Hmdb loader

Showing metabocard for beta-GalCer (HMDB0249129)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 03:37:09 UTC
Update Date2021-09-26 22:59:47 UTC
HMDB IDHMDB0249129
Secondary Accession NumbersNone
Metabolite Identification
Common Namebeta-GalCer
DescriptionN-(3-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octadec-4-en-2-yl)tetracosanimidic acid belongs to the class of organic compounds known as glycosphingolipids. These are sphingolipids containing a saccharide moiety glycosidically attached to the sphingoid base. Although saccharide moieties are mostly O-glycosidically linked to the ceramide moiety, other sphingolipids with glycosidic bonds of other types (e.g. S-,C-, or N-type) has been reported. Based on a literature review very few articles have been published on N-(3-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octadec-4-en-2-yl)tetracosanimidic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Beta-galcer is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically beta-GalCer is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0249129 (beta-GalCer)


  Mrv1533004241518182D          

 57 57  0  0  0  0            999 V2000
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M  END
Download

3D MOL for HMDB0249129 (beta-GalCer)

HMDB0249129
     RDKit          3D
beta-GalCer
150150  0  0  0  0  0  0  0  0999 V2000
   14.8633    6.1093    1.8659 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4952    5.6013    0.4759 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0064    5.5829    0.3616 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5768    5.0901   -1.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1000    3.7039   -1.1958 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5811    2.7891   -0.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0743    2.6806   -0.1917 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6435    1.7153    0.8953 C   0  0  0  0  0  0  0  0  0  0  0  0
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   12.6235    6.6375    0.4375 H   0  0  0  0  0  0  0  0  0  0  0  0
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   13.0903    5.7574   -1.7462 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4960    5.1179   -1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7430    3.2897   -2.1901 H   0  0  0  0  0  0  0  0  0  0  0  0
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   12.9765    1.7590   -0.3910 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6719    3.7107    0.0279 H   0  0  0  0  0  0  0  0  0  0  0  0
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   11.2451    0.7887    0.7912 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6906    2.4873    1.0692 H   0  0  0  0  0  0  0  0  0  0  0  0
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   10.3264   -0.2170   -1.0943 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7673   -1.3208    1.1778 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8987   -2.3205   -0.2629 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1371   -3.0638    1.1973 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4846   -2.6334   -0.3741 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2637   -0.8344    2.1761 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.4655    0.2831   -0.8575 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0249129 (beta-GalCer)


  Mrv1533004241518182D          

 57 57  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0249129

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1OC(CO)C(O)C(O)C1O)C(O)C=CCCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C48H93NO8/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-44(52)49-41(40-56-48-47(55)46(54)45(53)43(39-50)57-48)42(51)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h35,37,41-43,45-48,50-51,53-55H,3-34,36,38-40H2,1-2H3,(H,49,52)

> <INCHI_KEY>
POQRWMRXUOPCLD-UHFFFAOYSA-N

> <FORMULA>
C48H93NO8

> <MOLECULAR_WEIGHT>
812.271

> <EXACT_MASS>
811.690118959

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
150

> <JCHEM_AVERAGE_POLARIZABILITY>
105.27306293048487

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-(3-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octadec-4-en-2-yl)tetracosanamide

> <ALOGPS_LOGP>
9.15

> <JCHEM_LOGP>
12.651068818000004

> <ALOGPS_LOGS>
-6.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.015713374329472

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.181223595454354

> <JCHEM_PKA_STRONGEST_BASIC>
-1.0489165328949452

> <JCHEM_POLAR_SURFACE_AREA>
148.71

> <JCHEM_REFRACTIVITY>
234.99699999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
41

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.86e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-(3-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octadec-4-en-2-yl)tetracosanamide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0249129 (beta-GalCer)

HMDB0249129
     RDKit          3D
beta-GalCer
150150  0  0  0  0  0  0  0  0999 V2000
   14.8633    6.1093    1.8659 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4952    5.6013    0.4759 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0064    5.5829    0.3616 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5768    5.0901   -1.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1000    3.7039   -1.1958 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5811    2.7891   -0.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0743    2.6806   -0.1917 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6435    1.7153    0.8953 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0249129 (beta-GalCer)

