Showing metabocard for Glycerol (MMDBc0000036)

Plant
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:28:02 UTC
Update Date2022-08-30 23:13:28 UTC
Metabolite IDMMDBc0000036
Metabolite Identification
Common NameGlycerol
DescriptionGlycerol or glycerin is a colourless, odourless, viscous liquid that is sweet-tasting and mostly non-toxic. It is widely used in the food industry as a sweetener and humectant and in pharmaceutical formulations. Glycerol is an important component of triglycerides (i.e. fats and oils) and of phospholipids. Glycerol is a three-carbon substance that forms the backbone of fatty acids in fats. When the body uses stored fat as a source of energy, glycerol and fatty acids are released into the bloodstream. The glycerol component can be converted into glucose by the liver and provides energy for cellular metabolism. Normally, glycerol shows very little acute toxicity and very high oral doses or acute exposures can be tolerated. On the other hand, chronically high levels of glycerol in the blood are associated with glycerol kinase deficiency (GKD). GKD causes the condition known as hyperglycerolemia, an accumulation of glycerol in the blood and urine. There are three clinically distinct forms of GKD: infantile, juvenile, and adult. The infantile form is the most severe and is associated with vomiting, lethargy, severe developmental delay, and adrenal insufficiency. The mechanisms of glycerol toxicity in infants are not known, but it appears to shift metabolism towards chronic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart, liver, and kidney abnormalities, seizures, coma, and possibly death. These are also the characteristic symptoms of untreated GKD. Many affected children with organic acidemias experience intellectual disability or delayed development. Patients with the adult form of GKD generally have no symptoms and are often detected fortuitously.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be1ac1e60>


  Mrv1652309032023532D          

  6  5  0  0  0  0            999 V2000
 9998.3738 9998.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.0880 9998.9835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.8056 9998.5712    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.6591 9998.9835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.9445 9998.5712    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.3738 9997.7466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  4  5  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000560be1ac1e60>

HMDB0000131
     RDKit          3D
Glycerol
 14 13  0  0  0  0  0  0  0  0999 V2000
   -1.4107    1.4932    0.3222 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3058    0.2253   -0.1957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1558   -0.5556    0.3989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -1.8233   -0.2267 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1823    0.0505    0.0489 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3796    1.2993    0.5798 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2389    1.5312    0.8782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2260   -0.3914   -0.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1522    0.2356   -1.2946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2205   -0.6748    1.4813 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7049   -2.2298    0.0101 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9630   -0.6322    0.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3436    0.0998   -1.0502 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3151    1.3723    0.9506 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
M  END
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3D SDF for #<Metabolite:0x0000560be1ac1e60>


  Mrv1652309032023532D          

  6  5  0  0  0  0            999 V2000
 9998.3738 9998.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.0880 9998.9835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.8056 9998.5712    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.6591 9998.9835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.9445 9998.5712    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.3738 9997.7466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  4  5  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000036

> <DATABASE_NAME>
MIME

> <SMILES>
OCC(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2

> <INCHI_KEY>
PEDCQBHIVMGVHV-UHFFFAOYSA-N

> <FORMULA>
C3H8O3

> <MOLECULAR_WEIGHT>
92.0938

> <EXACT_MASS>
92.047344122

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
8.934349980067854

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
propane-1,2,3-triol

> <ALOGPS_LOGP>
-1.93

> <JCHEM_LOGP>
-1.8390140226666665

> <ALOGPS_LOGS>
1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.167747933654137

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.605499310321004

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9679773519640786

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
20.516099999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.17e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycerol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000560be1ac1e60>

HMDB0000131
     RDKit          3D
Glycerol
 14 13  0  0  0  0  0  0  0  0999 V2000
   -1.4107    1.4932    0.3222 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3058    0.2253   -0.1957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1558   -0.5556    0.3989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -1.8233   -0.2267 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1823    0.0505    0.0489 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3796    1.2993    0.5798 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2389    1.5312    0.8782 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2260   -0.3914   -0.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1522    0.2356   -1.2946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2205   -0.6748    1.4813 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7049   -2.2298    0.0101 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9630   -0.6322    0.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3436    0.0998   -1.0502 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3151    1.3723    0.9506 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
M  END
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PDB for #<Metabolite:0x0000560be1ac1e60>

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  C   UNK     0    8663.6318664.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8664.9648664.769   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8666.3048664.000   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0    8662.2978664.769   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8660.9638664.000   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8663.6318662.460   0.000  0.00  0.00           O+0
CONECT    1    2    4    6                                                  
CONECT    2    1    3                                                       
CONECT    3    2                                                            
CONECT    4    1    5                                                       
CONECT    5    4                                                            
CONECT    6    1                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for #<Metabolite:0x0000560be1ac1e60>

