Hmdb loader

Showing metabocard for (S)-2-Methyl-1-butanol (HMDB0031527)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:43:50 UTC
Update Date2023-02-21 17:20:45 UTC
HMDB IDHMDB0031527
Secondary Accession Numbers
  • HMDB31527
Metabolite Identification
Common Name(S)-2-Methyl-1-butanol
Description(S)-2-Methyl-1-butanol, also known as sec-butylcarbinol or 2-methyl butanol-1, belongs to the class of organic compounds known as primary alcohols. Primary alcohols are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl). (S)-2-Methyl-1-butanol is a very hydrophobic molecule, practically insoluble in water, and relatively neutral. Thus, (S)-2-methyl-1-butanol is considered to be a fatty alcohol lipid molecule. (S)-2-Methyl-1-butanol exists in all eukaryotes, ranging from yeast to humans. (S)-2-Methyl-1-butanol is a malt tasting compound. (S)-2-Methyl-1-butanol is found, on average, in the highest concentration within milk (cow) and it has also been detected, but not quantified, in several different foods, such as red raspberries, nectarines, carobs, wild leeks, and black-eyed pea. This could make (S)-2-methyl-1-butanol a potential biomarker for the consumption of these foods.
Structure
Data?1677000045
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031527 ((S)-2-Methyl-1-butanol)


  Mrv1652305261923502D          

  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
    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
    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
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
Download

3D MOL for HMDB0031527 ((S)-2-Methyl-1-butanol)

HMDB0031527
     RDKit          3D
(S)-2-Methyl-1-butanol
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.1103   -0.1034    0.0754 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8873   -0.1804   -0.8184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3071    0.3232   -0.0491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4679   -0.5700    1.1670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5754    0.2958   -0.8254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5949    0.7814   -0.0110 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1606    0.9131    0.5005 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0238   -0.3424   -0.5445 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0862   -0.8969    0.8517 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7933   -1.2501   -1.0966 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1168    0.4606   -1.7018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0912    1.3402    0.3341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4280   -0.2657    1.6485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4919   -1.6375    0.8457 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3769   -0.3579    1.8335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5667    0.8445   -1.7644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8291   -0.7725   -1.0788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2032    1.4179    0.6336 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
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
Download

3D SDF for HMDB0031527 ((S)-2-Methyl-1-butanol)


  Mrv1652305261923502D          

  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
    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
    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
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031527

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC(C)CO

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

> <INCHI_KEY>
QPRQEDXDYOZYLA-UHFFFAOYSA-N

> <FORMULA>
C5H12O

> <MOLECULAR_WEIGHT>
88.1482

> <EXACT_MASS>
88.088815006

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
10.992265927493843

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylbutan-1-ol

> <ALOGPS_LOGP>
1.24

> <JCHEM_LOGP>
1.1702947723333335

> <ALOGPS_LOGS>
-0.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.501123795275216

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7048084519466205

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
26.606499999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methyl-1-butanol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031527 ((S)-2-Methyl-1-butanol)

HMDB0031527
     RDKit          3D
(S)-2-Methyl-1-butanol
 18 17  0  0  0  0  0  0  0  0999 V2000
    2.1103   -0.1034    0.0754 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8873   -0.1804   -0.8184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3071    0.3232   -0.0491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4679   -0.5700    1.1670 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5754    0.2958   -0.8254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5949    0.7814   -0.0110 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1606    0.9131    0.5005 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0238   -0.3424   -0.5445 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0862   -0.8969    0.8517 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7933   -1.2501   -1.0966 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1168    0.4606   -1.7018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0912    1.3402    0.3341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4280   -0.2657    1.6485 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4919   -1.6375    0.8457 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3769   -0.3579    1.8335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5667    0.8445   -1.7644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8291   -0.7725   -1.0788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2032    1.4179    0.6336 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
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
Download

PDB for HMDB0031527 ((S)-2-Methyl-1-butanol)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0       4.620  -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       1.540   0.000   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  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    5                                                            
CONECT    3    1    5                                                       
CONECT    4    5    6                                                       
CONECT    5    2    3    4                                                  
CONECT    6    4                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
Download

3D PDB for HMDB0031527 ((S)-2-Methyl-1-butanol)