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0     -30.729  -5.288   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -29.341  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -28.069  -5.488   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -26.681  -4.820   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -25.409  -5.688   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -24.021  -5.021   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -22.749  -5.889   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -21.361  -5.221   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -20.089  -6.089   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -18.702  -5.421   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0     -17.430  -6.289   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -16.042  -5.622   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -14.770  -6.489   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -13.382  -5.822   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -12.110  -6.690   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -10.722  -6.022   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -9.450  -6.890   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -8.062  -6.222   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.790  -7.090   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.402  -6.423   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.130  -7.291   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.743  -6.623   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.471  -7.491   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.083  -6.823   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.033  -5.288   0.000  0.00  0.00           O+0
HETATM   26  N   UNK     0       1.189  -7.691   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0       2.577  -7.024   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.693  -5.488   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       1.421  -4.620   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       1.536  -3.084   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       0.264  -2.216   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       0.380  -0.681   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.892   0.187   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -0.777   1.723   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       1.767  -0.013   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       1.883   1.523   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       3.040  -0.881   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       4.427  -0.213   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       2.924  -2.417   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       4.196  -3.285   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0       3.849  -7.892   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       3.733  -9.427   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0       5.237  -7.224   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       6.509  -8.092   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       7.897  -7.424   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       9.169  -8.292   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      10.556  -7.625   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      11.829  -8.493   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      13.216  -7.825   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      14.488  -8.693   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      15.876  -8.025   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      17.148  -8.893   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      18.536  -8.225   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      19.808  -9.093   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      21.196  -8.426   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      22.468  -9.294   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      23.856  -8.626   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28   41                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   39                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   32   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   30   40                                                  
CONECT   40   39                                                            
CONECT   41   27   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56                                                            
MASTER        0    0    0    0    0    0    0    0   57    0  114    0
END
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3D PDB for HMDB0249129 (beta-GalCer)

