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Showing metabocard for Pentane-2,3-diol (HMDB0256276)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:37:51 UTC
Update Date2021-09-26 23:11:48 UTC
HMDB IDHMDB0256276
Secondary Accession NumbersNone
Metabolite Identification
Common NamePentane-2,3-diol
Descriptionpentane-2,3-diol belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions. Based on a literature review very few articles have been published on pentane-2,3-diol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pentane-2,3-diol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pentane-2,3-diol 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256276 (Pentane-2,3-diol)


  Mrv1652309112118382D          

  7  6  0  0  0  0            999 V2000
    0.8250   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  4  6  1  0  0  0  0
  3  7  1  0  0  0  0
M  END
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3D MOL for HMDB0256276 (Pentane-2,3-diol)

HMDB0256276
     RDKit          3D
Pentane-2,3-diol
 19 18  0  0  0  0  0  0  0  0999 V2000
    1.9458    0.6732   -0.4572 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2386   -0.1247    0.5699 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0907   -0.9502    0.0877 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4426   -1.6233    1.1893 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0104   -0.1696   -0.5450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5668    0.9277    0.2780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0088   -1.0547   -0.9437 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3351    1.0394   -1.2889 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3639    1.5932    0.0459 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8353    0.1460   -0.8616 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9729   -0.8196    1.0405 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8673    0.5186    1.3949 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3965   -1.7454   -0.6335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0229   -1.3275    2.0467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6045    0.2767   -1.4893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0887    1.0800    1.2579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5239    1.9219   -0.2491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6691    0.7735    0.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1083   -1.1353   -1.9070 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
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
M  END
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3D SDF for HMDB0256276 (Pentane-2,3-diol)


  Mrv1652309112118382D          

  7  6  0  0  0  0            999 V2000
    0.8250   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  4  6  1  0  0  0  0
  3  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256276

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC(O)C(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O2/c1-3-5(7)4(2)6/h4-7H,3H2,1-2H3

> <INCHI_KEY>
XLMFDCKSFJWJTP-UHFFFAOYSA-N

> <FORMULA>
C5H12O2

> <MOLECULAR_WEIGHT>
104.149

> <EXACT_MASS>
104.083729626

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
11.815114083985545

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentane-2,3-diol

> <ALOGPS_LOGP>
-0.18

> <JCHEM_LOGP>
0.14699336366666674

> <ALOGPS_LOGS>
0.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.549050757761595

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.048346613815042

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0100299397814174

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
27.9152

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.55e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentane-2,3-diol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0256276 (Pentane-2,3-diol)

HMDB0256276
     RDKit          3D
Pentane-2,3-diol
 19 18  0  0  0  0  0  0  0  0999 V2000
    1.9458    0.6732   -0.4572 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2386   -0.1247    0.5699 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0907   -0.9502    0.0877 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4426   -1.6233    1.1893 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0104   -0.1696   -0.5450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5668    0.9277    0.2780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0088   -1.0547   -0.9437 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3351    1.0394   -1.2889 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3639    1.5932    0.0459 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8353    0.1460   -0.8616 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9729   -0.8196    1.0405 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8673    0.5186    1.3949 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3965   -1.7454   -0.6335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0229   -1.3275    2.0467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6045    0.2767   -1.4893 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0887    1.0800    1.2579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5239    1.9219   -0.2491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6691    0.7735    0.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1083   -1.1353   -1.9070 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
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
M  END
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PDB for HMDB0256276 (Pentane-2,3-diol)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       1.540  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0256276 (Pentane-2,3-diol)

COMPND    HMDB0256276
HETATM    1  C1  UNL     1       1.946   0.673  -0.457  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.239  -0.125   0.570  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.091  -0.950   0.088  1.00  0.00           C  
HETATM    4  O1  UNL     1      -0.443  -1.623   1.189  1.00  0.00           O  
HETATM    5  C4  UNL     1      -1.010  -0.170  -0.545  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.567   0.928   0.278  1.00  0.00           C  
HETATM    7  O2  UNL     1      -2.009  -1.055  -0.944  1.00  0.00           O  
HETATM    8  H1  UNL     1       1.335   1.039  -1.289  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.364   1.593   0.046  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.835   0.146  -0.862  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.973  -0.820   1.040  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.867   0.519   1.395  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.396  -1.745  -0.633  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.023  -1.327   2.047  1.00  0.00           H  
HETATM   15  H8  UNL     1      -0.604   0.277  -1.489  1.00  0.00           H  
HETATM   16  H9  UNL     1      -1.089   1.080   1.258  1.00  0.00           H  
HETATM   17  H10 UNL     1      -1.524   1.922  -0.249  1.00  0.00           H  
HETATM   18  H11 UNL     1      -2.669   0.774   0.464  1.00  0.00           H  
HETATM   19  H12 UNL     1      -2.108  -1.135  -1.907  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4    5   13
CONECT    4   14
CONECT    5    6    7   15
CONECT    6   16   17   18
CONECT    7   19
END
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SMILES for HMDB0256276 (Pentane-2,3-diol)

CCC(O)C(C)O
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INCHI for HMDB0256276 (Pentane-2,3-diol)

InChI=1S/C5H12O2/c1-3-5(7)4(2)6/h4-7H,3H2,1-2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2,3-PentanediolMeSH
Chemical FormulaC5H12O2
Average Molecular Weight104.149
Monoisotopic Molecular Weight104.083729626
IUPAC Namepentane-2,3-diol
Traditional Namepentane-2,3-diol
CAS Registry NumberNot Available
SMILES
CCC(O)C(C)O
InChI Identifier
InChI=1S/C5H12O2/c1-3-5(7)4(2)6/h4-7H,3H2,1-2H3
InChI KeyXLMFDCKSFJWJTP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct Parent1,2-diols
Alternative Parents
Substituents
  • Secondary alcohol
  • 1,2-diol
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
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
PropertyValueSource
logP-0.18ALOGPS
logP0.15ChemAxon
logS0.53ALOGPS
pKa (Strongest Acidic)14.05ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity27.92 m³·mol⁻¹ChemAxon
Polarizability11.82 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+126.02830932474
DeepCCS[M-H]-124.07730932474
DeepCCS[M-2H]-159.88430932474
DeepCCS[M+Na]+134.45130932474
AllCCS[M+H]+128.532859911
AllCCS[M+H-H2O]+124.232859911
AllCCS[M+NH4]+132.532859911
AllCCS[M+Na]+133.732859911
AllCCS[M-H]-127.232859911
AllCCS[M+Na-2H]-131.132859911
AllCCS[M+HCOO]-135.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Pentane-2,3-diolCCC(O)C(C)O1549.2Standard polar33892256
Pentane-2,3-diolCCC(O)C(C)O826.7Standard non polar33892256
Pentane-2,3-diolCCC(O)C(C)O892.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pentane-2,3-diol GC-MS (Non-derivatized) - 70eV, Positivesplash10-054n-9000000000-50a5a862f23cf84476eb2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentane-2,3-diol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentane-2,3-diol GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentane-2,3-diol GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentane-2,3-diol GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentane-2,3-diol GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentane-2,3-diol GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pentane-2,3-diol GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-25Wishart LabView Spectrum
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 ID110100
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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 ]