Hmdb loader

Showing metabocard for Tridecane (HMDB0034284)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 19:05:22 UTC
Update Date2022-03-07 02:54:03 UTC
HMDB IDHMDB0034284
Secondary Accession Numbers
  • HMDB34284
Metabolite Identification
Common NameTridecane
DescriptionTridecane, also known as CH3-[CH2]11-CH3 or tridekan, belongs to the class of organic compounds known as alkanes. These are acyclic branched or unbranched hydrocarbons having the general formula CnH2n+2 , and therefore consisting entirely of hydrogen atoms and saturated carbon atoms. Thus, tridecane is considered to be a hydrocarbon. Tridecane is an alkane tasting compound. Tridecane is found, on average, in the highest concentration within a few different foods, such as black walnuts (Juglans nigra), limes (Citrus aurantiifolia), and safflowers (Carthamus tinctorius). Tridecane has also been detected, but not quantified in, several different foods, such as sweet bays (Laurus nobilis), citrus, cauliflowers (Brassica oleracea var. botrytis), allspices (Pimenta dioica), and cardamoms (Elettaria cardamomum). This could make tridecane a potential biomarker for the consumption of these foods. Tridecane is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Tridecane.
Structure
Data?1563862539
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034284 (Tridecane)


  Mrv1652303202019002D          

 13 12  0  0  0  0            999 V2000
   -3.6020   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9717   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2572   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1730   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5427   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4586   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8283   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7441   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1138   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0296   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3993   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 13 12  1  0  0  0  0
M  END
Download

3D MOL for HMDB0034284 (Tridecane)

HMDB0034284
     RDKit          3D
Tridecane
 41 40  0  0  0  0  0  0  0  0999 V2000
    4.6954    1.9590    0.5066 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6017    0.7437    1.3779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4254   -0.1566    0.8910 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6512   -0.5793   -0.5033 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7481   -1.4932   -1.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3252   -1.2156   -1.3961 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4363   -1.1163   -0.1987 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0142   -0.8347   -0.6656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9185   -0.7333    0.5460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3383   -0.4632    0.1848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5221    0.8314   -0.5741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9776    1.0656   -0.9195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7981    1.1356    0.3379 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2193    1.6653   -0.4386 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6865    2.3551    0.3375 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3390    2.6992    0.9961 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5058    0.1330    1.2195 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4470    0.9685    2.4499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5840    0.6096    0.8970 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2446   -0.9022    1.6432 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8604    0.3207   -1.1523 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6832   -1.0834   -0.5001 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8770   -2.5796   -0.8094 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1890   -1.6320   -2.2473 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8375   -2.0223   -2.0460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1611   -0.2752   -2.0226 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3342   -2.1270    0.3065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7067   -0.4303    0.5822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0252    0.0824   -1.2523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3401   -1.7032   -1.2547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5333    0.0064    1.2916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8762   -1.7208    1.0505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9693   -0.4848    1.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6833   -1.2851   -0.4850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9053    0.8279   -1.4961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2241    1.6652    0.1018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0208    2.0642   -1.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3928    0.2754   -1.5618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8114    1.5285    0.0992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8956    0.1233    0.7888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3123    1.7781    1.0906 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  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  2 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
  8 29  1  0
  8 30  1  0
  9 31  1  0
  9 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 11 36  1  0
 12 37  1  0
 12 38  1  0
 13 39  1  0
 13 40  1  0
 13 41  1  0
M  END
Download

3D SDF for HMDB0034284 (Tridecane)


  Mrv1652303202019002D          

 13 12  0  0  0  0            999 V2000
   -3.6020   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9717   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2572   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1730   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5427   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4586   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8283   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7441   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1138   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0296   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3993   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 13 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034284

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C13H28/c1-3-5-7-9-11-13-12-10-8-6-4-2/h3-13H2,1-2H3

> <INCHI_KEY>
IIYFAKIEWZDVMP-UHFFFAOYSA-N

> <FORMULA>
C13H28

> <MOLECULAR_WEIGHT>
184.3614

> <EXACT_MASS>
184.219100896

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
26.95794596956523

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
tridecane

> <ALOGPS_LOGP>
6.85

> <JCHEM_LOGP>
6.243118547666667

> <ALOGPS_LOGS>
-6.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
61.615199999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.60e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tridecane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0034284 (Tridecane)