COMPND    HMDB0000131
HETATM    1  O1  UNL     1      -1.411   1.493   0.322  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.306   0.225  -0.196  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.156  -0.556   0.399  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.179  -1.823  -0.227  1.00  0.00           O  
HETATM    5  C3  UNL     1       1.182   0.050   0.049  1.00  0.00           C  
HETATM    6  O3  UNL     1       1.380   1.299   0.580  1.00  0.00           O  
HETATM    7  H1  UNL     1      -2.239   1.531   0.878  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.226  -0.391  -0.002  1.00  0.00           H  
HETATM    9  H3  UNL     1      -1.152   0.236  -1.295  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.220  -0.675   1.481  1.00  0.00           H  
HETATM   11  H5  UNL     1       0.705  -2.230   0.010  1.00  0.00           H  
HETATM   12  H6  UNL     1       1.963  -0.632   0.442  1.00  0.00           H  
HETATM   13  H7  UNL     1       1.344   0.100  -1.050  1.00  0.00           H  
HETATM   14  H8  UNL     1       2.315   1.372   0.951  1.00  0.00           H  
CONECT    1    2    7
CONECT    2    3    8    9
CONECT    3    4    5   10
CONECT    4   11
CONECT    5    6   12   13
CONECT    6   14
END
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SMILES for #<Metabolite:0x0000560be1ac1e60>

OCC(O)CO
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INCHI for #<Metabolite:0x0000560be1ac1e60>

InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
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Synonyms
ValueSource
1,2,3-PropanetriolChEBI
1,2,3-TrihydroxypropaneChEBI
GlycerinChEBI
GlycerineChEBI
GlyceritolChEBI
GlycerolumChEBI
Glycyl alcoholChEBI
GlyzerinChEBI
GroChEBI
OelsuessChEBI
PropanetriolChEBI
TrihydroxypropaneChEBI
Concentrated glycerinKegg
Glycerin, concentratedKegg
BulboldHMDB
CristalHMDB
e 422HMDB
Emery 916HMDB
Glyceol opthalganHMDB
GlyrolHMDB
GlysaninHMDB
IFPHMDB
Incorporation factorHMDB
Mackstat H 66HMDB
OsmoglynHMDB
Pricerine 9091HMDB
RG-SHMDB
TryhydroxypropaneHMDB
2,5-Dihydroxyphenylacetic acidHMDB
2-(3,6-DIHYDROXYPHENYL)acetIC ACIDHMDB
2,5-DihydroxyphenylacetateHMDB
2-(3,6-DIHYDROXYPHENYL)acetateHMDB
HomogentisateHMDB
(2,5-Dihydroxyphenyl)-acetateHMDB
(2,5-Dihydroxyphenyl)-acetic acidHMDB
2,5-Dihydroxy-a-toluateHMDB
2,5-Dihydroxy-a-toluic acidHMDB
2,5-Dihydroxy-alpha-toluateHMDB
2,5-Dihydroxy-alpha-toluic acidHMDB
2,5-Dihydroxy-benzeneacetateHMDB
2,5-Dihydroxy-benzeneacetic acidHMDB
AlcaptonHMDB
Homogentisate acidHMDB
HomogentisinateHMDB
Homogentisinic acidHMDB
Melanic acidHMDB
Acid, homogentisicHMDB
GlcAaHMDB
GlcAalphaHMDB
D-GlucuronateHMDB
alpha-D-Glucopyranuronic acidHMDB
alpha-D-Glucuronic acidHMDB
alpha-delta-Glucopyranuronic acidHMDB
alpha-delta-Glucuronic acidHMDB
D-(+)-GlucuronateHMDB
D-(+)-Glucuronic acidHMDB
delta-(+)-GlucuronateHMDB
delta-(+)-Glucuronic acidHMDB
delta-GlucuronateHMDB
GCUHMDB
GlucosiduronateHMDB
Glucosiduronic acidHMDB
GlucuronateHMDB
Glucuronic acidHMDB
(2E)-2-Butenedioic acidHMDB
(e)-2-Butenedioic acidHMDB
e297HMDB
FumarsaeureHMDB
trans-1,2-Ethylenedicarboxylic acidHMDB
trans-But-2-enedioic acidHMDB
trans-Butenedioic acidHMDB
(2E)-2-ButenedioateHMDB
(e)-2-ButenedioateHMDB
trans-1,2-EthylenedicarboxylateHMDB
trans-But-2-enedioateHMDB
trans-ButenedioateHMDB
FumarateHMDB
(2E)-But-2-enedioateHMDB
(2E)-But-2-enedioic acidHMDB
2-(e)-ButenedioateHMDB
2-(e)-Butenedioic acidHMDB
AllomaleateHMDB
Allomaleic acidHMDB
BoletateHMDB
Boletic acidHMDB
FC 33HMDB
LichenateHMDB
Lichenic acidHMDB
Sodium fumarateHMDB
trans-2-ButenedioateHMDB
trans-2-Butenedioic acidHMDB
FuramagHMDB
Ammonium fumarateHMDB
Magnesium fumarateHMDB
MafusolHMDB
Molecular FormulaC3H8O3
Average Mass92.0938
Monoisotopic Mass92.047344122
IUPAC Namepropane-1,2,3-triol
Traditional Nameglycerol
CAS Registry Number56-81-5
SMILES
OCC(O)CO
InChI Identifier
InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
InChI KeyPEDCQBHIVMGVHV-UHFFFAOYSA-N