Hmdb loader

Showing metabocard for 3-Methylpentane (HMDB0061885)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2014-10-08 15:56:35 UTC
Update Date2021-09-07 17:05:39 UTC
HMDB IDHMDB0061885
Secondary Accession Numbers
  • HMDB61885
Metabolite Identification
Common Name3-Methylpentane
Description3-Methylpentane belongs to the class of organic compounds known as branched alkanes. These are acyclic branched hydrocarbons having the general formula CnH2n+2. These solvents are also used as cleaning agents in the printing, textile, furniture, and shoemaking industries. Breathing large amounts of hexane causes numbness in the feet and hands, followed by muscle weakness in the feet and lower legs. 3-Methylpentane is possibly neutral. 3-Methylpentane is a potentially toxic compound. Inhalation of high concentrations produces first a state of mild euphoria, followed by somnolence with headaches and nausea.
Structure
Data?1563866243
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0061885 (3-Methylpentane)


  Mrv1652303202019012D          

  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 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 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 HMDB0061885 (3-Methylpentane)

HMDB0061885
     RDKit          3D
3-Methylpentane
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.0642    0.7916   -0.4183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3677    0.2285    0.7825 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0069   -0.3082    0.4941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0158   -1.4294   -0.5221 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9981    0.7592    0.1431 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3505    0.1262   -0.1348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6719    1.7952   -0.6471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1425    0.8962   -0.1796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9794    0.1278   -1.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3171    0.9565    1.5916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9845   -0.6272    1.1617 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3646   -0.7755    1.4521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1823   -1.0602   -1.5513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8435   -2.1237   -0.2010 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9176   -2.0125   -0.4095 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7123    1.3180   -0.7646 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1638    1.4734    0.9744 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2962   -0.6002   -0.9754 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6503   -0.4214    0.7986 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1225    0.8858   -0.3004 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
  6 19  1  0
  6 20  1  0
M  END
Download

3D SDF for HMDB0061885 (3-Methylpentane)


  Mrv1652303202019012D          

  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 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 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>
HMDB0061885

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC(C)CC

> <INCHI_IDENTIFIER>
InChI=1S/C6H14/c1-4-6(3)5-2/h6H,4-5H2,1-3H3

> <INCHI_KEY>
PFEOZHBOMNWTJB-UHFFFAOYSA-N

> <FORMULA>
C6H14

> <MOLECULAR_WEIGHT>
86.1754

> <EXACT_MASS>
86.109550448

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
12.017164929835634

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylpentane

> <ALOGPS_LOGP>
3.98

> <JCHEM_LOGP>
2.973588324

> <ALOGPS_LOGS>
-3.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
29.355800000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.58e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methylpentane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0061885 (3-Methylpentane)

HMDB0061885
     RDKit          3D
3-Methylpentane
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.0642    0.7916   -0.4183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3677    0.2285    0.7825 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0069   -0.3082    0.4941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0158   -1.4294   -0.5221 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9981    0.7592    0.1431 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3505    0.1262   -0.1348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6719    1.7952   -0.6471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1425    0.8962   -0.1796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9794    0.1278   -1.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3171    0.9565    1.5916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9845   -0.6272    1.1617 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3646   -0.7755    1.4521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1823   -1.0602   -1.5513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8435   -2.1237   -0.2010 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9176   -2.0125   -0.4095 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7123    1.3180   -0.7646 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1638    1.4734    0.9744 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2962   -0.6002   -0.9754 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6503   -0.4214    0.7986 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1225    0.8858   -0.3004 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
  6 19  1  0
  6 20  1  0
M  END
Download

PDB for HMDB0061885 (3-Methylpentane)

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  C   UNK     0       1.540  -2.667   0.000  0.00  0.00           C+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 HMDB0061885 (3-Methylpentane)

COMPND    HMDB0061885
HETATM    1  C1  UNL     1      -2.064   0.792  -0.418  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.368   0.228   0.783  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.007  -0.308   0.494  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.016  -1.429  -0.522  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.998   0.759   0.143  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.351   0.126  -0.135  1.00  0.00           C  
HETATM    7  H1  UNL     1      -1.672   1.795  -0.647  1.00  0.00           H  
HETATM    8  H2  UNL     1      -3.143   0.896  -0.180  1.00  0.00           H  
HETATM    9  H3  UNL     1      -1.979   0.128  -1.294  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.317   0.956   1.592  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.985  -0.627   1.162  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.365  -0.775   1.452  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.182  -1.060  -1.551  1.00  0.00           H  
HETATM   14  H8  UNL     1      -0.844  -2.124  -0.201  1.00  0.00           H  
HETATM   15  H9  UNL     1       0.918  -2.013  -0.410  1.00  0.00           H  
HETATM   16  H10 UNL     1       0.712   1.318  -0.765  1.00  0.00           H  
HETATM   17  H11 UNL     1       1.164   1.473   0.974  1.00  0.00           H  
HETATM   18  H12 UNL     1       2.296  -0.600  -0.975  1.00  0.00           H  
HETATM   19  H13 UNL     1       2.650  -0.421   0.799  1.00  0.00           H  
HETATM   20  H14 UNL     1       3.122   0.886  -0.300  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   19   20
END
Download

