Hmdb loader

Showing metabocard for N-Glycoloylganglioside GM2 (HMDB0000770)

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enzymes (46) Show 46 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-03-07 02:49:06 UTC
HMDB IDHMDB0000770
Secondary Accession Numbers
  • HMDB00770
Metabolite Identification
Common NameN-Glycoloylganglioside GM2
DescriptionN-Glycoloylganglioside GM2 is a glycosphingolipid (ceramide and oligosaccharide)or oligoglycosylceramide with one or more sialic acids (i.e. n-acetylneuraminic acid) linked on the sugar chain. It is a component the cell plasma membrane which modulates cell signal transduction events. Gangliosides have been found to be highly important in immunology. Ganglioside AII carries a net-negative charge at pH 7.0 and is acidic. Gangliosides can amount to 6% of the weight of lipids from brain, but they are found at low levels in all animal tissues.
Structure
Data?1582752155
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000770 (N-Glycoloylganglioside GM2)


  Mrv1652305231920032D          

 52 52  0  0  1  0            999 V2000
   12.5594  -16.6272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9884  -16.6272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7015  -15.8022    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5594  -18.2772    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7015  -18.2772    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1305  -19.1021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1305  -16.6272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.7028  -14.5647    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.2739  -14.5647    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.9884  -15.8022    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   16.8462  -15.8022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   18.2751  -15.8022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9896  -15.3897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   16.8462   -8.3773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8462   -9.2023    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.4185  -15.3897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5607   -7.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1318   -9.6148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.1329  -15.8022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5607   -7.1398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1318  -10.4398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.8474  -15.3897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2751   -6.7273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   15.4173  -11.6773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2763  -15.3897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9896   -5.4898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7028  -12.0897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9907  -15.8022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   19.7040   -4.2524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7015  -16.6272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   11.8449  -17.0396    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   13.9884  -14.1522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 12  1  0  0  0  0
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 10  2  1  6  0  0  0
  3 43  1  0  0  0  0
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  7 47  1  0  0  0  0
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 47 49  1  0  0  0  0
 48 50  1  0  0  0  0
 49 51  1  0  0  0  0
 50 51  1  0  0  0  0
M  END
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3D MOL for HMDB0000770 (N-Glycoloylganglioside GM2)

HMDB0000770
     RDKit          3D
N-Glycoloylganglioside GM2
137137  0  0  0  0  0  0  0  0999 V2000
   13.6453   -0.3594    0.2265 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7379    0.4003   -0.7358 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3128    0.3693   -0.1733 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3720    1.0892   -1.1035 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6787    2.5052   -1.3584 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7587    3.4896   -0.2779 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6161    3.7835    0.6114 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1535    2.7268    1.5212 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9632    3.0754    2.3479 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6741    3.0864    1.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4962    3.9394    0.4440 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.7333    2.3838   -0.3200 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3622    2.2946   -0.9600 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0325    0.8340   -1.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8702    0.1208    0.0667 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5613   -1.3262    0.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3697   -1.7011   -0.7073 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1305   -1.1529   -1.7881 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4601   -2.7015   -0.2295 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6898   -3.0882   -1.0037 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4380   -4.1652   -0.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7065   -5.3058   -0.1529 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3078   -5.8852   -1.3268 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1049   -7.0892   -1.4484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9785   -7.4517   -2.7910 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1108   -8.2681   -3.3191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3196   -7.5445   -3.2103 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3476   -8.2129   -2.8877 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9157   -7.9751   -4.1212 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2317   -7.8328   -1.7181 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7692   -8.5163   -0.5797 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1129   -6.3444   -1.3769 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8881   -5.6509   -2.2807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5727   -1.8891   -1.3422 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6833   -2.3806   -2.0855 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.8837    0.0507   -0.6671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4689    0.9241    0.3644 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.6493    0.1931   -0.2948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0196    1.3188    0.6619 C   0  0  0  0  0  0  0  0  0  0  0  0
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   13.0313    1.4581   -0.7704 H   0  0  0  0  0  0  0  0  0  0  0  0
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    9.3424    0.8010   -0.9088 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9716    2.8331   -2.1919 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.6768    2.5179   -1.9379 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.6838    3.3311    0.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0341    4.4913   -0.7669 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0753    4.5900    1.3518 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8618    4.3674    0.0896 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0003    2.4583    2.2220 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8491    1.7765    0.9776 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1244    4.0550    2.9041 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9278    2.2769    3.1635 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8275    3.1747    2.3718 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4818    1.9839    1.2481 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0324    3.5473   -0.4785 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6885    5.0090    0.6114 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4128    4.2178    0.7998 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8587    4.4939   -0.9116 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4990    1.8522   -0.8983 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7001    1.8989    0.7013 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5908    2.7759   -0.2946 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3957    2.8143   -1.9331 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0923    0.8280   -1.8327 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8913    0.4458   -1.8289 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0666    0.6314    0.6841 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8144    0.2190    0.7062 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.2881   -3.3687   -2.0299 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.0835   -8.0891    0.2551 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6261   -6.2478   -0.3900 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3265   -5.1633   -2.9008 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0000770 (N-Glycoloylganglioside GM2)