HMDB0034284
     RDKit          3D
Tridecane
 41 40  0  0  0  0  0  0  0  0999 V2000
    4.6954    1.9590    0.5066 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6017    0.7437    1.3779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4254   -0.1566    0.8910 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6512   -0.5793   -0.5033 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7481   -1.4932   -1.1890 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3252   -1.2156   -1.3961 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4363   -1.1163   -0.1987 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0142   -0.8347   -0.6656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9185   -0.7333    0.5460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3383   -0.4632    0.1848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5221    0.8314   -0.5741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9776    1.0656   -0.9195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7981    1.1356    0.3379 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2193    1.6653   -0.4386 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6865    2.3551    0.3375 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3390    2.6992    0.9961 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5058    0.1330    1.2195 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4470    0.9685    2.4499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5840    0.6096    0.8970 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2446   -0.9022    1.6432 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8604    0.3207   -1.1523 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6832   -1.0834   -0.5001 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8770   -2.5796   -0.8094 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1890   -1.6320   -2.2473 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8375   -2.0223   -2.0460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1611   -0.2752   -2.0226 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3342   -2.1270    0.3065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7067   -0.4303    0.5822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0252    0.0824   -1.2523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3401   -1.7032   -1.2547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5333    0.0064    1.2916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8762   -1.7208    1.0505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9693   -0.4848    1.0756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6833   -1.2851   -0.4850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9053    0.8279   -1.4961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2241    1.6652    0.1018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0208    2.0642   -1.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3928    0.2754   -1.5618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8114    1.5285    0.0992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8956    0.1233    0.7888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3123    1.7781    1.0906 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  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  2 18  1  0
  3 19  1  0
  3 20  1  0
  4 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  7 27  1  0
  7 28  1  0
  8 29  1  0
  8 30  1  0
  9 31  1  0
  9 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 11 36  1  0
 12 37  1  0
 12 38  1  0
 13 39  1  0
 13 40  1  0
 13 41  1  0
M  END
Download

PDB for HMDB0034284 (Tridecane)

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      -6.724  -3.231   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.281  -3.231   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.390  -4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.947  -4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.056  -3.231   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.613  -3.231   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.723  -4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.279  -4.001   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.389  -3.231   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.946  -3.231   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.055  -4.001   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.612  -4.001   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.278  -3.231   0.000  0.00  0.00           C+0
CONECT    1    3                                                            
CONECT    2    4                                                            
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    8                                                       
CONECT    7    5    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    8   12                                                       
CONECT   11    9   13                                                       
CONECT   12   10   13                                                       
CONECT   13   11   12                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
Download

3D PDB for HMDB0034284 (Tridecane)

COMPND    HMDB0034284
HETATM    1  C1  UNL     1       4.695   1.959   0.507  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.602   0.744   1.378  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.425  -0.157   0.891  1.00  0.00           C  
HETATM    4  C4  UNL     1       3.651  -0.579  -0.503  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.748  -1.493  -1.189  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.325  -1.216  -1.396  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.436  -1.116  -0.199  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.014  -0.835  -0.666  1.00  0.00           C  
HETATM    9  C9  UNL     1      -1.918  -0.733   0.546  1.00  0.00           C  
HETATM   10  C10 UNL     1      -3.338  -0.463   0.185  1.00  0.00           C  
HETATM   11  C11 UNL     1      -3.522   0.831  -0.574  1.00  0.00           C  
HETATM   12  C12 UNL     1      -4.978   1.066  -0.919  1.00  0.00           C  
HETATM   13  C13 UNL     1      -5.798   1.136   0.338  1.00  0.00           C  
HETATM   14  H1  UNL     1       5.219   1.665  -0.439  1.00  0.00           H  
HETATM   15  H2  UNL     1       3.686   2.355   0.338  1.00  0.00           H  
HETATM   16  H3  UNL     1       5.339   2.699   0.996  1.00  0.00           H  
HETATM   17  H4  UNL     1       5.506   0.133   1.219  1.00  0.00           H  
HETATM   18  H5  UNL     1       4.447   0.968   2.450  1.00  0.00           H  
HETATM   19  H6  UNL     1       2.584   0.610   0.897  1.00  0.00           H  
HETATM   20  H7  UNL     1       3.245  -0.902   1.643  1.00  0.00           H  
HETATM   21  H8  UNL     1       3.860   0.321  -1.152  1.00  0.00           H  
HETATM   22  H9  UNL     1       4.683  -1.083  -0.500  1.00  0.00           H  
HETATM   23  H10 UNL     1       2.877  -2.580  -0.809  1.00  0.00           H  
HETATM   24  H11 UNL     1       3.189  -1.632  -2.247  1.00  0.00           H  
HETATM   25  H12 UNL     1       0.837  -2.022  -2.046  1.00  0.00           H  
HETATM   26  H13 UNL     1       1.161  -0.275  -2.023  1.00  0.00           H  
HETATM   27  H14 UNL     1       0.334  -2.127   0.306  1.00  0.00           H  
HETATM   28  H15 UNL     1       0.707  -0.430   0.582  1.00  0.00           H  
HETATM   29  H16 UNL     1      -1.025   0.082  -1.252  1.00  0.00           H  
HETATM   30  H17 UNL     1      -1.340  -1.703  -1.255  1.00  0.00           H  
HETATM   31  H18 UNL     1      -1.533   0.006   1.292  1.00  0.00           H  
HETATM   32  H19 UNL     1      -1.876  -1.721   1.050  1.00  0.00           H  
HETATM   33  H20 UNL     1      -3.969  -0.485   1.076  1.00  0.00           H  
HETATM   34  H21 UNL     1      -3.683  -1.285  -0.485  1.00  0.00           H  
HETATM   35  H22 UNL     1      -2.905   0.828  -1.496  1.00  0.00           H  
HETATM   36  H23 UNL     1      -3.224   1.665   0.102  1.00  0.00           H  
HETATM   37  H24 UNL     1      -5.021   2.064  -1.418  1.00  0.00           H  
HETATM   38  H25 UNL     1      -5.393   0.275  -1.562  1.00  0.00           H  
HETATM   39  H26 UNL     1      -6.811   1.529   0.099  1.00  0.00           H  
HETATM   40  H27 UNL     1      -5.896   0.123   0.789  1.00  0.00           H  
HETATM   41  H28 UNL     1      -5.312   1.778   1.091  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3   17   18
CONECT    3    4   19   20
CONECT    4    5   21   22
CONECT    5    6   23   24
CONECT    6    7   25   26
CONECT    7    8   27   28
CONECT    8    9   29   30
CONECT    9   10   31   32
CONECT   10   11   33   34
CONECT   11   12   35   36
CONECT   12   13   37   38
CONECT   13   39   40   41
END
Download

