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Showing NP-Card for DL-alpha-Glycerol phosphate (NP0002647)

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Record Information
Version2.0
Created at2020-11-23 18:26:00 UTC
Updated at2021-08-12 19:51:45 UTC
NP-MRD IDNP0002647
Secondary Accession NumbersNone
Natural Product Identification
Common NameDL-alpha-Glycerol phosphate
Provided ByBMRBBMRB logo
DescriptionSn-glycerol 1-phosphate, also known as sn-gro-1-p, belongs to the class of organic compounds known as glycerophosphates. Glycerophosphates are compounds containing a glycerol linked to a phosphate group. DL-alpha-Glycerol phosphate is found in Apis cerana and Musca domestica. DL-alpha-Glycerol phosphate was first documented in 1995 (PMID: 8586635). Based on a literature review a small amount of articles have been published on sn-glycerol 1-phosphate (PMID: 15066037) (PMID: 16428851) (PMID: 32047114) (PMID: 31282866) (PMID: 27795311).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002647 (DL-alpha-Glycerol phosphate)


     RDKit          2D

 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.9580   -2.3836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5040   -0.9540    0.0000 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.0499    0.4756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9336   -0.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0743   -1.4081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0337   -0.3970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1417    0.6141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2498    1.6252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1528   -0.4939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1639   -1.6020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0610    1.5837    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2552    0.9652    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5465   -1.1192    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9774    0.7111    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1307    1.7221    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9282    3.0903    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5762   -1.1663    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2608    0.5171    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6290   -1.2804    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  1
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  6
  6 14  1  0
  7 15  1  6
  8 16  1  0
  9 17  1  6
  9 18  1  0
 10 19  1  0
M  END
Download

3D MOL for NP0002647 (DL-alpha-Glycerol phosphate)

NP0002647
     RDKit          3D

 19 18  0  0  0  0  0  0  0  0999 V2000
   -3.2516   -0.1282   -1.0322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4665    0.1254    0.2222 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.0398    1.7559    0.2805 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4654   -0.1820    1.5576 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1171   -0.8658    0.3426 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0905   -0.4810   -0.5281 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1098   -0.0680    0.2817 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4443   -1.1093    1.1358 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2802    0.1746   -0.6631 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4099    0.5935    0.0144 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3640    2.2302   -0.5144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5070   -1.1657    1.6688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4211    0.3129   -1.2252 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1410   -1.3915   -1.1339 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8588    0.8301    0.8632 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7852   -1.8477    0.5537 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9913    0.8544   -1.4797 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4957   -0.8241   -1.1193 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2067    1.1862    0.7756 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
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  1
  8 16  1  0
  9 17  1  0
  9 18  1  0
 10 19  1  0
M  END
Download

3D SDF for NP0002647 (DL-alpha-Glycerol phosphate)


     RDKit          2D

 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.9580   -2.3836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5040   -0.9540    0.0000 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.0499    0.4756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9336   -0.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0743   -1.4081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0337   -0.3970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1417    0.6141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2498    1.6252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1528   -0.4939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1639   -1.6020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0610    1.5837    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2552    0.9652    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5465   -1.1192    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9774    0.7111    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1307    1.7221    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9282    3.0903    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5762   -1.1663    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2608    0.5171    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6290   -1.2804    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  1
  2  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  6
  6 14  1  0
  7 15  1  6
  8 16  1  0
  9 17  1  6
  9 18  1  0
 10 19  1  0
M  END
> <DATABASE_ID>
NP0002647

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@](O)(CO)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)/t3-/m0/s1

> <INCHI_KEY>
AWUCVROLDVIAJX-VKHMYHEASA-N

> <FORMULA>
C3H9O6P

> <MOLECULAR_WEIGHT>
172.0737

> <EXACT_MASS>
172.013674532

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
13.446752984898623

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-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>
glycerophosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002647 (DL-alpha-Glycerol phosphate)