COMPND    HMDB0249129
HETATM    1  C1  UNL     1      14.863   6.109   1.866  1.00  0.00           C  
HETATM    2  C2  UNL     1      14.495   5.601   0.476  1.00  0.00           C  
HETATM    3  C3  UNL     1      13.006   5.583   0.362  1.00  0.00           C  
HETATM    4  C4  UNL     1      12.577   5.090  -1.004  1.00  0.00           C  
HETATM    5  C5  UNL     1      13.100   3.704  -1.196  1.00  0.00           C  
HETATM    6  C6  UNL     1      12.581   2.789  -0.152  1.00  0.00           C  
HETATM    7  C7  UNL     1      11.074   2.681  -0.192  1.00  0.00           C  
HETATM    8  C8  UNL     1      10.644   1.715   0.895  1.00  0.00           C  
HETATM    9  C9  UNL     1       9.177   1.478   0.961  1.00  0.00           C  
HETATM   10  C10 UNL     1       8.619   0.898  -0.326  1.00  0.00           C  
HETATM   11  C11 UNL     1       9.269  -0.374  -0.714  1.00  0.00           C  
HETATM   12  C12 UNL     1       9.228  -1.518   0.203  1.00  0.00           C  
HETATM   13  C13 UNL     1       7.923  -2.138   0.558  1.00  0.00           C  
HETATM   14  C14 UNL     1       6.933  -1.294   1.222  1.00  0.00           C  
HETATM   15  C15 UNL     1       5.712  -1.025   0.822  1.00  0.00           C  
HETATM   16  C16 UNL     1       5.051  -1.512  -0.394  1.00  0.00           C  
HETATM   17  O1  UNL     1       5.008  -0.403  -1.332  1.00  0.00           O  
HETATM   18  C17 UNL     1       3.631  -1.952  -0.236  1.00  0.00           C  
HETATM   19  C18 UNL     1       3.323  -3.108   0.633  1.00  0.00           C  
HETATM   20  O2  UNL     1       3.737  -4.344   0.423  1.00  0.00           O  
HETATM   21  C19 UNL     1       5.022  -4.727   0.446  1.00  0.00           C  
HETATM   22  O3  UNL     1       5.186  -5.501   1.622  1.00  0.00           O  
HETATM   23  C20 UNL     1       4.642  -6.745   1.566  1.00  0.00           C  
HETATM   24  C21 UNL     1       3.178  -6.831   1.270  1.00  0.00           C  
HETATM   25  O4  UNL     1       2.864  -8.213   1.279  1.00  0.00           O  
HETATM   26  C22 UNL     1       5.479  -7.608   0.653  1.00  0.00           C  
HETATM   27  O5  UNL     1       6.515  -8.148   1.413  1.00  0.00           O  
HETATM   28  C23 UNL     1       6.081  -6.835  -0.481  1.00  0.00           C  
HETATM   29  O6  UNL     1       5.995  -7.619  -1.633  1.00  0.00           O  
HETATM   30  C24 UNL     1       5.439  -5.517  -0.765  1.00  0.00           C  
HETATM   31  O7  UNL     1       6.326  -4.794  -1.548  1.00  0.00           O  
HETATM   32  N1  UNL     1       2.899  -0.769   0.286  1.00  0.00           N  
HETATM   33  C25 UNL     1       1.947  -0.067  -0.482  1.00  0.00           C  
HETATM   34  O8  UNL     1       1.751  -0.465  -1.649  1.00  0.00           O  
HETATM   35  C26 UNL     1       1.227   1.071   0.088  1.00  0.00           C  
HETATM   36  C27 UNL     1       0.096   1.600  -0.754  1.00  0.00           C  
HETATM   37  C28 UNL     1      -0.897   0.501  -0.981  1.00  0.00           C  
HETATM   38  C29 UNL     1      -2.128   0.967  -1.779  1.00  0.00           C  
HETATM   39  C30 UNL     1      -2.950  -0.289  -1.965  1.00  0.00           C  
HETATM   40  C31 UNL     1      -4.234  -0.131  -2.669  1.00  0.00           C  
HETATM   41  C32 UNL     1      -5.253   0.766  -1.950  1.00  0.00           C  
HETATM   42  C33 UNL     1      -5.567   0.238  -0.611  1.00  0.00           C  
