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Showing metabocard for Cyclopentanol (HMDB0302463)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:58:42 UTC
Update Date2021-09-23 17:58:43 UTC
HMDB IDHMDB0302463
Secondary Accession NumbersNone
Metabolite Identification
Common NameCyclopentanol
DescriptionCyclopentanol, also known as cyclopentyl alcohol or hydroxycyclopentane, is a member of the class of compounds known as cyclopentanols. Cyclopentanols are compounds containing a cyclopentane ring that carries an alcohol group. Cyclopentanol is soluble (in water) and an extremely weak acidic compound (based on its pKa). Cyclopentanol can be found in a number of food items such as walnut, cashew nut, cauliflower, and linden, which makes cyclopentanol a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302463 (Cyclopentanol)

 
  Mrv0541 02241221042D          
 
  6  6  0  0  0  0            999 V2000
   10.8936   -9.8290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1821   -9.4165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6051   -9.4165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8899  -10.6502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1821   -8.5915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6051   -8.5915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for HMDB0302463 (Cyclopentanol)

HMDB0302463
     RDKit          3D
Cyclopentanol
 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.0068    1.0921   -0.3478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9460    0.4241    0.2128 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3486    1.2095    0.0032 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4030    0.1832    0.3129 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7582   -1.1802    0.0941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5963   -0.8583   -0.5508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8530    0.6713   -0.0769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0935    0.1370    1.2634 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4013    2.1048    0.6321 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3998    1.4185   -1.0873 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2914    0.2520   -0.3534 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7639    0.2267    1.3630 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3632   -1.8229   -0.5511 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5099   -1.6261    1.0807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4146   -0.5822   -1.5977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3291   -1.6495   -0.3972 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  2  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
M  END
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3D SDF for HMDB0302463 (Cyclopentanol)

 
  Mrv0541 02241221042D          
 
  6  6  0  0  0  0            999 V2000
   10.8936   -9.8290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1821   -9.4165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6051   -9.4165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8899  -10.6502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1821   -8.5915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6051   -8.5915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302463

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1CCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O/c6-5-3-1-2-4-5/h5-6H,1-4H2

> <INCHI_KEY>
XCIXKGXIYUWCLL-UHFFFAOYSA-N

> <FORMULA>
C5H10O

> <MOLECULAR_WEIGHT>
86.1323

> <EXACT_MASS>
86.073164942

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
10.070144774572457

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclopentanol

> <ALOGPS_LOGP>
0.76

> <JCHEM_LOGP>
0.8361247979999998

> <ALOGPS_LOGS>
-0.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.949725982471424

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5085898552669992

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
24.6745

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.85e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclopentanol

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0302463 (Cyclopentanol)

HMDB0302463
     RDKit          3D
Cyclopentanol
 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.0068    1.0921   -0.3478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9460    0.4241    0.2128 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3486    1.2095    0.0032 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4030    0.1832    0.3129 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7582   -1.1802    0.0941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5963   -0.8583   -0.5508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8530    0.6713   -0.0769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0935    0.1370    1.2634 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4013    2.1048    0.6321 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3998    1.4185   -1.0873 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2914    0.2520   -0.3534 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7639    0.2267    1.3630 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3632   -1.8229   -0.5511 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5099   -1.6261    1.0807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4146   -0.5822   -1.5977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3291   -1.6495   -0.3972 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  2  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
M  END
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PDB for HMDB0302463 (Cyclopentanol)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      20.335 -18.347   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.007 -17.577   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      21.663 -17.577   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      20.328 -19.880   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      19.007 -16.037   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      21.663 -16.037   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1                                                            
CONECT    5    2    6                                                       
CONECT    6    3    5                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0302463 (Cyclopentanol)

