2743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1896   -1.0993    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9040   -1.5118    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.6185   -1.9243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4916   -2.2262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3165   -0.7973    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2393   -0.2742    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  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
  1 10  1  0  0  0  0
M  END
Download

3D MOL for NP0054955 (Glycerol 2-phosphate)

     RDKit          3D

 19 18  0  0  0  0  0  0  0  0999 V2000
    1.7090   -0.9267    1.7879 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0994   -0.6709    0.3752 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.4033    0.4348    0.3920 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7018   -2.1131   -0.2784 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8515   -0.1169   -0.5925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3371    0.0647    0.0700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8417    1.5081   -0.0557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0467    1.5460    0.6596 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3931   -0.7931   -0.6257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6235   -0.6372    0.0196 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0377    1.3178    0.1442 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8395   -2.0682   -1.2456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3140   -0.1744    1.1350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1516    2.1958    0.4751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0273    1.7765   -1.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5697    2.3479    0.4901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0940   -1.8554   -0.6266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5299   -0.4690   -1.6755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7136   -1.3669    0.6501 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  9  1  0
  9 10  1  0
  6  5  1  0
  5  2  1  0
  2  3  1  0
  2  4  1  0
  2  1  2  0
  8 16  1  0
  7 14  1  0
  7 15  1  0
  6 13  1  0
  9 17  1  0
  9 18  1  0
 10 19  1  0
  3 11  1  0
  4 12  1  0
M  END
Download

3D SDF for NP0054955 (Glycerol 2-phosphate)

      
  Mrv1652305101917272D          

 10  9  0  0  0  0            999 V2000
    0.4751    0.1381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1896   -0.2743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9040    0.1381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6185   -0.2743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1896   -1.0993    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9040   -1.5118    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.6185   -1.9243    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4916   -2.2262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3165   -0.7973    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2393   -0.2742    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  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
  1 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0054955

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC(CO)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H9O6P/c4-1-3(2-5)9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)

> <INCHI_KEY>
DHCLVCXQIBBOPH-UHFFFAOYSA-N

> <FORMULA>
C3H9O6P

> <MOLECULAR_WEIGHT>
172.0737

> <EXACT_MASS>
172.013674532

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
13.288127184427333

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1,3-dihydroxypropan-2-yl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-1.84

> <JCHEM_LOGP>
-1.9625800539999998

> <ALOGPS_LOGS>
-0.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.165546869512347

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.134625237612609

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9891179827681142

> <JCHEM_POLAR_SURFACE_AREA>
107.22

> <JCHEM_REFRACTIVITY>
31.389

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.07e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-glycerophosphorate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0054955 (Glycerol 2-phosphate)

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PDB for NP0054955 (Glycerol 2-phosphate)
HEADER    PROTEIN                                 10-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAY-19         0                                  
HETATM    1  C   UNK     0       0.887   0.258   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.221  -0.512   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.554   0.258   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.888  -0.512   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.221  -2.052   0.000  0.00  0.00           O+0
HETATM    6  P   UNK     0       3.554  -2.822   0.000  0.00  0.00           P+0
HETATM    7  O   UNK     0       4.888  -3.592   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.784  -4.156   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.324  -1.488   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -0.447  -0.512   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
CONECT   10    1                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0054955 (Glycerol 2-phosphate)
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SMILES for NP0054955 (Glycerol 2-phosphate)
OCC(CO)OP(O)(O)=O
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INCHI for NP0054955 (Glycerol 2-phosphate)
InChI=1S/C3H9O6P/c4-1-3(2-5)9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)
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View in JSmol
Synonyms
ValueSource
1,2,3-Propanetriol, 2-(dihydrogen phosphate)ChEBI
1,3-Hydroxy-2-propyl dihydrogen phosphateChEBI
2-GlycerophosphateChEBI
2-HYDROXY-1-(hydroxymethyl)ethyl dihydrogen phosphATEChEBI
beta-GlycerophosphateChEBI
1,2,3-Propanetriol, 2-(dihydrogen phosphoric acid)Generator
1,3-Hydroxy-2-propyl dihydrogen phosphoric acidGenerator
2-Glycerophosphoric acidGenerator
2-HYDROXY-1-(hydroxymethyl)ethyl dihydrogen phosphoric acidGenerator
b-GlycerophosphateGenerator
b-Glycerophosphoric acidGenerator
Β-glycerophosphateGenerator
Β-glycerophosphoric acidGenerator
beta-GlycerophosphorateHMDB
Glycerol-2-phosphateHMDB
beta-Glycerol phosphateHMDB
beta-Glycerophosphoric acid, calcium saltHMDB
beta-Glycerophosphoric acid, disodium saltHMDB
beta-Glycerophosphoric acid, sodium saltHMDB
beta-Glycerophosphoric acid, calcium salt (1:1)HMDB
beta-Glycerophosphoric acid, iron saltHMDB
beta-Glycerophosphoric acid, iron(3+) salt(3:2)HMDB
Glycerol 2-phosphoric acidHMDB
BGAHMDB
Glycerol 2-phosphateHMDB
Dihydrogen beta-glycerophosphateHMDB
Dihydrogen β-glycerophosphateHMDB
beta-Glyceryl phosphateHMDB
Β-glyceryl phosphateHMDB
beta-Glycerophosphoric acidChEBI
Glycerol-2-phosphoric acidGenerator
Chemical FormulaC3H9O6P
Average Mass172.0737 Da
Monoisotopic Mass172.01367 Da
IUPAC Name[(1,3-dihydroxypropan-2-yl)oxy]phosphonic acid
Traditional Nameβ-glycerophosphorate
CAS Registry NumberNot Available
SMILES
OCC(CO)OP(O)(O)=O
InChI Identifier
InChI=1S/C3H9O6P/c4-1-3(2-5)9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)
InChI KeyDHCLVCXQIBBOPH-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
Arabidopsis thalianaPlant
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
Chlamydomonas reinhardtiiLOTUS Database
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Solanum lycopersicumLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Trypanosoma bruceiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycerophosphates. Glycerophosphates are compounds containing a glycerol linked to a phosphate group.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassGlycerophospholipids  
Sub ClassGlycerophosphates  
Direct ParentGlycerophosphates  
Alternative Parents
Substituents
  • Sn-glycerol-2-phosphate
    • 

  • Monoalkyl phosphate
    • 

  • Alkyl phosphate
    • 

  • Phosphoric acid ester
    • 

  • Organic phosphoric acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • 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-1.8ALOGPS
logP-2ChemAxon
logS-0.75ALOGPS
pKa (Strongest Acidic)1.13ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area107.22 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.39 m³·mol⁻¹ChemAxon
Polarizability13.29 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002520  
DrugBank IDDB01779  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023021  
KNApSAcK IDC00007407  
Chemspider ID2431  
KEGG Compound IDC02979  
BioCyc IDCPD-536  
BiGG IDNot Available
Wikipedia LinkGlycerol_2-phosphate  
METLIN ID6708  
PubChem Compound2526  
PDB IDNot Available
ChEBI ID17270  
Good Scents IDNot Available
References
General References
  1. Yang K, Wang M, Metcalf WW: Uptake of glycerol-2-phosphate via the ugp-encoded transporter in Escherichia coli K-12. J Bacteriol. 2009 Jul;191(14):4667-70. doi: 10.1128/JB.00235-09. Epub 2009 May 8. [PubMed:19429609  ]