COMPND    HMDB0031527
HETATM    1  C1  UNL     1       2.110  -0.103   0.075  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.887  -0.180  -0.818  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.307   0.323  -0.049  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.468  -0.570   1.167  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.575   0.296  -0.825  1.00  0.00           C  
HETATM    6  O1  UNL     1      -2.595   0.781  -0.011  1.00  0.00           O  
HETATM    7  H1  UNL     1       2.161   0.913   0.500  1.00  0.00           H  
HETATM    8  H2  UNL     1       3.024  -0.342  -0.545  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.086  -0.897   0.852  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.793  -1.250  -1.097  1.00  0.00           H  
HETATM   11  H5  UNL     1       1.117   0.461  -1.702  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.091   1.340   0.334  1.00  0.00           H  
HETATM   13  H7  UNL     1      -1.428  -0.266   1.649  1.00  0.00           H  
HETATM   14  H8  UNL     1      -0.492  -1.638   0.846  1.00  0.00           H  
HETATM   15  H9  UNL     1       0.377  -0.358   1.833  1.00  0.00           H  
HETATM   16  H10 UNL     1      -1.567   0.844  -1.764  1.00  0.00           H  
HETATM   17  H11 UNL     1      -1.829  -0.772  -1.079  1.00  0.00           H  
HETATM   18  H12 UNL     1      -2.203   1.418   0.634  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3   10   11
CONECT    3    4    5   12
CONECT    4   13   14   15
CONECT    5    6   16   17
CONECT    6   18
END
Download

SMILES for HMDB0031527 ((S)-2-Methyl-1-butanol)

CCC(C)CO
Download

INCHI for HMDB0031527 ((S)-2-Methyl-1-butanol)

InChI=1S/C5H12O/c1-3-5(2)4-6/h5-6H,3-4H2,1-2H3
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Methyl butanol-1ChEBI
2-Methyl-1-butanolChEBI
2-Methyl-N-butanolChEBI
2-MethylbutanolChEBI
2-Methylbutyl alcoholChEBI
Active amyl alcoholChEBI
Active primary amyl alcoholChEBI
CH3CH2CH(CH3)CH2OHChEBI
Methyl-2-butan-1-olChEBI
Primary active amyl alcoholChEBI
Sec-butylcarbinolChEBI
(+/-)-2-methyl-1-butanolHMDB
(1)-2-Methylbutan-1-olHMDB
(S)-(-)-2-Methyl-1-butanolHMDB
(S)-2-Methylbutan-1-olHMDB
2-Methyl-(.+/-.)-1-butanolHMDB
2-Methyl-(2S)-1-butanolHMDB
2-Methyl-(S)-1-butanolHMDB
2-Methylbutan-1-olHMDB
D-2-METHYL-1-butanolHMDB
DL-2-Methyl-1-butanolHMDB
DL-2-METHYL-1-butanol, practHMDB
DL-Sec-butyl carbinolHMDB
L-2-Methyl-1-butanolHMDB
Sec-butyl carbinolHMDB
Chemical FormulaC5H12O
Average Molecular Weight88.1482
Monoisotopic Molecular Weight88.088815006
IUPAC Name2-methylbutan-1-ol
Traditional Name2-methyl-1-butanol
CAS Registry Number1565-80-6
SMILES
CCC(C)CO
InChI Identifier
InChI=1S/C5H12O/c1-3-5(2)4-6/h5-6H,3-4H2,1-2H3
InChI KeyQPRQEDXDYOZYLA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as primary alcohols. Primary alcohols are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentPrimary alcohols
Alternative Parents
Substituents
  • Hydrocarbon derivative
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point128.00 to 130.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility32200 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.290The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility42 g/LALOGPS
logP1.24ALOGPS
logP1.17ChemAxon
logS-0.32ALOGPS
pKa (Strongest Acidic)17.5ChemAxon
pKa (Strongest Basic)-1.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area20.23 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity26.61 m³·mol⁻¹ChemAxon
Polarizability10.99 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
DarkChem[M+H]+117.91331661259
DarkChem[M-H]-112.39331661259
DeepCCS[M+H]+126.83230932474
DeepCCS[M-H]-124.88130932474
DeepCCS[M-2H]-160.39630932474
DeepCCS[M+Na]+134.99330932474
AllCCS[M+H]+123.132859911
AllCCS[M+H-H2O]+118.632859911
AllCCS[M+NH4]+127.232859911
AllCCS[M+Na]+128.432859911
AllCCS[M-H]-131.132859911
AllCCS[M+Na-2H]-135.832859911
AllCCS[M+HCOO]-141.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.2.24 minutes32390414
Predicted by Siyang on May 30, 202211.5993 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.19 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid38.9 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1457.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid406.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid134.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid256.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid117.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid435.3 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 Acid468.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)114.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid861.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid338.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1100.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid294.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid317.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate406.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA347.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water58.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(S)-2-Methyl-1-butanolCCC(C)CO1169.3Standard polar33892256
(S)-2-Methyl-1-butanolCCC(C)CO696.9Standard non polar33892256
(S)-2-Methyl-1-butanolCCC(C)CO725.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
(S)-2-Methyl-1-butanol,1TMS,isomer #1CCC(C)CO[Si](C)(C)C848.0Semi standard non polar33892256
(S)-2-Methyl-1-butanol,1TBDMS,isomer #1CCC(C)CO[Si](C)(C)C(C)(C)C1064.6Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008130
KNApSAcK IDC00050415
Chemspider ID8398
KEGG Compound IDNot Available
BioCyc IDCPD-7033
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound8723
PDB IDNot Available
ChEBI ID48945
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1059521
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .