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Showing metabocard for Glycerol (HMDB0000131)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (41)transporters (1) Show 42 proteinsXML
enzymes (41)transporters (1) Show 42 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:32 UTC
HMDB IDHMDB0000131
Secondary Accession Numbers
  • HMDB00131
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
Data?1676999672
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000131 (Glycerol)


  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 HMDB0000131 (Glycerol)

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 HMDB0000131 (Glycerol)


  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>
HMDB0000131

> <DATABASE_NAME>
hmdb

> <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 HMDB0000131 (Glycerol)

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 HMDB0000131 (Glycerol)

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 HMDB0000131 (Glycerol)

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 HMDB0000131 (Glycerol)

OCC(O)CO
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INCHI for HMDB0000131 (Glycerol)

InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
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View in JSmolView NMR AssignmentsView Stereo Labels
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
Chemical FormulaC3H8O3
Average Molecular Weight92.0938
Monoisotopic Molecular Weight92.047344122
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
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar alcohols
Alternative Parents
Substituents
  • Sugar alcohol
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effectOrganoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process