Np mrd loader

Showing NP-Card for α-glycerophosphorate (NP0213780)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version1.0
Created at2022-09-05 12:52:16 UTC
Updated at2022-09-05 12:52:16 UTC
NP-MRD IDNP0213780
Secondary Accession NumbersNone
Natural Product Identification
Common Nameα-glycerophosphorate
DescriptionGlycerol 1-monophosphate, also known as 1-glycerophosphoric acid or alpha-phosphoglycerol, belongs to the class of organic compounds known as glycerophosphates. Glycerophosphates are compounds containing a glycerol linked to a phosphate group. α-glycerophosphorate is found in Arabidopsis thaliana, Chlamydomonas reinhardtii, Lemna aequinoctialis, Musca domestica, Populus tremula and Synechococcus elongatus. It was first documented in 1984 (PMID: 6083437). Glycerol 1-monophosphate is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 22770225) (PMID: 29438107) (PMID: 1694860).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0213780 (α-glycerophosphorate)


  Mrv1652305221920472D          

 10  9  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 C   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
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  9  2  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
M  END
Download

3D MOL for NP0213780 (α-glycerophosphorate)

Download
3D SDF for NP0213780 (α-glycerophosphorate)

  Mrv1652305221920472D          

 10  9  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 C   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
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  9  2  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0213780

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
AWUCVROLDVIAJX-UHFFFAOYSA-N

> <FORMULA>
C3H9O6P

> <MOLECULAR_WEIGHT>
172.0737

> <EXACT_MASS>
172.013674532

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
13.450137666564107

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2,3-dihydroxypropoxy)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>
6.533552281214722

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5077547010974532

> <JCHEM_PKA_STRONGEST_BASIC>
-2.968964717967575

> <JCHEM_POLAR_SURFACE_AREA>
107.22000000000001

> <JCHEM_REFRACTIVITY>
31.389

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-glycerophosphate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0213780 (α-glycerophosphorate)
Download
PDB for NP0213780 (α-glycerophosphorate)
HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.160  -2.667   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       4.620  -0.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
CONECT    1    3    4                                                       
CONECT    2    3    9                                                       
CONECT    3    1    2    5                                                  
CONECT    4    1                                                            
CONECT    5    3                                                            
CONECT    6   10                                                            
CONECT    7   10                                                            
CONECT    8   10                                                            
CONECT    9    2   10                                                       
CONECT   10    6    7    8    9                                             
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