COMPND    HMDB0302463
HETATM    1  O1  UNL     1      -2.007   1.092  -0.348  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.946   0.424   0.213  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.349   1.209   0.003  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.403   0.183   0.313  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.758  -1.180   0.094  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.596  -0.858  -0.551  1.00  0.00           C  
HETATM    7  H1  UNL     1      -2.853   0.671  -0.077  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.094   0.137   1.263  1.00  0.00           H  
HETATM    9  H3  UNL     1       0.401   2.105   0.632  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.400   1.419  -1.087  1.00  0.00           H  
HETATM   11  H5  UNL     1       2.291   0.252  -0.353  1.00  0.00           H  
HETATM   12  H6  UNL     1       1.764   0.227   1.363  1.00  0.00           H  
HETATM   13  H7  UNL     1       1.363  -1.823  -0.551  1.00  0.00           H  
HETATM   14  H8  UNL     1       0.510  -1.626   1.081  1.00  0.00           H  
HETATM   15  H9  UNL     1      -0.415  -0.582  -1.598  1.00  0.00           H  
HETATM   16  H10 UNL     1      -1.329  -1.650  -0.397  1.00  0.00           H  
CONECT    1    2    7
CONECT    2    3    6    8
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5    6   13   14
CONECT    6   15   16
END
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SMILES for HMDB0302463 (Cyclopentanol)

OC1CCCC1
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INCHI for HMDB0302463 (Cyclopentanol)

InChI=1S/C5H10O/c6-5-3-1-2-4-5/h5-6H,1-4H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Cyclopentyl alcoholChEBI
HydroxycyclopentaneChEBI
Chemical FormulaC5H10O
Average Molecular Weight86.1323
Monoisotopic Molecular Weight86.073164942
IUPAC Namecyclopentanol
Traditional Namecyclopentanol
CAS Registry NumberNot Available
SMILES
OC1CCCC1
InChI Identifier
InChI=1S/C5H10O/c6-5-3-1-2-4-5/h5-6H,1-4H2
InChI KeyXCIXKGXIYUWCLL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclopentanols. Cyclopentanols are compounds containing a cyclopentane ring that carries an alcohol group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentCyclopentanols
Alternative Parents
Substituents
  • Cyclopentanol
  • Cyclic alcohol
  • Hydrocarbon derivative
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
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
logP0.76ALOGPS
logP0.84ChemAxon
logS-0.04ALOGPS
pKa (Strongest Acidic)17.95ChemAxon
pKa (Strongest Basic)-1.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity24.67 m³·mol⁻¹ChemAxon
Polarizability10.07 ųChemAxon
Number of Rings1ChemAxon
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]+120.50832859911
AllCCS[M+H-H2O]+115.48232859911
AllCCS[M+Na]+126.56432859911
AllCCS[M+NH4]+125.20632859911
AllCCS[M-H]-118.34332859911
AllCCS[M+Na-2H]-122.15732859911
AllCCS[M+HCOO]-126.36432859911
DeepCCS[M+H]+124.19230932474
DeepCCS[M-H]-122.22230932474
DeepCCS[M-2H]-157.61430932474
DeepCCS[M+Na]+132.00330932474

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopentanol GC-MS (TMS_1_1) - 70eV, PositiveNot Available2022-08-08Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 10V, Positive-QTOFsplash10-014r-9000000000-7ba7870aec86994d28152016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 20V, Positive-QTOFsplash10-014r-9000000000-d6ba57d2adba589d97eb2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 40V, Positive-QTOFsplash10-014l-9000000000-c344792850a8e654eec92016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 10V, Negative-QTOFsplash10-000i-9000000000-0c197ad9e8e761effcd22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 20V, Negative-QTOFsplash10-000i-9000000000-bf9e07cf2b1811509ff82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 40V, Negative-QTOFsplash10-052u-9000000000-bb7b685f2854f6871b112016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 10V, Positive-QTOFsplash10-014i-9000000000-8e4c0ecd8363627c51db2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 20V, Positive-QTOFsplash10-00kf-9000000000-c0838ae20e30cce799192021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 40V, Positive-QTOFsplash10-00kf-9000000000-d45ed9789f0b9dc5e7ff2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 10V, Negative-QTOFsplash10-000i-9000000000-2091e44a102d8284a8132021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 20V, Negative-QTOFsplash10-014r-9000000000-bf93438ac1b77f7faf212021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentanol 40V, Negative-QTOFsplash10-0ap0-9000000000-47490602fb4a891575df2021-10-21Wishart 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 IDFDB004659
KNApSAcK IDNot Available
Chemspider ID7026
KEGG Compound IDC02020
BioCyc IDCYCLOPENTANOL
BiGG IDNot Available
Wikipedia LinkCyclopentanol
METLIN IDNot Available
PubChem Compound7298
PDB IDNot Available
ChEBI ID16133
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1171331
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available