HETATM   43  C34 UNL     1      -6.468   0.875   0.327  1.00  0.00           C  
HETATM   44  C35 UNL     1      -7.900   1.129   0.003  1.00  0.00           C  
HETATM   45  C36 UNL     1      -8.196   2.133  -1.038  1.00  0.00           C  
HETATM   46  C37 UNL     1      -9.578   2.266  -1.496  1.00  0.00           C  
HETATM   47  C38 UNL     1     -10.642   2.561  -0.523  1.00  0.00           C  
HETATM   48  C39 UNL     1     -10.993   1.510   0.477  1.00  0.00           C  
HETATM   49  C40 UNL     1     -12.164   2.054   1.344  1.00  0.00           C  
HETATM   50  C41 UNL     1     -12.484   0.999   2.384  1.00  0.00           C  
HETATM   51  C42 UNL     1     -12.892  -0.286   1.779  1.00  0.00           C  
HETATM   52  C43 UNL     1     -14.153  -0.146   0.910  1.00  0.00           C  
HETATM   53  C44 UNL     1     -15.276   0.293   1.754  1.00  0.00           C  
HETATM   54  C45 UNL     1     -16.620   0.402   1.186  1.00  0.00           C  
HETATM   55  C46 UNL     1     -16.985   1.313   0.100  1.00  0.00           C  
HETATM   56  C47 UNL     1     -16.362   1.170  -1.246  1.00  0.00           C  
HETATM   57  C48 UNL     1     -17.030   2.241  -2.174  1.00  0.00           C  
HETATM   58  H1  UNL     1      14.387   5.427   2.604  1.00  0.00           H  
HETATM   59  H2  UNL     1      15.957   6.089   1.924  1.00  0.00           H  
HETATM   60  H3  UNL     1      14.461   7.128   2.029  1.00  0.00           H  
HETATM   61  H4  UNL     1      14.921   4.576   0.367  1.00  0.00           H  
HETATM   62  H5  UNL     1      14.934   6.205  -0.321  1.00  0.00           H  
HETATM   63  H6  UNL     1      12.624   6.637   0.437  1.00  0.00           H  
HETATM   64  H7  UNL     1      12.510   5.018   1.175  1.00  0.00           H  
HETATM   65  H8  UNL     1      13.090   5.757  -1.746  1.00  0.00           H  
HETATM   66  H9  UNL     1      11.496   5.118  -1.103  1.00  0.00           H  
HETATM   67  H10 UNL     1      12.743   3.290  -2.190  1.00  0.00           H  
HETATM   68  H11 UNL     1      14.212   3.672  -1.296  1.00  0.00           H  
HETATM   69  H12 UNL     1      12.954   3.007   0.870  1.00  0.00           H  
HETATM   70  H13 UNL     1      12.977   1.759  -0.391  1.00  0.00           H  
HETATM   71  H14 UNL     1      10.672   3.711   0.028  1.00  0.00           H  
HETATM   72  H15 UNL     1      10.726   2.414  -1.193  1.00  0.00           H  
HETATM   73  H16 UNL     1      10.957   2.175   1.857  1.00  0.00           H  
HETATM   74  H17 UNL     1      11.245   0.789   0.791  1.00  0.00           H  
HETATM   75  H18 UNL     1       8.691   2.487   1.069  1.00  0.00           H  
HETATM   76  H19 UNL     1       8.929   0.910   1.855  1.00  0.00           H  
HETATM   77  H20 UNL     1       8.842   1.658  -1.115  1.00  0.00           H  
HETATM   78  H21 UNL     1       7.551   0.805  -0.239  1.00  0.00           H  
HETATM   79  H22 UNL     1       8.743  -0.707  -1.671  1.00  0.00           H  
HETATM   80  H23 UNL     1      10.326  -0.217  -1.094  1.00  0.00           H  
HETATM   81  H24 UNL     1       9.767  -1.321   1.178  1.00  0.00           H  
HETATM   82  H25 UNL     1       9.899  -2.321  -0.263  1.00  0.00           H  
HETATM   83  H26 UNL     1       8.137  -3.064   1.197  1.00  0.00           H  
HETATM   84  H27 UNL     1       7.485  -2.633  -0.374  1.00  0.00           H  