  Mrv1652305231920032D          

 52 52  0  0  1  0            999 V2000
   12.5594  -16.6272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9884  -16.6272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1 12  1  0  0  0  0
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 50 51  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000770

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)[C@@H](O)CCCCCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C43H85NO8/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-39(47)44-36(35-51-43-42(50)41(49)40(48)38(34-45)52-43)37(46)32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h36-38,40-43,45-46,48-50H,3-35H2,1-2H3,(H,44,47)/t36-,37-,38+,40+,41-,42+,43+/m0/s1

> <INCHI_KEY>
SYMIJCRAJBNLEL-YPQBUIQASA-N

> <FORMULA>
C43H85NO8

> <MOLECULAR_WEIGHT>
744.1369

> <EXACT_MASS>
743.627518701

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
137

> <JCHEM_AVERAGE_POLARIZABILITY>
95.72465997273954

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2S,3S)-3-hydroxy-1-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}nonadecan-2-yl]octadecanamide

> <ALOGPS_LOGP>
8.25

> <JCHEM_LOGP>
10.634239689666668

> <ALOGPS_LOGS>
-6.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.071169926754877

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.191471743671366

> <JCHEM_PKA_STRONGEST_BASIC>
-1.0432406014040918

> <JCHEM_POLAR_SURFACE_AREA>
148.71

> <JCHEM_REFRACTIVITY>
211.0294

> <JCHEM_ROTATABLE_BOND_COUNT>
37

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.08e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2S,3S)-3-hydroxy-1-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}nonadecan-2-yl]octadecanamide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000770 (N-Glycoloylganglioside GM2)

HMDB0000770
     RDKit          3D
N-Glycoloylganglioside GM2
137137  0  0  0  0  0  0  0  0999 V2000
   13.6453   -0.3594    0.2265 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7379    0.4003   -0.7358 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3128    0.3693   -0.1733 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3720    1.0892   -1.1035 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6787    2.5052   -1.3584 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7587    3.4896   -0.2779 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6161    3.7835    0.6114 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1535    2.7268    1.5212 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9632    3.0754    2.3479 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6741    3.0864    1.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4962    3.9394    0.4440 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0209    3.8310   -0.0482 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7333    2.3838   -0.3200 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3622    2.2946   -0.9600 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0325    0.8340   -1.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8702    0.1208    0.0667 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5613   -1.3262    0.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3697   -1.7011   -0.7073 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1305   -1.1529   -1.7881 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4601   -2.7015   -0.2295 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6898   -3.0882   -1.0037 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4380   -4.1652   -0.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7065   -5.3058   -0.1529 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0000770 (N-Glycoloylganglioside GM2)

HEADER    PROTEIN                                 23-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAY-19         0                                  
HETATM    1  O   UNK     0      23.444 -31.037   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      26.112 -31.037   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      18.109 -29.497   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      23.444 -34.117   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      18.109 -34.117   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      20.777 -35.657   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      20.777 -31.037   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      27.445 -27.187   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      24.778 -27.187   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      26.112 -29.497   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      24.778 -28.727   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      23.444 -29.497   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      27.445 -28.727   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      28.779 -29.497   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      30.113 -28.727   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      31.446 -29.497   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      32.780 -28.727   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      34.114 -29.497   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      35.447 -28.727   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      36.781 -29.497   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      31.446 -15.638   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      31.446 -17.178   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      38.115 -28.727   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      32.780 -14.868   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      30.113 -17.948   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      39.448 -29.497   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      32.780 -13.328   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      30.113 -19.488   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      40.782 -28.727   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      34.114 -12.558   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      28.779 -20.257   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      42.116 -29.497   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      34.114 -11.018   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      28.779 -21.798   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      43.449 -28.727   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      35.447 -10.248   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      27.445 -22.567   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      44.783 -29.497   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      35.447  -8.708   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      27.445 -24.107   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      46.117 -28.727   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      36.781  -7.938   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      18.109 -31.037   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      26.112 -24.877   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      47.450 -29.497   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      36.781  -6.398   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      22.110 -31.807   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      19.443 -31.807   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      22.110 -33.347   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      19.443 -33.347   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      20.777 -34.117   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      26.112 -26.417   0.000  0.00  0.00           C+0
CONECT    1   12   47                                                       
CONECT    2   10                                                            
CONECT    3   43                                                            
CONECT    4   49                                                            
CONECT    5   50                                                            
CONECT    6   51                                                            
CONECT    7   47   48                                                       
CONECT    8   52                                                            
CONECT    9   11   52                                                       
CONECT   10    2   11   13                                                  
CONECT   11    9   10   12                                                  
CONECT   12    1   11                                                       
CONECT   13   10   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   23                                                       
CONECT   21   22   24                                                       
CONECT   22   21   25                                                       
CONECT   23   20   26                                                       
CONECT   24   21   27                                                       
CONECT   25   22   28                                                       
CONECT   26   23   29                                                       
CONECT   27   24   30                                                       
CONECT   28   25   31                                                       
CONECT   29   26   32                                                       
CONECT   30   27   33                                                       
CONECT   31   28   34                                                       
CONECT   32   29   35                                                       
CONECT   33   30   36                                                       
CONECT   34   31   37                                                       
CONECT   35   32   38                                                       
CONECT   36   33   39                                                       
CONECT   37   34   40                                                       
CONECT   38   35   41                                                       
CONECT   39   36   42                                                       
CONECT   40   37   44                                                       
CONECT   41   38   45                                                       
CONECT   42   39   46                                                       
CONECT   43    3   48                                                       
CONECT   44   40   52                                                       
CONECT   45   41                                                            
CONECT   46   42                                                            
CONECT   47    1    7   49                                                  
CONECT   48    7   43   50                                                  
CONECT   49    4   47   51                                                  
CONECT   50    5   48   51                                                  
CONECT   51    6   49   50                                                  
CONECT   52    8    9   44                                                  
MASTER        0    0    0    0    0    0    0    0   52    0  104    0
END
Download

3D PDB for HMDB0000770 (N-Glycoloylganglioside GM2)