SMILES for HMDB0034284 (Tridecane)

CCCCCCCCCCCCC
Download

INCHI for HMDB0034284 (Tridecane)

InChI=1S/C13H28/c1-3-5-7-9-11-13-12-10-8-6-4-2/h3-13H2,1-2H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
CH3-[CH2]11-CH3ChEBI
N-TridecaneChEBI
TridekanChEBI
(2S,3S)-2-Hydroxytridecane-1,2,3-tricarboxylateHMDB
Alkanes, C12-14HMDB
Lipid fragmentHMDB
TRDHMDB
Chemical FormulaC13H28
Average Molecular Weight184.3614
Monoisotopic Molecular Weight184.219100896
IUPAC Nametridecane
Traditional Nametridecane
CAS Registry Number629-50-5
SMILES
CCCCCCCCCCCCC
InChI Identifier
InChI=1S/C13H28/c1-3-5-7-9-11-13-12-10-8-6-4-2/h3-13H2,1-2H3
InChI KeyIIYFAKIEWZDVMP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkanes. These are acyclic branched or unbranched hydrocarbons having the general formula CnH2n+2 , and therefore consisting entirely of hydrogen atoms and saturated carbon atoms.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassSaturated hydrocarbons
Sub ClassAlkanes
Direct ParentAlkanes
Alternative ParentsNot Available
Substituents
  • Acyclic alkane
  • Alkane
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological roleEnvironmental role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-5.5 °CNot Available
Boiling Point235.00 to 236.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility4.7e-06 mg/mL at 25 °CNot Available
LogP7.331 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility9.6e-05 g/LALOGPS
logP6.85ALOGPS
logP6.24ChemAxon
logS-6.3ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity61.62 m³·mol⁻¹ChemAxon
Polarizability26.96 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+147.94331661259
DarkChem[M-H]-146.07431661259
DeepCCS[M+H]+153.84630932474
DeepCCS[M-H]-150.6130932474
DeepCCS[M-2H]-187.69230932474
DeepCCS[M+Na]+163.21430932474
AllCCS[M+H]+154.232859911
AllCCS[M+H-H2O]+150.532859911
AllCCS[M+NH4]+157.732859911
AllCCS[M+Na]+158.732859911
AllCCS[M-H]-154.932859911
AllCCS[M+Na-2H]-156.632859911
AllCCS[M+HCOO]-158.432859911

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, 2022.9.78 minutes32390414
Predicted by Siyang on May 30, 202225.186 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.83 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid51.8 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2908.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid906.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid332.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid593.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid524.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1089.9 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 Acid1099.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)176.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2265.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid687.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2045.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid865.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid648.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate920.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA713.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water8.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
TridecaneCCCCCCCCCCCCC1306.6Standard polar33892256
TridecaneCCCCCCCCCCCCC1301.1Standard non polar33892256
TridecaneCCCCCCCCCCCCC1297.9Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Breath
  • Feces
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BreathDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not Specified
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
    • Zerihun T. Dame, ...
 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BreathDetected but not QuantifiedNot QuantifiedChildren (1-13 years old)Not SpecifiedAsthma details
Associated Disorders and Diseases
Disease References
Asthma
  1. Dallinga JW, Robroeks CM, van Berkel JJ, Moonen EJ, Godschalk RW, Jobsis Q, Dompeling E, Wouters EF, van Schooten FJ: Volatile organic compounds in exhaled breath as a diagnostic tool for asthma in children. Clin Exp Allergy. 2010 Jan;40(1):68-76. doi: 10.1111/j.1365-2222.2009.03343.x. Epub 2009 Sep 28. [PubMed:19793086 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB012622
KNApSAcK IDC00048561
Chemspider ID11882
KEGG Compound IDC13834
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkTridecane
METLIN IDNot Available
PubChem Compound12388
PDB IDTRD
ChEBI ID35998
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1292341
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .