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Showing metabocard for 2-Methylpentan-3-ol (HMDB0302390)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:25:29 UTC
Update Date2021-09-23 17:25:29 UTC
HMDB IDHMDB0302390
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Methylpentan-3-ol
Description2-methylpentan-3-ol is a member of the class of 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). 2-methylpentan-3-ol is soluble (in water) and an extremely weak acidic compound (based on its pKa). 2-methylpentan-3-ol can be found in tea, which makes 2-methylpentan-3-ol a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302390 (2-Methylpentan-3-ol)


  Mrv1533007131513362D          

  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
    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 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
    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
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
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3D MOL for HMDB0302390 (2-Methylpentan-3-ol)

HMDB0302390
     RDKit          3D
2-Methylpentan-3-ol
 21 20  0  0  0  0  0  0  0  0999 V2000
    2.2665    0.2908    0.5720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5109   -0.0692   -0.6565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1672   -0.6959   -0.3922 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3138   -1.8715    0.3416 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7700    0.1969    0.3636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0656    1.4851   -0.3517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0947   -0.5569    0.4832 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4468    1.4023    0.5822 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7600    0.0193    1.5174 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2844   -0.1597    0.5755 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1037   -0.8443   -1.2187 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4036    0.7882   -1.3523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2955   -0.8914   -1.3863 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1381   -2.6250   -0.2578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4500    0.4365    1.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2084    1.2551   -1.4235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0325    1.8742    0.0820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2741    2.2616   -0.1931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8825    0.0496    0.9421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3874   -0.8055   -0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9342   -1.5401    0.9687 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
  7 20  1  0
  7 21  1  0
M  END
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3D SDF for HMDB0302390 (2-Methylpentan-3-ol)


  Mrv1533007131513362D          

  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
    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 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
    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
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302390

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H14O/c1-4-6(7)5(2)3/h5-7H,4H2,1-3H3

> <INCHI_KEY>
ISTJMQSHILQAEC-UHFFFAOYSA-N

> <FORMULA>
C6H14O

> <MOLECULAR_WEIGHT>
102.177

> <EXACT_MASS>
102.104465071

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
12.847141614268361

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylpentan-3-ol

> <ALOGPS_LOGP>
1.58

> <JCHEM_LOGP>
1.6648235270000002

> <ALOGPS_LOGS>
-0.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.70098014244407

> <JCHEM_PKA_STRONGEST_BASIC>
-1.179991285694964

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
30.9483

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methyl-3-pentanol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0302390 (2-Methylpentan-3-ol)

HMDB0302390
     RDKit          3D
2-Methylpentan-3-ol
 21 20  0  0  0  0  0  0  0  0999 V2000
    2.2665    0.2908    0.5720 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5109   -0.0692   -0.6565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1672   -0.6959   -0.3922 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3138   -1.8715    0.3416 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7700    0.1969    0.3636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0656    1.4851   -0.3517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0947   -0.5569    0.4832 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4468    1.4023    0.5822 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7600    0.0193    1.5174 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2844   -0.1597    0.5755 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1037   -0.8443   -1.2187 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4036    0.7882   -1.3523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2955   -0.8914   -1.3863 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1381   -2.6250   -0.2578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4500    0.4365    1.3827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2084    1.2551   -1.4235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0325    1.8742    0.0820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2741    2.2616   -0.1931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8825    0.0496    0.9421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3874   -0.8055   -0.5787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9342   -1.5401    0.9687 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
  7 20  1  0
  7 21  1  0
M  END
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PDB for HMDB0302390 (2-Methylpentan-3-ol)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       1.540  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.850   1.334   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       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    4                                                            
CONECT    2    5                                                            
CONECT    3    5                                                            
CONECT    4    1    6                                                       
CONECT    5    2    3    6                                                  
CONECT    6    4    5    7                                                  
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0302390 (2-Methylpentan-3-ol)

COMPND    HMDB0302390
HETATM    1  C1  UNL     1       2.266   0.291   0.572  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.511  -0.069  -0.656  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.167  -0.696  -0.392  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.314  -1.872   0.342  1.00  0.00           O  
HETATM    5  C4  UNL     1      -0.770   0.197   0.364  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.066   1.485  -0.352  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.095  -0.557   0.483  1.00  0.00           C  
HETATM    8  H1  UNL     1       2.447   1.402   0.582  1.00  0.00           H  
HETATM    9  H2  UNL     1       1.760   0.019   1.517  1.00  0.00           H  
HETATM   10  H3  UNL     1       3.284  -0.160   0.575  1.00  0.00           H  
HETATM   11  H4  UNL     1       2.104  -0.844  -1.219  1.00  0.00           H  
HETATM   12  H5  UNL     1       1.404   0.788  -1.352  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.295  -0.891  -1.386  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.138  -2.625  -0.258  1.00  0.00           H  
HETATM   15  H8  UNL     1      -0.450   0.437   1.383  1.00  0.00           H  
HETATM   16  H9  UNL     1      -1.208   1.255  -1.424  1.00  0.00           H  
HETATM   17  H10 UNL     1      -2.032   1.874   0.082  1.00  0.00           H  
HETATM   18  H11 UNL     1      -0.274   2.262  -0.193  1.00  0.00           H  
HETATM   19  H12 UNL     1      -2.883   0.050   0.942  1.00  0.00           H  
HETATM   20  H13 UNL     1      -2.387  -0.805  -0.579  1.00  0.00           H  
HETATM   21  H14 UNL     1      -1.934  -1.540   0.969  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   20   21
END
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SMILES for HMDB0302390 (2-Methylpentan-3-ol)

CCC(O)C(C)C
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INCHI for HMDB0302390 (2-Methylpentan-3-ol)

InChI=1S/C6H14O/c1-4-6(7)5(2)3/h5-7H,4H2,1-3H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC6H14O
Average Molecular Weight102.177
Monoisotopic Molecular Weight102.104465071
IUPAC Name2-methylpentan-3-ol
Traditional Name2-methyl-3-pentanol
CAS Registry NumberNot Available
SMILES
CCC(O)C(C)C
InChI Identifier
InChI=1S/C6H14O/c1-4-6(7)5(2)3/h5-7H,4H2,1-3H3
InChI KeyISTJMQSHILQAEC-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 DescriptorsNot Available
Ontology
Physiological effectNot Available
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
logP1.58ALOGPS
logP1.66ChemAxon
logS-0.7ALOGPS
pKa (Strongest Acidic)18.7ChemAxon
pKa (Strongest Basic)-1.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity30.95 m³·mol⁻¹ChemAxon
Polarizability12.85 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]+126.9632859911
AllCCS[M+H-H2O]+122.66532859911
AllCCS[M+Na]+132.12332859911
AllCCS[M+NH4]+130.96732859911
AllCCS[M-H]-130.98532859911
AllCCS[M+Na-2H]-134.98532859911
AllCCS[M+HCOO]-139.40532859911
DeepCCS[M+H]+127.1730932474
DeepCCS[M-H]-125.15430932474
DeepCCS[M-2H]-160.99830932474
DeepCCS[M+Na]+135.66130932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202211.5621 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.26 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1618.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid393.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid130.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid230.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid94.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid468.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid518.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)102.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid824.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid352.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1121.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid277.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid288.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate374.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA402.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water33.2 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 10V, Positive-QTOFsplash10-0f79-9600000000-90a65cedface04ce83f02016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 20V, Positive-QTOFsplash10-0f79-9300000000-0186da412c53e6a4387b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 40V, Positive-QTOFsplash10-00ko-9000000000-7844b63b0891571924722016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 10V, Negative-QTOFsplash10-0udi-1900000000-fe46952772a57544b5412016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 20V, Negative-QTOFsplash10-0udi-6900000000-86962914295fdd3375db2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 40V, Negative-QTOFsplash10-0kg9-9100000000-33f1ce6ddc718a929cf32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 10V, Positive-QTOFsplash10-0006-9000000000-be1664bd8d70e329c0832021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 20V, Positive-QTOFsplash10-0006-9000000000-47ef32a0a1defce0dbc82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 40V, Positive-QTOFsplash10-0006-9000000000-6ae91b711bd1eb58d0622021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 10V, Negative-QTOFsplash10-0udi-0900000000-3ab02485eaffb4e83bff2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 20V, Negative-QTOFsplash10-001i-9100000000-a40fe4dcfd51674ee41c2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Methylpentan-3-ol 40V, Negative-QTOFsplash10-0a4i-9000000000-9b4e3cecb14338396a6c2021-10-21Wishart 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 IDFDB004398
KNApSAcK IDNot Available
Chemspider ID10790
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11264
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 ReferencesNot Available