COMPND    HMDB0000770
HETATM    1  C1  UNL     1      13.645  -0.359   0.226  1.00  0.00           C  
HETATM    2  C2  UNL     1      12.738   0.400  -0.736  1.00  0.00           C  
HETATM    3  C3  UNL     1      11.313   0.369  -0.173  1.00  0.00           C  
HETATM    4  C4  UNL     1      10.372   1.089  -1.104  1.00  0.00           C  
HETATM    5  C5  UNL     1      10.679   2.505  -1.358  1.00  0.00           C  
HETATM    6  C6  UNL     1      10.759   3.490  -0.278  1.00  0.00           C  
HETATM    7  C7  UNL     1       9.616   3.784   0.611  1.00  0.00           C  
HETATM    8  C8  UNL     1       9.154   2.727   1.521  1.00  0.00           C  
HETATM    9  C9  UNL     1       7.963   3.075   2.348  1.00  0.00           C  
HETATM   10  C10 UNL     1       6.674   3.086   1.616  1.00  0.00           C  
HETATM   11  C11 UNL     1       6.496   3.939   0.444  1.00  0.00           C  
HETATM   12  C12 UNL     1       5.021   3.831  -0.048  1.00  0.00           C  
HETATM   13  C13 UNL     1       4.733   2.384  -0.320  1.00  0.00           C  
HETATM   14  C14 UNL     1       3.362   2.295  -0.960  1.00  0.00           C  
HETATM   15  C15 UNL     1       3.032   0.834  -1.210  1.00  0.00           C  
HETATM   16  C16 UNL     1       2.870   0.121   0.067  1.00  0.00           C  
HETATM   17  C17 UNL     1       2.561  -1.326   0.066  1.00  0.00           C  
HETATM   18  C18 UNL     1       1.370  -1.701  -0.707  1.00  0.00           C  
HETATM   19  O1  UNL     1       1.130  -1.153  -1.788  1.00  0.00           O  
HETATM   20  N1  UNL     1       0.460  -2.702  -0.229  1.00  0.00           N  
HETATM   21  C19 UNL     1      -0.690  -3.088  -1.004  1.00  0.00           C  
HETATM   22  C20 UNL     1      -1.438  -4.165  -0.339  1.00  0.00           C  
HETATM   23  O2  UNL     1      -0.707  -5.306  -0.153  1.00  0.00           O  
HETATM   24  C21 UNL     1      -0.308  -5.885  -1.327  1.00  0.00           C  
HETATM   25  O3  UNL     1      -1.105  -7.089  -1.448  1.00  0.00           O  
HETATM   26  C22 UNL     1      -0.978  -7.452  -2.791  1.00  0.00           C  
HETATM   27  C23 UNL     1      -2.111  -8.268  -3.319  1.00  0.00           C  
HETATM   28  O4  UNL     1      -3.320  -7.545  -3.210  1.00  0.00           O  
HETATM   29  C24 UNL     1       0.348  -8.213  -2.888  1.00  0.00           C  
HETATM   30  O5  UNL     1       0.916  -7.975  -4.121  1.00  0.00           O  
HETATM   31  C25 UNL     1       1.232  -7.833  -1.718  1.00  0.00           C  
HETATM   32  O6  UNL     1       0.769  -8.516  -0.580  1.00  0.00           O  
HETATM   33  C26 UNL     1       1.113  -6.344  -1.377  1.00  0.00           C  
HETATM   34  O7  UNL     1       1.888  -5.651  -2.281  1.00  0.00           O  
HETATM   35  C27 UNL     1      -1.573  -1.889  -1.342  1.00  0.00           C  
HETATM   36  O8  UNL     1      -2.683  -2.381  -2.085  1.00  0.00           O  
HETATM   37  C28 UNL     1      -2.079  -1.134  -0.159  1.00  0.00           C  
HETATM   38  C29 UNL     1      -2.884   0.051  -0.667  1.00  0.00           C  
HETATM   39  C30 UNL     1      -3.469   0.924   0.364  1.00  0.00           C  
HETATM   40  C31 UNL     1      -4.490   0.336   1.267  1.00  0.00           C  
HETATM   41  C32 UNL     1      -5.695  -0.201   0.485  1.00  0.00           C  
HETATM   42  C33 UNL     1      -6.244   0.942  -0.331  1.00  0.00           C  
HETATM   43  C34 UNL     1      -7.455   0.606  -1.135  1.00  0.00           C  
HETATM   44  C35 UNL     1      -8.649   0.193  -0.295  1.00  0.00           C  
HETATM   45  C36 UNL     1      -9.020   1.319   0.662  1.00  0.00           C  
HETATM   46  C37 UNL     1      -9.342   2.579  -0.111  1.00  0.00           C  
HETATM   47  C38 UNL     1      -9.678   3.717   0.812  1.00  0.00           C  
HETATM   48  C39 UNL     1     -10.878   3.388   1.644  1.00  0.00           C  