NP0002647
     RDKit          3D

 19 18  0  0  0  0  0  0  0  0999 V2000
   -3.2516   -0.1282   -1.0322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4665    0.1254    0.2222 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.0398    1.7559    0.2805 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4654   -0.1820    1.5576 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1171   -0.8658    0.3426 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0905   -0.4810   -0.5281 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1098   -0.0680    0.2817 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4443   -1.1093    1.1358 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2802    0.1746   -0.6631 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4099    0.5935    0.0144 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3640    2.2302   -0.5144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5070   -1.1657    1.6688 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4211    0.3129   -1.2252 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1410   -1.3915   -1.1339 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8588    0.8301    0.8632 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7852   -1.8477    0.5537 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9913    0.8544   -1.4797 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4957   -0.8241   -1.1193 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2067    1.1862    0.7756 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
  2  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  1
  8 16  1  0
  9 17  1  0
  9 18  1  0
 10 19  1  0
M  END
Download

PDB for NP0002647 (DL-alpha-Glycerol phosphate)

HEADER    PROTEIN                                 31-MAY-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   31-MAY-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   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
HETATM   11  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    3    9                                                       
CONECT    3    1    2    5   11                                             
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                                             
CONECT   11    3                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for NP0002647 (DL-alpha-Glycerol phosphate)

COMPND    NP0002647
HETATM    1  O1  UNL     1      -3.252  -0.128  -1.032  1.00  0.00           O  
HETATM    2  P1  UNL     1      -2.466   0.125   0.222  1.00  0.00           P  
HETATM    3  O2  UNL     1      -2.040   1.756   0.280  1.00  0.00           O  
HETATM    4  O3  UNL     1      -3.465  -0.182   1.558  1.00  0.00           O  
HETATM    5  O4  UNL     1      -1.117  -0.866   0.343  1.00  0.00           O  
HETATM    6  C1  UNL     1      -0.090  -0.481  -0.528  1.00  0.00           C  
HETATM    7  C2  UNL     1       1.110  -0.068   0.282  1.00  0.00           C  
HETATM    8  O5  UNL     1       1.444  -1.109   1.136  1.00  0.00           O  
HETATM    9  C3  UNL     1       2.280   0.175  -0.663  1.00  0.00           C  
HETATM   10  O6  UNL     1       3.410   0.594   0.014  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.364   2.230  -0.514  1.00  0.00           H  
HETATM   12  H2  UNL     1      -3.507  -1.166   1.669  1.00  0.00           H  
HETATM   13  H3  UNL     1      -0.421   0.313  -1.225  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.141  -1.392  -1.134  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.859   0.830   0.863  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.785  -1.848   0.554  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.991   0.854  -1.480  1.00  0.00           H  
HETATM   18  H8  UNL     1       2.496  -0.824  -1.119  1.00  0.00           H  
HETATM   19  H9  UNL     1       3.207   1.186   0.776  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4    5
CONECT    3   11
CONECT    4   12
CONECT    5    6
CONECT    6    7   13   14
CONECT    7    8    9   15
CONECT    8   16
CONECT    9   10   17   18
CONECT   10   19
END
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SMILES for NP0002647 (DL-alpha-Glycerol phosphate)

[H][C@](O)(CO)COP(O)(O)=O
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INCHI for NP0002647 (DL-alpha-Glycerol phosphate)

InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)/t3-/m0/s1
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View in JSmol
Synonyms
ValueSource
D-(Glycerol 3-phosphate)ChEBI
L-(Glycerol 1-phosphate)ChEBI
L-Glycerol 1-phosphateChEBI
sn-GLYCEROL-1-phosphATEChEBI
sn-Gro-1-pChEBI
D-(Glycerol 3-phosphoric acid)Generator
L-(Glycerol 1-phosphoric acid)Generator
L-Glycerol 1-phosphoric acidGenerator
sn-GLYCEROL-1-phosphoric acidGenerator
sn-Glycerol 1-phosphoric acidGenerator
Chemical FormulaC3H9O6P
Average Mass172.0737 Da
Monoisotopic Mass172.01367 Da
IUPAC Name[(2S)-2,3-dihydroxypropoxy]phosphonic acid
Traditional Nameglycerophosphate
CAS Registry NumberNot Available
SMILES
[H][C@](O)(CO)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)/t3-/m0/s1
InChI KeyAWUCVROLDVIAJX-VKHMYHEASA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Apis ceranaLOTUS Database
Musca domesticaLOTUS 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 IDNot Available
KNApSAcK IDNot Available
Chemspider ID388409
KEGG Compound IDC00623
BioCyc IDSN-GLYCEROL-1-PHOSPHATE
BiGG IDNot Available
Wikipedia LinkGlycerol 1-phosphate
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID16221
Good Scents IDNot Available
References
General References
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