Download
3D PDB for NP0213780 (α-glycerophosphorate)
Download
SMILES for NP0213780 (α-glycerophosphorate)
OCC(O)COP(O)(O)=O
Download
INCHI for NP0213780 (α-glycerophosphorate)
InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)
Download
View in JSmol
Synonyms
ValueSource
1,2,3-Propanetriol, 1-(dihydrogen phosphate)ChEBI
1-GlycerophosphateChEBI
1-Glycerophosphoric acidChEBI
1-PhosphoglycerolChEBI
2,3-Dihydroxypropyl dihydrogen phosphateChEBI
2,3-Hydroxy-1-propyl dihydrogen phosphateChEBI
3-GlycerophosphateChEBI
alpha-Glycerophosphoric acidChEBI
alpha-PhosphoglycerolChEBI
D,L-alpha-Glycerol-phosphateChEBI
DL-Glycerol 1-phosphateChEBI
DL-Glycerol 3-phosphateChEBI
DL-Glyceryl 1-phosphateChEBI
Glycerol alpha-phosphateChEBI
PGChEBI
rac-Glycerol 1-phosphateChEBI
Glycerol 1-phosphateKegg
Glycerol-3-phosphateKegg
1,2,3-Propanetriol, 1-(dihydrogen phosphoric acid)Generator
2,3-Dihydroxypropyl dihydrogen phosphoric acidGenerator
2,3-Hydroxy-1-propyl dihydrogen phosphoric acidGenerator
3-Glycerophosphoric acidGenerator
a-GlycerophosphateGenerator
a-Glycerophosphoric acidGenerator
alpha-GlycerophosphateGenerator
Α-glycerophosphateGenerator
Α-glycerophosphoric acidGenerator
a-PhosphoglycerolGenerator
Α-phosphoglycerolGenerator
D,L-a-Glycerol-phosphateGenerator
D,L-a-Glycerol-phosphoric acidGenerator
D,L-alpha-Glycerol-phosphoric acidGenerator
D,L-Α-glycerol-phosphateGenerator
D,L-Α-glycerol-phosphoric acidGenerator
DL-Glycerol 1-phosphoric acidGenerator
DL-Glycerol 3-phosphoric acidGenerator
DL-Glyceryl 1-phosphoric acidGenerator
Glycerol a-phosphateGenerator
Glycerol a-phosphoric acidGenerator
Glycerol alpha-phosphoric acidGenerator
Glycerol α-phosphateGenerator
Glycerol α-phosphoric acidGenerator
rac-Glycerol 1-phosphoric acidGenerator
Glycerol 1-phosphoric acidGenerator
Glycerol-3-phosphoric acidGenerator
Glycerol 1-monophosphoric acidGenerator
alpha-Glycerophosphoric acid, 1,2,3-propanetriol-1-(18)O,3-(dihydrogen phosphate)-labeledMeSH
alpha-Glycerophosphoric acid, fe(+3) salt (3:2)MeSH
alpha-Glycerophosphoric acid, disodium saltMeSH
Disodium glycerophosphateMeSH
Glycerol 3-phosphateMeSH
alpha-Glycerophosphoric acid, fe saltMeSH
alpha-Glycerophosphoric acid, monocalcium salt (S)-isomerMeSH
alpha-Glycerophosphoric acid, monomagnesium saltMeSH
alpha-Glycerophosphoric acid, sodium saltMeSH
alpha-Glycerophosphoric acid, (R)-isomerMeSH
alpha-Glycerophosphoric acid, (S)-isomerMeSH
alpha-Glycerophosphoric acid, disodium salt hexahydrate(+-)-isomerMeSH
alpha-Glycerophosphoric acid, monocalcium saltMeSH
Sodium glycerophosphateMeSH
alpha-Glycerophosphoric acid, (DL)-isomerMeSH
alpha-Glycerophosphoric acid, 1,2,3-propanetriol-2-(18)O,3-(dihydrogen phosphate)-labeledMeSH
alpha-Glycerophosphoric acid, calcium saltMeSH
alpha-Glycerophosphoric acid, disodium salt (+-)-isomerMeSH
Chemical FormulaC3H9O6P
Average Mass172.0737 Da
Monoisotopic Mass172.01367 Da
IUPAC Name(2,3-dihydroxypropoxy)phosphonic acid
Traditional Nameα-glycerophosphate
CAS Registry NumberNot Available
SMILES
OCC(O)COP(O)(O)=O
InChI Identifier
InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)
InChI KeyAWUCVROLDVIAJX-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaLOTUS Database
Chlamydomonas reinhardtiiLOTUS Database
Lemna aequinoctialisLOTUS Database
Musca domesticaLOTUS Database
Populus tremulaLOTUS Database
Synechococcus elongatusLOTUS 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-3-phosphate
    • 

  • Monoalkyl phosphate
    • 

  • Alkyl phosphate
    • 

  • Phosphoric acid ester
    • 

  • Organic phosphoric acid derivative
    • 

  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • 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)1.51ChemAxon
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
Polarizability13.45 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021800  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC03189  
BioCyc IDGlycerol-1-phosphate  
BiGG IDNot Available
Wikipedia LinkGlycerol_1-phosphate  
METLIN IDNot Available
PubChem Compound754  
PDB IDNot Available
ChEBI ID14336  
Good Scents IDNot Available
References
General References
  1. Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C: Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem. 2012 Aug 7;84(15):6429-37. doi: 10.1021/ac300829f. Epub 2012 Jul 17. [PubMed:22770225  ] 
  2. Ostrov DA, Alkanani A, McDaniel KA, Case S, Baschal EE, Pyle L, Ellis S, Pollinger B, Seidl KJ, Shah VN, Garg SK, Atkinson MA, Gottlieb PA, Michels AW: Methyldopa blocks MHC class II binding to disease-specific antigens in autoimmune diabetes. J Clin Invest. 2018 May 1;128(5):1888-1902. doi: 10.1172/JCI97739. Epub 2018 Apr  3. [PubMed:29438107  ] 
  3. Levy RA, Gharavi AE, Sammaritano LR, Habina L, Lockshin MD: Fatty acid chain is a critical epitope for antiphospholipid antibody. J Clin Immunol. 1990 May;10(3):141-5. doi: 10.1007/BF00917913. [PubMed:1694860  ] 
  4. Hamada S, Furuta T, Okahashi N, Nisizawa T, Yamamoto T, Chiba J: Characterization of a monoclonal antibody specific for lipoteichoic acid from various gram-positive bacteria. Microbiol Immunol. 1984;28(9):1009-21. doi: 10.1111/j.1348-0421.1984.tb00757.x. [PubMed:6083437  ] 
  5. LOTUS database [Link]