Hmdb loader

Showing metabocard for 1-O-Pentylglycerol (HMDB0243976)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:10:59 UTC
Update Date2021-09-26 22:51:24 UTC
HMDB IDHMDB0243976
Secondary Accession NumbersNone
Metabolite Identification
Common Name1-O-Pentylglycerol
Description1-O-Pentylglycerol belongs to the class of organic compounds known as monoalkylglycerols. These are glycerolipids containing exactly one aliphatic chain linked to the glycerol moiety. This chain is the only one linked to the glycerol. Based on a literature review a small amount of articles have been published on 1-O-Pentylglycerol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-o-pentylglycerol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-O-Pentylglycerol is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0243976 (1-O-Pentylglycerol)

  Mrv1652309102123112D          

 11 10  0  0  0  0            999 V2000
    2.2836    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    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
  4  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
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  8 11  1  0  0  0  0
M  END
Download

3D MOL for HMDB0243976 (1-O-Pentylglycerol)

HMDB0243976
     RDKit          3D
1-O-Pentylglycerol
 29 28  0  0  0  0  0  0  0  0999 V2000
    4.7044    0.5633   -0.4153 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2981    1.0648   -0.1585 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3572   -0.0694   -0.5014 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9038    0.3183   -0.2816 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0914   -0.8948   -0.6598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2603   -0.7688   -0.5492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6710   -0.4868    0.7455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1841   -0.3763    0.8073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7069   -1.5972    0.3956 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7084    0.6960   -0.1041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0984    0.6892   -0.0022 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4210    1.3973   -0.5536 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6485   -0.0897   -1.3076 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9842   -0.0883    0.4418 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1775    1.3275    0.9091 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1233    1.9520   -0.8153 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6125   -0.9154    0.1682 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5329   -0.4253   -1.5364 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7689    0.4984    0.8171 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6071    1.1596   -0.9053 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4183   -1.2433   -1.6622 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4294   -1.7060    0.0536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3886   -1.3165    1.4270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1955    0.4335    1.1723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4606   -0.1472    1.8434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0832   -1.9870   -0.2516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4490    0.4956   -1.1599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3732    1.7078    0.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4993   -0.1915   -0.0986 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
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
M  END
Download

3D SDF for HMDB0243976 (1-O-Pentylglycerol)

  Mrv1652309102123112D          

 11 10  0  0  0  0            999 V2000
    2.2836    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    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
  4  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
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  8 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0243976

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCOCC(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C8H18O3/c1-2-3-4-5-11-7-8(10)6-9/h8-10H,2-7H2,1H3

> <INCHI_KEY>
FQJXITFHANYMET-UHFFFAOYSA-N

> <FORMULA>
C8H18O3

> <MOLECULAR_WEIGHT>
162.229

> <EXACT_MASS>
162.12559444

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
19.212322433199304

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-(pentyloxy)propane-1,2-diol

> <ALOGPS_LOGP>
0.60

> <JCHEM_LOGP>
0.572580160666667

> <ALOGPS_LOGS>
-0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.565284452957464

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.64153171924703

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9681925647994625

> <JCHEM_POLAR_SURFACE_AREA>
49.69

> <JCHEM_REFRACTIVITY>
43.741899999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.95e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-O-pentylglycerol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0243976 (1-O-Pentylglycerol)

HMDB0243976
     RDKit          3D
1-O-Pentylglycerol
 29 28  0  0  0  0  0  0  0  0999 V2000
    4.7044    0.5633   -0.4153 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2981    1.0648   -0.1585 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3572   -0.0694   -0.5014 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9038    0.3183   -0.2816 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0914   -0.8948   -0.6598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2603   -0.7688   -0.5492 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6710   -0.4868    0.7455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1841   -0.3763    0.8073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7069   -1.5972    0.3956 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7084    0.6960   -0.1041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0984    0.6892   -0.0022 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4210    1.3973   -0.5536 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6485   -0.0897   -1.3076 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9842   -0.0883    0.4418 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1775    1.3275    0.9091 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1233    1.9520   -0.8153 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6125   -0.9154    0.1682 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5329   -0.4253   -1.5364 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7689    0.4984    0.8171 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6071    1.1596   -0.9053 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4183   -1.2433   -1.6622 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4294   -1.7060    0.0536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3886   -1.3165    1.4270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1955    0.4335    1.1723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4606   -0.1472    1.8434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0832   -1.9870   -0.2516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4490    0.4956   -1.1599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3732    1.7078    0.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4993   -0.1915   -0.0986 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
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  3 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
M  END
Download

PDB for HMDB0243976 (1-O-Pentylglycerol)

