Showing metabocard for Glycerol 2-phosphate (MMDBc0030316)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 00:03:08 UTC
Update Date2024-10-11 03:29:18 UTC
Metabolite IDMMDBc0030316
Metabolite Identification
Common NameGlycerol 2-phosphate
DescriptionGlycerol-2-phosphate is a component of glycerolipid metabolism. It is formed in minor quanitites, as the alpha glycerophosphorate is preferentially formed in this manner. Also used as a biological buffer (Sigma-Aldrich).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9258025e30>

      
  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
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3D MOL for #<Metabolite:0x00007f9258025e30>

HMDB0002520
     RDKit          3D
beta-Glycerophosphoric acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.0033    1.5134   -0.9920 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8785    0.5596    0.1565 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.9204    0.9981    1.4011 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2998   -0.9899   -0.3955 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2668    0.4530    0.7012 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4328   -0.2669   -0.2595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5781    0.5513   -0.8359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1251    1.7122   -1.4371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0246   -1.5412    0.3229 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9060   -1.2918    1.3566 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0217    1.9810    1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9794   -1.3850    0.2013 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1991   -0.5848   -1.1123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1420   -0.0270   -1.5935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3119    0.7760   -0.0211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6525    2.5024   -1.0923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2271   -2.2509    0.5625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6155   -2.0031   -0.5108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5535   -0.7063    2.0555 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
  6  9  1  0
  9 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  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:0x00007f9258025e30>

      
  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>
MMDBc0030316

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f9258025e30>

HMDB0002520
     RDKit          3D
beta-Glycerophosphoric acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.0033    1.5134   -0.9920 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8785    0.5596    0.1565 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.9204    0.9981    1.4011 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2998   -0.9899   -0.3955 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2668    0.4530    0.7012 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4328   -0.2669   -0.2595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5781    0.5513   -0.8359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1251    1.7122   -1.4371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0246   -1.5412    0.3229 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9060   -1.2918    1.3566 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0217    1.9810    1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9794   -1.3850    0.2013 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1991   -0.5848   -1.1123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1420   -0.0270   -1.5935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3119    0.7760   -0.0211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6525    2.5024   -1.0923 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2271   -2.2509    0.5625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6155   -2.0031   -0.5108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5535   -0.7063    2.0555 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
  6  9  1  0
  9 10  1  0
  3 11  1  0
  4 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  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:0x00007f9258025e30>

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 #<Metabolite:0x00007f9258025e30>

COMPND    HMDB0002520
HETATM    1  O1  UNL     1       2.003   1.513  -0.992  1.00  0.00           O  
HETATM    2  P1  UNL     1       1.878   0.560   0.156  1.00  0.00           P  
HETATM    3  O2  UNL     1       2.920   0.998   1.401  1.00  0.00           O  
HETATM    4  O3  UNL     1       2.300  -0.990  -0.396  1.00  0.00           O  
HETATM    5  O4  UNL     1       0.267   0.453   0.701  1.00  0.00           O  
HETATM    6  C1  UNL     1      -0.433  -0.267  -0.260  1.00  0.00           C  
HETATM    7  C2  UNL     1      -1.578   0.551  -0.836  1.00  0.00           C  
HETATM    8  O5  UNL     1      -1.125   1.712  -1.437  1.00  0.00           O  
HETATM    9  C3  UNL     1      -1.025  -1.541   0.323  1.00  0.00           C  
HETATM   10  O6  UNL     1      -1.906  -1.292   1.357  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.022   1.981   1.492  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.979  -1.385   0.201  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.199  -0.585  -1.112  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.142  -0.027  -1.593  1.00  0.00           H  
HETATM   15  H5  UNL     1      -2.312   0.776  -0.021  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.652   2.502  -1.092  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.227  -2.251   0.563  1.00  0.00           H  
HETATM   18  H8  UNL     1      -1.615  -2.003  -0.511  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.553  -0.706   2.056  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    9   13
CONECT    7    8   14   15
CONECT    8   16
CONECT    9   10   17   18
CONECT   10   19
END
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SMILES for #<Metabolite:0x00007f9258025e30>

OCC(CO)OP(O)(O)=O
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INCHI for #<Metabolite:0x00007f9258025e30>

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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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
Glycerol 2-phosphateMeSH
beta-Glycerol phosphateMeSH
beta-Glycerophosphoric acid, calcium saltMeSH
beta-Glycerophosphoric acid, calcium salt (1:1)MeSH
beta-Glycerophosphoric acid, disodium saltMeSH
beta-Glycerophosphoric acid, iron saltMeSH
beta-Glycerophosphoric acid, iron(3+) salt(3:2)MeSH
beta-Glycerophosphoric acid, sodium saltMeSH
beta-GlycerophosphorateHMDB
Glycerol-2-phosphateHMDB
beta-Glycerophosphoric acidChEBI
Glycerol 2-phosphoric acidGenerator, HMDB
BGAHMDB
Dihydrogen beta-glycerophosphateHMDB
Dihydrogen β-glycerophosphateHMDB
beta-Glyceryl phosphateHMDB
β-Glyceryl phosphateHMDB
Glycerol-2-phosphoric acidGenerator
Molecular FormulaC3H9O6P
Average Mass172.0737
Monoisotopic Mass172.013674532
IUPAC Name[(1,3-dihydroxypropan-2-yl)oxy]phosphonic acid
Traditional Nameβ-glycerophosphorate
CAS Registry Number17181-54-3
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