SMILES for HMDB0061885 (3-Methylpentane)

CCC(C)CC
Download

INCHI for HMDB0061885 (3-Methylpentane)

InChI=1S/C6H14/c1-4-6(3)5-2/h6H,4-5H2,1-3H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
3-Methyl-pentaneHMDB
Chemical FormulaC6H14
Average Molecular Weight86.1754
Monoisotopic Molecular Weight86.109550448
IUPAC Name3-methylpentane
Traditional Name3-methylpentane
CAS Registry NumberNot Available
SMILES
CCC(C)CC
InChI Identifier
InChI=1S/C6H14/c1-4-6(3)5-2/h6H,4-5H2,1-3H3
InChI KeyPFEOZHBOMNWTJB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as branched alkanes. These are acyclic branched hydrocarbons having the general formula CnH2n+2.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassSaturated hydrocarbons
Sub ClassAlkanes
Direct ParentBranched alkanes
Alternative ParentsNot Available
Substituents
  • Branched alkane
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Water Solubility0.046 g/LALOGPS
logP3.98ALOGPS
logP2.97ChemAxon
logS-3.3ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity29.36 m³·mol⁻¹ChemAxon
Polarizability12.02 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]+118.56131661259
DarkChem[M-H]-112.67731661259
DeepCCS[M+H]+129.55930932474
DeepCCS[M-H]-127.48530932474
DeepCCS[M-2H]-163.2230932474
DeepCCS[M+Na]+137.96130932474
AllCCS[M+H]+122.532859911
AllCCS[M+H-H2O]+118.132859911
AllCCS[M+NH4]+126.732859911
AllCCS[M+Na]+127.932859911
AllCCS[M-H]-134.232859911
AllCCS[M+Na-2H]-138.932859911
AllCCS[M+HCOO]-144.132859911

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, 2022.4.22 minutes32390414
Predicted by Siyang on May 30, 202217.9118 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.06 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1973.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid718.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid273.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid486.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid348.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid784.2 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 Acid745.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)297.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1425.7 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid544.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1575.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid506.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid437.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate581.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA543.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water79.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-MethylpentaneCCC(C)CC567.3Standard polar33892256
3-MethylpentaneCCC(C)CC586.5Standard non polar33892256
3-MethylpentaneCCC(C)CC584.8Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Methylpentane
METLIN IDNot Available
PubChem Compound7282
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. Brugnone F, Perbellini L, Grigolini L, Apostoli P: Solvent exposure in a shoe upper factory. II. Methylcyclopentane, 2-methylpentane, and 3-methylpentane concentration in alveolar and in environmental air and in blood. Int Arch Occup Environ Health. 1979 Jan 15;42(3-4):355-63. [PubMed:422277 ]
  2. Galvin JB, Bond G: 3-Methylpentane. CAS# 96-14-0. J Toxicol Environ Health A. 1999 Sep 10-24;58(1-2):93-102. [PubMed:10537375 ]
  3. PRETI M: [Some aspects of the general pharmacology of 2,2-bis(carbamoyloxymethyl)-3-methylpentane (mebutamate)]. Arch Ital Sci Farmacol. 1961 Jul;11:216-24. [PubMed:14488675 ]
  4. Favaro G, Romani A, Ortica F: The complex photochromic behaviour of 5,6-benzo(2H)dimethylchromene in 3-methylpentane solution. Photochem Photobiol Sci. 2003 Oct;2(10):1032-7. [PubMed:14606759 ]
  5. Huang W, Shahriari S, Richert R: Dynamics of glass-forming liquids. X. Dielectric relaxation of 3-bromopentane as molecular probes in 3-methylpentane. J Chem Phys. 2005 Oct 22;123(16):164504. [PubMed:16268709 ]
  6. Iwanowski I, Leluk K, Rudowski M, Kaatze U: Critical dynamics of the binary system nitroethane/3-methylpentane: relaxation rate and scaling function. J Phys Chem A. 2006 Apr 6;110(13):4313-9. [PubMed:16571033 ]
  7. Iwanowski I, Mirzaev SZ, Kaatze U: Relaxation rate and scaling function of the critical system 3-methylpentane-nitroethane-cyclohexane. J Chem Phys. 2008 Aug 14;129(6):064516. doi: 10.1063/1.2965521. [PubMed:18715094 ]
  8. Wikipedia [Link]
  9. Helmut Heinrich BUSCHMANN, Joerg HOLENZ, 'Process for Preparing Substituted 3-(1-amino-2-methylpentane-3-yl)phenyl Compounds.' U.S. Patent US20110306793, issued December 15, 2011. [Link]
  10. Werner Aquila, Walter Himmele, Werner Fliege, Hardo Siegel, 'Production of 3-methylpentane-1,5-diol.' U.S. Patent US3966827, issued January, 1971. [Link]