HEADER    PROTEIN                                 10-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-21         0                                  
HETATM    1  C   UNK     0       4.263   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      10.931   4.771   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      13.598   6.311   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
Download

3D PDB for HMDB0243976 (1-O-Pentylglycerol)

COMPND    HMDB0243976
HETATM    1  C1  UNL     1       4.704   0.563  -0.415  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.298   1.065  -0.158  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.357  -0.069  -0.501  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.904   0.318  -0.282  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.091  -0.895  -0.660  1.00  0.00           C  
HETATM    6  O1  UNL     1      -1.260  -0.769  -0.549  1.00  0.00           O  
HETATM    7  C6  UNL     1      -1.671  -0.487   0.745  1.00  0.00           C  
HETATM    8  C7  UNL     1      -3.184  -0.376   0.807  1.00  0.00           C  
HETATM    9  O2  UNL     1      -3.707  -1.597   0.396  1.00  0.00           O  
HETATM   10  C8  UNL     1      -3.708   0.696  -0.104  1.00  0.00           C  
HETATM   11  O3  UNL     1      -5.098   0.689  -0.002  1.00  0.00           O  
HETATM   12  H1  UNL     1       5.421   1.397  -0.554  1.00  0.00           H  
HETATM   13  H2  UNL     1       4.648  -0.090  -1.308  1.00  0.00           H  
HETATM   14  H3  UNL     1       4.984  -0.088   0.442  1.00  0.00           H  
HETATM   15  H4  UNL     1       3.178   1.328   0.909  1.00  0.00           H  
HETATM   16  H5  UNL     1       3.123   1.952  -0.815  1.00  0.00           H  
HETATM   17  H6  UNL     1       2.612  -0.915   0.168  1.00  0.00           H  
HETATM   18  H7  UNL     1       2.533  -0.425  -1.536  1.00  0.00           H  
HETATM   19  H8  UNL     1       0.769   0.498   0.817  1.00  0.00           H  
HETATM   20  H9  UNL     1       0.607   1.160  -0.905  1.00  0.00           H  
HETATM   21  H10 UNL     1       0.418  -1.243  -1.662  1.00  0.00           H  
HETATM   22  H11 UNL     1       0.429  -1.706   0.054  1.00  0.00           H  
HETATM   23  H12 UNL     1      -1.389  -1.316   1.427  1.00  0.00           H  
HETATM   24  H13 UNL     1      -1.195   0.434   1.172  1.00  0.00           H  
HETATM   25  H14 UNL     1      -3.461  -0.147   1.843  1.00  0.00           H  
HETATM   26  H15 UNL     1      -3.083  -1.987  -0.252  1.00  0.00           H  
HETATM   27  H16 UNL     1      -3.449   0.496  -1.160  1.00  0.00           H  
HETATM   28  H17 UNL     1      -3.373   1.708   0.179  1.00  0.00           H  
HETATM   29  H18 UNL     1      -5.499  -0.192  -0.099  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3   15   16
CONECT    3    4   17   18
CONECT    4    5   19   20
CONECT    5    6   21   22
CONECT    6    7
CONECT    7    8   23   24
CONECT    8    9   10   25
CONECT    9   26
CONECT   10   11   27   28
CONECT   11   29
END
Download

SMILES for HMDB0243976 (1-O-Pentylglycerol)

CCCCCOCC(O)CO
Download

INCHI for HMDB0243976 (1-O-Pentylglycerol)

InChI=1S/C8H18O3/c1-2-3-4-5-11-7-8(10)6-9/h8-10H,2-7H2,1H3
Download
View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC8H18O3
Average Molecular Weight162.229
Monoisotopic Molecular Weight162.12559444
IUPAC Name3-(pentyloxy)propane-1,2-diol
Traditional Name1-O-pentylglycerol
CAS Registry NumberNot Available
SMILES
CCCCCOCC(O)CO
InChI Identifier
InChI=1S/C8H18O3/c1-2-3-4-5-11-7-8(10)6-9/h8-10H,2-7H2,1H3
InChI KeyFQJXITFHANYMET-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monoalkylglycerols. These are glycerolipids containing exactly one aliphatic chain linked to the glycerol moiety. This chain is the only one linked to the glycerol.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerolipids
Sub ClassMonoradylglycerols
Direct ParentMonoalkylglycerols
Alternative Parents
Substituents
  • Monoalkylglycerol
  • 1-o-alkylglycerol
  • Glycerol ether
  • Secondary alcohol
  • 1,2-diol
  • Ether
  • Dialkyl ether
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID82002
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound90819
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]