HETATM   85  H28 UNL     1       7.264  -0.834   2.176  1.00  0.00           H  
HETATM   86  H29 UNL     1       5.094  -0.357   1.452  1.00  0.00           H  
HETATM   87  H30 UNL     1       5.615  -2.257  -0.979  1.00  0.00           H  
HETATM   88  H31 UNL     1       4.465   0.283  -0.858  1.00  0.00           H  
HETATM   89  H32 UNL     1       3.165  -2.131  -1.249  1.00  0.00           H  
HETATM   90  H33 UNL     1       2.158  -3.153   0.627  1.00  0.00           H  
HETATM   91  H34 UNL     1       3.470  -2.784   1.734  1.00  0.00           H  
HETATM   92  H35 UNL     1       5.694  -3.874   0.624  1.00  0.00           H  
HETATM   93  H36 UNL     1       4.759  -7.184   2.603  1.00  0.00           H  
HETATM   94  H37 UNL     1       2.641  -6.366   2.102  1.00  0.00           H  
HETATM   95  H38 UNL     1       2.863  -6.479   0.287  1.00  0.00           H  
HETATM   96  H39 UNL     1       2.024  -8.391   0.798  1.00  0.00           H  
HETATM   97  H40 UNL     1       4.855  -8.458   0.329  1.00  0.00           H  
HETATM   98  H41 UNL     1       6.770  -7.466   2.105  1.00  0.00           H  
HETATM   99  H42 UNL     1       7.187  -6.676  -0.310  1.00  0.00           H  
HETATM  100  H43 UNL     1       5.040  -7.945  -1.679  1.00  0.00           H  
HETATM  101  H44 UNL     1       4.522  -5.677  -1.398  1.00  0.00           H  
HETATM  102  H45 UNL     1       7.222  -4.902  -1.104  1.00  0.00           H  
HETATM  103  H46 UNL     1       3.110  -0.476   1.252  1.00  0.00           H  
HETATM  104  H47 UNL     1       1.901   1.924   0.348  1.00  0.00           H  
HETATM  105  H48 UNL     1       0.731   0.689   1.034  1.00  0.00           H  
HETATM  106  H49 UNL     1      -0.381   2.435  -0.196  1.00  0.00           H  
HETATM  107  H50 UNL     1       0.494   1.930  -1.736  1.00  0.00           H  
HETATM  108  H51 UNL     1      -1.230   0.038  -0.020  1.00  0.00           H  
HETATM  109  H52 UNL     1      -0.469  -0.319  -1.572  1.00  0.00           H  
HETATM  110  H53 UNL     1      -2.643   1.686  -1.110  1.00  0.00           H  
HETATM  111  H54 UNL     1      -1.831   1.451  -2.713  1.00  0.00           H  
HETATM  112  H55 UNL     1      -2.332  -1.023  -2.570  1.00  0.00           H  
HETATM  113  H56 UNL     1      -3.007  -0.768  -0.967  1.00  0.00           H  
HETATM  114  H57 UNL     1      -4.030   0.431  -3.627  1.00  0.00           H  
HETATM  115  H58 UNL     1      -4.720  -1.064  -2.978  1.00  0.00           H  
HETATM  116  H59 UNL     1      -6.179   0.594  -2.598  1.00  0.00           H  
HETATM  117  H60 UNL     1      -4.957   1.786  -2.073  1.00  0.00           H  
HETATM  118  H61 UNL     1      -5.905  -0.863  -0.704  1.00  0.00           H  
HETATM  119  H62 UNL     1      -4.581   0.064  -0.030  1.00  0.00           H  
HETATM  120  H63 UNL     1      -6.075   1.886   0.709  1.00  0.00           H  
HETATM  121  H64 UNL     1      -6.406   0.274   1.304  1.00  0.00           H  
HETATM  122  H65 UNL     1      -8.274   1.620   0.990  1.00  0.00           H  
HETATM  123  H66 UNL     1      -8.509   0.204  -0.064  1.00  0.00           H  
HETATM  124  H67 UNL     1      -7.448   2.196  -1.876  1.00  0.00           H  
HETATM  125  H68 UNL     1      -7.934   3.155  -0.511  1.00  0.00           H  
HETATM  126  H69 UNL     1      -9.661   2.997  -2.370  1.00  0.00           H  
HETATM  127  H70 UNL     1      -9.849   1.258  -1.991  1.00  0.00           H  
HETATM  128  H71 UNL     1     -10.417   3.532   0.056  1.00  0.00           H  
HETATM  129  H72 UNL     1     -11.596   2.895  -1.073  1.00  0.00           H  
HETATM  130  H73 UNL     1     -10.238   1.264   1.188  1.00  0.00           H  
HETATM  131  H74 UNL     1     -11.364   0.577  -0.025  1.00  0.00           H  
HETATM  132  H75 UNL     1     -11.793   2.949   1.876  1.00  0.00           H  
HETATM  133  H76 UNL     1     -13.023   2.309   0.700  1.00  0.00           H  
HETATM  134  H77 UNL     1     -13.248   1.386   3.068  1.00  0.00           H  
HETATM  135  H78 UNL     1     -11.529   0.881   2.994  1.00  0.00           H  
HETATM  136  H79 UNL     1     -12.149  -0.813   1.173  1.00  0.00           H  
HETATM  137  H80 UNL     1     -13.149  -0.985   2.626  1.00  0.00           H  
HETATM  138  H81 UNL     1     -13.889   0.520   0.083  1.00  0.00           H  
HETATM  139  H82 UNL     1     -14.335  -1.165   0.507  1.00  0.00           H  
HETATM  140  H83 UNL     1     -15.333  -0.441   2.622  1.00  0.00           H  
HETATM  141  H84 UNL     1     -15.010   1.258   2.300  1.00  0.00           H  
HETATM  142  H85 UNL     1     -16.927  -0.669   0.909  1.00  0.00           H  
HETATM  143  H86 UNL     1     -17.350   0.611   2.054  1.00  0.00           H  
HETATM  144  H87 UNL     1     -16.840   2.381   0.459  1.00  0.00           H  
HETATM  145  H88 UNL     1     -18.123   1.289  -0.080  1.00  0.00           H  
HETATM  146  H89 UNL     1     -15.293   1.419  -1.269  1.00  0.00           H  
HETATM  147  H90 UNL     1     -16.502   0.166  -1.682  1.00  0.00           H  
HETATM  148  H91 UNL     1     -16.402   2.381  -3.055  1.00  0.00           H  
HETATM  149  H92 UNL     1     -17.125   3.179  -1.618  1.00  0.00           H  
HETATM  150  H93 UNL     1     -18.044   1.876  -2.394  1.00  0.00           H  
CONECT    1    2   58   59   60
CONECT    2    3   61   62
CONECT    3    4   63   64
CONECT    4    5   65   66
CONECT    5    6   67   68
CONECT    6    7   69   70
CONECT    7    8   71   72
CONECT    8    9   73   74
CONECT    9   10   75   76
CONECT   10   11   77   78
CONECT   11   12   79   80
CONECT   12   13   81   82
CONECT   13   14   83   84
CONECT   14   15   15   85
CONECT   15   16   86
CONECT   16   17   18   87
CONECT   17   88
CONECT   18   19   32   89
CONECT   19   20   90   91
CONECT   20   21
CONECT   21   22   30   92
CONECT   22   23
CONECT   23   24   26   93
CONECT   24   25   94   95
CONECT   25   96
CONECT   26   27   28   97
CONECT   27   98
CONECT   28   29   30   99
CONECT   29  100
CONECT   30   31  101
CONECT   31  102
CONECT   32   33  103
CONECT   33   34   34   35
CONECT   35   36  104  105
CONECT   36   37  106  107
CONECT   37   38  108  109
CONECT   38   39  110  111
CONECT   39   40  112  113
CONECT   40   41  114  115
CONECT   41   42  116  117
CONECT   42   43  118  119
CONECT   43   44  120  121
CONECT   44   45  122  123
CONECT   45   46  124  125
CONECT   46   47  126  127
CONECT   47   48  128  129
CONECT   48   49  130  131
CONECT   49   50  132  133
CONECT   50   51  134  135
CONECT   51   52  136  137
CONECT   52   53  138  139
CONECT   53   54  140  141
CONECT   54   55  142  143
CONECT   55   56  144  145
CONECT   56   57  146  147
CONECT   57  148  149  150
END
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SMILES for HMDB0249129 (beta-GalCer)

CCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1OC(CO)C(O)C(O)C1O)C(O)C=CCCCCCCCCCCCCC
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INCHI for HMDB0249129 (beta-GalCer)

InChI=1S/C48H93NO8/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-44(52)49-41(40-56-48-47(55)46(54)45(53)43(39-50)57-48)42(51)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h35,37,41-43,45-48,50-51,53-55H,3-34,36,38-40H2,1-2H3,(H,49,52)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
N-(3-Hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octadec-4-en-2-yl)tetracosanimidateGenerator
beta-D-Galactosyl-N-(N-acyl)-D-sphingosineMeSH
CerasineMeSH
KerasinMeSH
Chemical FormulaC48H93NO8
Average Molecular Weight812.271
Monoisotopic Molecular Weight811.690118959
IUPAC NameN-(3-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octadec-4-en-2-yl)tetracosanamide
Traditional NameN-(3-hydroxy-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octadec-4-en-2-yl)tetracosanamide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCCCCCCCCCC(=O)NC(COC1OC(CO)C(O)C(O)C1O)C(O)C=CCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C48H93NO8/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-44(52)49-41(40-56-48-47(55)46(54)45(53)43(39-50)57-48)42(51)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h35,37,41-43,45-48,50-51,53-55H,3-34,36,38-40H2,1-2H3,(H,49,52)
InChI KeyPOQRWMRXUOPCLD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycosphingolipids. These are sphingolipids containing a saccharide moiety glycosidically attached to the sphingoid base. Although saccharide moieties are mostly O-glycosidically linked to the ceramide moiety, other sphingolipids with glycosidic bonds of other types (e.G. S-,C-, or N-type) has been reported.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassGlycosphingolipids
Direct ParentGlycosphingolipids
Alternative Parents
Substituents
  • Glycosphingolipid
  • Fatty acyl glycoside
  • Fatty acyl glycoside of mono- or disaccharide
  • Alkyl glycoside
  • Hexose monosaccharide
  • Glycosyl compound
  • O-glycosyl compound
  • Monosaccharide
  • Fatty acyl
  • Oxane
  • Secondary alcohol
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organoheterocyclic compound
  • Carboximidic acid
  • Carboximidic acid derivative
  • Oxacycle
  • Acetal
  • Polyol
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Alcohol
  • Organonitrogen compound
  • Organooxygen compound
  • Organopnictogen compound
  • Primary alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP9.15ALOGPS
logP12.65ChemAxon
logS-6.6ALOGPS
pKa (Strongest Acidic)12.18ChemAxon
pKa (Strongest Basic)-1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area148.71 ŲChemAxon
Rotatable Bond Count41ChemAxon
Refractivity235 m³·mol⁻¹ChemAxon
Polarizability105.27 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+298.53430932474
DeepCCS[M-H]-296.13930932474
DeepCCS[M-2H]-329.13930932474
DeepCCS[M+Na]+305.530932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
beta-GalCer,1TMS,isomer #1CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO[Si](C)(C)C)C(O)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC6375.7Semi standard non polar33892256
beta-GalCer,1TMS,isomer #1CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO[Si](C)(C)C)C(O)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC5806.5Standard non polar33892256
beta-GalCer,1TMS,isomer #1CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO[Si](C)(C)C)C(O)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC7394.7Standard polar33892256
beta-GalCer,1TMS,isomer #2CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O[Si](C)(C)C)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC6318.8Semi standard non polar33892256
beta-GalCer,1TMS,isomer #2CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O[Si](C)(C)C)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC5757.9Standard non polar33892256
beta-GalCer,1TMS,isomer #2CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O[Si](C)(C)C)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC7307.3Standard polar33892256
beta-GalCer,1TMS,isomer #3CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O)C(O[Si](C)(C)C)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC6323.8Semi standard non polar33892256
beta-GalCer,1TMS,isomer #3CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O)C(O[Si](C)(C)C)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC5751.9Standard non polar33892256
beta-GalCer,1TMS,isomer #3CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O)C(O[Si](C)(C)C)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC7331.6Standard polar33892256
beta-GalCer,1TMS,isomer #4CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O)C(O)C1O[Si](C)(C)C)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC6302.4Semi standard non polar33892256
beta-GalCer,1TMS,isomer #4CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O)C(O)C1O[Si](C)(C)C)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC5761.9Standard non polar33892256
beta-GalCer,1TMS,isomer #4CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O)C(O)C1O[Si](C)(C)C)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC7324.5Standard polar33892256
beta-GalCer,1TMS,isomer #5CCCCCCCCCCCCCC=CC(O[Si](C)(C)C)C(COC1OC(CO)C(O)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC6355.8Semi standard non polar33892256
beta-GalCer,1TMS,isomer #5CCCCCCCCCCCCCC=CC(O[Si](C)(C)C)C(COC1OC(CO)C(O)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC5751.9Standard non polar33892256
beta-GalCer,1TMS,isomer #5CCCCCCCCCCCCCC=CC(O[Si](C)(C)C)C(COC1OC(CO)C(O)C(O)C1O)NC(=O)CCCCCCCCCCCCCCCCCCCCCCC7306.2Standard polar33892256
beta-GalCer,1TMS,isomer #6CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O)C(O)C1O)N(C(=O)CCCCCCCCCCCCCCCCCCCCCCC)[Si](C)(C)C6294.0Semi standard non polar33892256
beta-GalCer,1TMS,isomer #6CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O)C(O)C1O)N(C(=O)CCCCCCCCCCCCCCCCCCCCCCC)[Si](C)(C)C5756.6Standard non polar33892256
beta-GalCer,1TMS,isomer #6CCCCCCCCCCCCCC=CC(O)C(COC1OC(CO)C(O)C(O)C1O)N(C(=O)CCCCCCCCCCCCCCCCCCCCCCC)[Si](C)(C)C7430.9Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - beta-GalCer 10V, Positive-QTOFsplash10-03ec-6100009570-72c4fafb1689f053b1332021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - beta-GalCer 20V, Positive-QTOFsplash10-01qc-6200109310-652d768095c695956ff82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - beta-GalCer 40V, Positive-QTOFsplash10-000x-9141002000-0ca2e30defedc8d5c8722021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - beta-GalCer 10V, Negative-QTOFsplash10-03di-0000000090-84bdb4292d1325f2ce512021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - beta-GalCer 20V, Negative-QTOFsplash10-03di-6110103790-59611867e850e6ad0a322021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - beta-GalCer 40V, Negative-QTOFsplash10-0c00-9242612000-dfabddbafcf3744f9a7c2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot 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 ID21230508
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound74950937
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]