Showing metabocard for Glycerol 3-phosphate (MMDBc0000335)

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Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:28:58 UTC
Update Date2024-10-13 06:29:08 UTC
Metabolite IDMMDBc0000335
Metabolite 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fd5d8144168>

  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 #<Metabolite:0x00007fd5d8144168>

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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3D SDF for #<Metabolite:0x00007fd5d8144168>

  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>
MMDBc0000335

> <DATABASE_NAME>
MIME

> <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

$$$$
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3D-SDF for #<Metabolite:0x00007fd5d8144168>

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 #<Metabolite:0x00007fd5d8144168>

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 #<Metabolite:0x00007fd5d8144168>

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 #<Metabolite:0x00007fd5d8144168>

OC[C@@H](O)COP(O)(O)=O
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INCHI for #<Metabolite:0x00007fd5d8144168>

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
Molecular FormulaC3H9O6P
Average Mass172.0737
Monoisotopic Mass172.013674532
IUPAC Name[(2R)-2,3-dihydroxypropoxy]phosphonic acid
Traditional Name3-phosphoglycerol
CAS Registry NumberNot Available
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