Hmdb loader

Showing metabocard for 3-pentanol (HMDB0303831)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 04:58:29 UTC
Update Date2021-09-24 04:58:29 UTC
HMDB IDHMDB0303831
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-pentanol
Description3-Pentanol, also known as (C2H5)2choh or 3-pentyl alcohol, belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R, R'=alkyl, aryl). 3-Pentanol is an extremely weak basic (essentially neutral) compound (based on its pKa). 3-Pentanol is a sweet, fruit, and herbal tasting compound. 3-Pentanol has been detected, but not quantified in, prickly pears. This could make 3-pentanol a potential biomarker for the consumption of these foods. 3-Pentanol is one of eight isomers of amyl alcohol. An amyl alcohol is any of 8 alcohols with the formula C5H12O. A mixture of amyl alcohols (also called amyl alcohol) can be obtained from fusel alcohol. Amyl alcohol is used as a solvent and in esterfication, by which is produced amyl acetate and other important products. The name amyl alcohol without further specification applies to the normal (straight-chain) form, 1-pentanol.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303831 (3-pentanol)


  Mrv1652303202018592D          

  6  5  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    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 O   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
    0.0000    0.0000    0.0000 C   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
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0303831 (3-pentanol)

HMDB0303831
     RDKit          3D
3-pentanol
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.0861    0.3443    0.1394 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2885   -0.6531   -0.6831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271   -0.7293   -0.1381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1045   -1.1367    1.1778 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8592    0.5831   -0.3315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2556    0.4265    0.2349 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0070    0.1618    1.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1735    0.1836   -0.1201 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7951    1.3844   -0.0784 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2858   -0.3114   -1.7358 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7719   -1.6451   -0.5850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6600   -1.5124   -0.7133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2584   -0.4370    1.8363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3131    1.4246    0.1286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9839    0.7753   -1.4172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9928    1.0330   -0.3506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3231    0.7629    1.2809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5300   -0.6545    0.1390 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
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  6 18  1  0
M  END
Download

3D SDF for HMDB0303831 (3-pentanol)


  Mrv1652303202018592D          

  6  5  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    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 O   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
    0.0000    0.0000    0.0000 C   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
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0303831

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC(O)CC

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O/c1-3-5(6)4-2/h5-6H,3-4H2,1-2H3

> <INCHI_KEY>
AQIXEPGDORPWBJ-UHFFFAOYSA-N

> <FORMULA>
C5H12O

> <MOLECULAR_WEIGHT>
88.15

> <EXACT_MASS>
88.088815006

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
11.00249240711231

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentan-3-ol

> <ALOGPS_LOGP>
1.22

> <JCHEM_LOGP>
1.2998507006666664

> <ALOGPS_LOGS>
-0.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.176239320824177

> <JCHEM_PKA_STRONGEST_BASIC>
-1.4095129210715047

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
26.4767

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.75e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-pentanol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0303831 (3-pentanol)

HMDB0303831
     RDKit          3D
3-pentanol
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.0861    0.3443    0.1394 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2885   -0.6531   -0.6831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1271   -0.7293   -0.1381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1045   -1.1367    1.1778 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8592    0.5831   -0.3315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2556    0.4265    0.2349 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0070    0.1618    1.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1735    0.1836   -0.1201 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7951    1.3844   -0.0784 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2858   -0.3114   -1.7358 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7719   -1.6451   -0.5850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6600   -1.5124   -0.7133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2584   -0.4370    1.8363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3131    1.4246    0.1286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9839    0.7753   -1.4172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9928    1.0330   -0.3506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3231    0.7629    1.2809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5300   -0.6545    0.1390 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
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  6 18  1  0
M  END
Download

PDB for HMDB0303831 (3-pentanol)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.540  -2.667   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
Download

3D PDB for HMDB0303831 (3-pentanol)

