Showing NP-Card for Glycerol 3-phosphate (NP0000128)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:13:03 UTC
NP-MRD IDNP0000128
Secondary Accession NumbersNone
Natural Product Identification
Common NameGlycerol 3-phosphate
DescriptionGlycerol 3-phosphate is a chemical intermediate in the glycolysis metabolic pathway. It is commonly confused with the similarly named glycerate 3-phosphate or glyceraldehyde 3-phosphate. Glycerol 3-phosphate is produced from glycerol, the triose sugar backbone of triglycerides and glycerophospholipids, by the enzyme glycerol kinase. Glycerol 3-phospate may then be converted by dehydrogenation to dihydroxyacetone phosphate (DHAP) by the enzyme glycerol-3-phosphate dehydrogenase. DHAP can then be rearranged into glyceraldehyde 3-phosphate (GA3P) by triose phosphate isomerase (TIM), and feed into glycolysis. The glycerol 3-phosphate shuttle is used to rapidly regenerate NAD+ in the brain and skeletal muscle cells of mammals (wikipedia).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000128 (Glycerol 3-phosphate)

  Mrv1652309032023532D          

 10  9  0  0  1  0            999 V2000
    1.7605   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.7145    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  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
M  END
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3D MOL for NP0000128 (Glycerol 3-phosphate)

HMDB0000126
     RDKit          3D
Glycerol 3-phosphate
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.6570   -0.5349    1.4044 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3094    0.3449    0.2279 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.1789    1.9489    0.7657 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4217    0.2536   -1.0088 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7414   -0.1130   -0.2867 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0221   -0.3714    0.8784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4006   -0.7926    0.5791 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4532   -1.9363   -0.1839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1227    0.3344   -0.1307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5310    0.5994   -1.3752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9373    2.5495    0.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8333   -0.6495   -1.0411 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5224   -1.1749    1.4656 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0517    0.5330    1.5154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9397   -0.9653    1.5288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9683   -2.6649    0.2036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0552    1.2740    0.4484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1879    0.0128   -0.2448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0168    1.3521   -1.7795 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 NP0000128 (Glycerol 3-phosphate)

  Mrv1652309032023532D          

 10  9  0  0  1  0            999 V2000
    1.7605   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.7145    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  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0000128

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H](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)/t3-/m1/s1

> <INCHI_KEY>
AWUCVROLDVIAJX-GSVOUGTGSA-N

> <FORMULA>
C3H9O6P

> <MOLECULAR_WEIGHT>
172.0737

> <EXACT_MASS>
172.013674532

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
13.581834516868902

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R)-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>
6.533552281214719

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5077547010974532

> <JCHEM_PKA_STRONGEST_BASIC>
-2.968964717967575

> <JCHEM_POLAR_SURFACE_AREA>
107.22

> <JCHEM_REFRACTIVITY>
31.389

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-phosphoglycerol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000128 (Glycerol 3-phosphate)

HMDB0000126
     RDKit          3D
Glycerol 3-phosphate
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.6570   -0.5349    1.4044 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3094    0.3449    0.2279 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.1789    1.9489    0.7657 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4217    0.2536   -1.0088 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7414   -0.1130   -0.2867 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0221   -0.3714    0.8784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4006   -0.7926    0.5791 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4532   -1.9363   -0.1839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1227    0.3344   -0.1307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5310    0.5994   -1.3752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9373    2.5495    0.0229 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8333   -0.6495   -1.0411 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5224   -1.1749    1.4656 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0517    0.5330    1.5154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9397   -0.9653    1.5288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9683   -2.6649    0.2036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0552    1.2740    0.4484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1879    0.0128   -0.2448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0168    1.3521   -1.7795 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
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PDB for NP0000128 (Glycerol 3-phosphate)

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  O   UNK     0       3.286  -3.437   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.954  -4.977   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.287  -2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       8.621  -3.437   0.000  0.00  0.00           O+0
HETATM    7  P   UNK     0       9.955  -2.667   0.000  0.00  0.00           P+0
HETATM    8  O   UNK     0      11.288  -1.897   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      10.725  -4.001   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       9.185  -1.334   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for NP0000128 (Glycerol 3-phosphate)

COMPND    HMDB0000126
HETATM    1  O1  UNL     1       2.657  -0.535   1.404  1.00  0.00           O  
HETATM    2  P1  UNL     1       2.309   0.345   0.228  1.00  0.00           P  
HETATM    3  O2  UNL     1       2.179   1.949   0.766  1.00  0.00           O  
HETATM    4  O3  UNL     1       3.422   0.254  -1.009  1.00  0.00           O  
HETATM    5  O4  UNL     1       0.741  -0.113  -0.287  1.00  0.00           O  
HETATM    6  C1  UNL     1       0.022  -0.371   0.878  1.00  0.00           C  
HETATM    7  C2  UNL     1      -1.401  -0.793   0.579  1.00  0.00           C  
HETATM    8  O5  UNL     1      -1.453  -1.936  -0.184  1.00  0.00           O  
HETATM    9  C3  UNL     1      -2.123   0.334  -0.131  1.00  0.00           C  
HETATM   10  O6  UNL     1      -1.531   0.599  -1.375  1.00  0.00           O  
HETATM   11  H1  UNL     1       1.937   2.549   0.023  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.833  -0.649  -1.041  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.522  -1.175   1.466  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.052   0.533   1.515  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.940  -0.965   1.529  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.968  -2.665   0.204  1.00  0.00           H  
HETATM   17  H7  UNL     1      -2.055   1.274   0.448  1.00  0.00           H  
HETATM   18  H8  UNL     1      -3.188   0.013  -0.245  1.00  0.00           H  
HETATM   19  H9  UNL     1      -2.017   1.352  -1.780  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 NP0000128 (Glycerol 3-phosphate)

OC[C@@H](O)COP(O)(O)=O
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INCHI for NP0000128 (Glycerol 3-phosphate)

InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)/t3-/m1/s1
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Synonyms
Chemical FormulaC3H9O6P
Average Mass172.0737 Da
Monoisotopic Mass172.01367 Da
IUPAC Name[(2R)-2,3-dihydroxypropoxy]phosphonic acid
Traditional Name3-phosphoglycerol
CAS Registry Number57-03-4
SMILES
OC[C@@H](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)/t3-/m1/s1
InChI KeyAWUCVROLDVIAJX-GSVOUGTGSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Escherichia coliKNApSAcK Database
Homo sapiens (Urine)KNApSAcK 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
StateSolid
Experimental Properties
PropertyValueReference
Melting Point102 - 104 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility30.6 g/LALOGPS
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
Polarizability13.58 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000126
DrugBank IDDB02515
Phenol Explorer Compound IDNot Available
FoodDB IDFDB031180
KNApSAcK IDC00007288
Chemspider ID388308
KEGG Compound IDC00093
BioCyc IDGLYCEROL-3P
BiGG ID137383
Wikipedia LinkGlycerol 3-phosphate
METLIN ID5161
PubChem Compound439162
PDB IDNot Available
ChEBI ID15978
Good Scents IDNot Available
References
General References