COMPND    HMDB0303831
HETATM    1  C1  UNL     1       2.086   0.344   0.139  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.289  -0.653  -0.683  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.127  -0.729  -0.138  1.00  0.00           C  
HETATM    4  O1  UNL     1      -0.105  -1.137   1.178  1.00  0.00           O  
HETATM    5  C4  UNL     1      -0.859   0.583  -0.331  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.256   0.426   0.235  1.00  0.00           C  
HETATM    7  H1  UNL     1       2.007   0.162   1.216  1.00  0.00           H  
HETATM    8  H2  UNL     1       3.174   0.184  -0.120  1.00  0.00           H  
HETATM    9  H3  UNL     1       1.795   1.384  -0.078  1.00  0.00           H  
HETATM   10  H4  UNL     1       1.286  -0.311  -1.736  1.00  0.00           H  
HETATM   11  H5  UNL     1       1.772  -1.645  -0.585  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.660  -1.512  -0.713  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.258  -0.437   1.836  1.00  0.00           H  
HETATM   14  H8  UNL     1      -0.313   1.425   0.129  1.00  0.00           H  
HETATM   15  H9  UNL     1      -0.984   0.775  -1.417  1.00  0.00           H  
HETATM   16  H10 UNL     1      -2.993   1.033  -0.351  1.00  0.00           H  
HETATM   17  H11 UNL     1      -2.323   0.763   1.281  1.00  0.00           H  
HETATM   18  H12 UNL     1      -2.530  -0.655   0.139  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3   10   11
CONECT    3    4    5   12
CONECT    4   13
CONECT    5    6   14   15
CONECT    6   16   17   18
END
Download

SMILES for HMDB0303831 (3-pentanol)

CCC(O)CC
Download

INCHI for HMDB0303831 (3-pentanol)

InChI=1S/C5H12O/c1-3-5(6)4-2/h5-6H,3-4H2,1-2H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
(C2H5)2chohChEBI
1-Ethyl-1-propanolChEBI
3-PentanolChEBI
3-Pentyl alcoholChEBI
Diethyl carbinolChEBI
Isoamyl alcoholChEBI
Pentanol-3ChEBI
Sec-amyl alcoholChEBI
Sec-pentanolChEBI
Sec-pentyl alcoholChEBI
Chemical FormulaC5H12O
Average Molecular Weight88.15
Monoisotopic Molecular Weight88.088815006
IUPAC Namepentan-3-ol
Traditional Name3-pentanol
CAS Registry NumberNot Available
SMILES
CCC(O)CC
InChI Identifier
InChI=1S/C5H12O/c1-3-5(6)4-2/h5-6H,3-4H2,1-2H3
InChI KeyAQIXEPGDORPWBJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentSecondary alcohols
Alternative Parents
Substituents
  • Secondary alcohol
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Source
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
logP1.22ALOGPS
logP1.3ChemAxon
logS-0.12ALOGPS
pKa (Strongest Acidic)18.18ChemAxon
pKa (Strongest Basic)-1.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity26.48 m³·mol⁻¹ChemAxon
Polarizability11 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+124.71532859911
AllCCS[M+H-H2O]+120.25132859911
AllCCS[M+Na]+130.08732859911
AllCCS[M+NH4]+128.88332859911
AllCCS[M-H]-130.91432859911
AllCCS[M+Na-2H]-135.56132859911
AllCCS[M+HCOO]-140.6832859911
DeepCCS[M+H]+125.14430932474
DeepCCS[M-H]-123.02130932474
DeepCCS[M-2H]-158.9130932474
DeepCCS[M+Na]+133.4630932474

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-pentanol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2020-06-30Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 10V, Positive-QTOFsplash10-00dr-9000000000-e64ea9482a134b64ca602019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 20V, Positive-QTOFsplash10-00dr-9000000000-22e624e212516c9bdcf02019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 40V, Positive-QTOFsplash10-00dl-9000000000-4472bf3dc5ac9186cfcb2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 10V, Negative-QTOFsplash10-000i-9000000000-a9965ed5f9b6380663652019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 20V, Negative-QTOFsplash10-000i-9000000000-97eaae02bdad4b161c552019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 40V, Negative-QTOFsplash10-052r-9000000000-ba851c071a2279611a0e2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 10V, Positive-QTOFsplash10-006x-9000000000-ed4d4b51d175c6022c882021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 20V, Positive-QTOFsplash10-0006-9000000000-510db6aa17eae30a6eaf2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 40V, Positive-QTOFsplash10-0006-9000000000-1da3cfde243ec41433d52021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 10V, Negative-QTOFsplash10-000i-9000000000-b889088fa29812fa83182021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 20V, Negative-QTOFsplash10-0a4i-9000000000-d6390cf6923303aed5742021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-pentanol 40V, Negative-QTOFsplash10-0a4r-9000000000-088ed77f90ff750efde72021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB029632
KNApSAcK IDC00053663
Chemspider ID10947
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Pentanol
METLIN IDNot Available
PubChem Compound11428
PDB IDNot Available
ChEBI ID77519
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1048801
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available