HETATM   49  C40 UNL     1     -11.107   4.610   2.544  1.00  0.00           C  
HETATM   50  C41 UNL     1     -12.307   4.386   3.410  1.00  0.00           C  
HETATM   51  C42 UNL     1     -12.461   5.648   4.271  1.00  0.00           C  
HETATM   52  C43 UNL     1     -11.201   5.770   5.087  1.00  0.00           C  
HETATM   53  H1  UNL     1      14.677   0.029   0.057  1.00  0.00           H  
HETATM   54  H2  UNL     1      13.589  -1.454   0.013  1.00  0.00           H  
HETATM   55  H3  UNL     1      13.365  -0.156   1.283  1.00  0.00           H  
HETATM   56  H4  UNL     1      13.031   1.458  -0.770  1.00  0.00           H  
HETATM   57  H5  UNL     1      12.687  -0.102  -1.716  1.00  0.00           H  
HETATM   58  H6  UNL     1      11.253   0.657   0.872  1.00  0.00           H  
HETATM   59  H7  UNL     1      11.025  -0.723  -0.235  1.00  0.00           H  
HETATM   60  H8  UNL     1      10.586   0.564  -2.126  1.00  0.00           H  
HETATM   61  H9  UNL     1       9.342   0.801  -0.909  1.00  0.00           H  
HETATM   62  H10 UNL     1       9.972   2.833  -2.192  1.00  0.00           H  
HETATM   63  H11 UNL     1      11.677   2.518  -1.938  1.00  0.00           H  
HETATM   64  H12 UNL     1      11.684   3.331   0.379  1.00  0.00           H  
HETATM   65  H13 UNL     1      11.034   4.491  -0.767  1.00  0.00           H  
HETATM   66  H14 UNL     1      10.075   4.590   1.352  1.00  0.00           H  
HETATM   67  H15 UNL     1       8.862   4.367   0.090  1.00  0.00           H  
HETATM   68  H16 UNL     1      10.000   2.458   2.222  1.00  0.00           H  
HETATM   69  H17 UNL     1       8.849   1.777   0.978  1.00  0.00           H  
HETATM   70  H18 UNL     1       8.124   4.055   2.904  1.00  0.00           H  
HETATM   71  H19 UNL     1       7.928   2.277   3.164  1.00  0.00           H  
HETATM   72  H20 UNL     1       5.828   3.175   2.372  1.00  0.00           H  
HETATM   73  H21 UNL     1       6.482   1.984   1.248  1.00  0.00           H  
HETATM   74  H22 UNL     1       7.032   3.547  -0.478  1.00  0.00           H  
HETATM   75  H23 UNL     1       6.688   5.009   0.611  1.00  0.00           H  
HETATM   76  H24 UNL     1       4.413   4.218   0.800  1.00  0.00           H  
HETATM   77  H25 UNL     1       4.859   4.494  -0.912  1.00  0.00           H  
HETATM   78  H26 UNL     1       5.499   1.852  -0.898  1.00  0.00           H  
HETATM   79  H27 UNL     1       4.700   1.899   0.701  1.00  0.00           H  
HETATM   80  H28 UNL     1       2.591   2.776  -0.295  1.00  0.00           H  
HETATM   81  H29 UNL     1       3.396   2.814  -1.933  1.00  0.00           H  
HETATM   82  H30 UNL     1       2.092   0.828  -1.833  1.00  0.00           H  
HETATM   83  H31 UNL     1       3.891   0.446  -1.829  1.00  0.00           H  
HETATM   84  H32 UNL     1       2.067   0.631   0.684  1.00  0.00           H  
HETATM   85  H33 UNL     1       3.814   0.219   0.706  1.00  0.00           H  
HETATM   86  H34 UNL     1       2.458  -1.652   1.145  1.00  0.00           H  
HETATM   87  H35 UNL     1       3.472  -1.889  -0.272  1.00  0.00           H  
HETATM   88  H36 UNL     1       0.641  -3.143   0.681  1.00  0.00           H  
HETATM   89  H37 UNL     1      -0.288  -3.369  -2.030  1.00  0.00           H  
HETATM   90  H38 UNL     1      -2.406  -4.427  -0.846  1.00  0.00           H  
HETATM   91  H39 UNL     1      -1.699  -3.815   0.722  1.00  0.00           H  
HETATM   92  H40 UNL     1      -0.573  -5.329  -2.243  1.00  0.00           H  
HETATM   93  H41 UNL     1      -0.897  -6.498  -3.377  1.00  0.00           H  
HETATM   94  H42 UNL     1      -2.203  -9.256  -2.857  1.00  0.00           H  
HETATM   95  H43 UNL     1      -1.940  -8.421  -4.412  1.00  0.00           H  
HETATM   96  H44 UNL     1      -3.615  -7.493  -2.274  1.00  0.00           H  
HETATM   97  H45 UNL     1       0.099  -9.306  -2.823  1.00  0.00           H  
HETATM   98  H46 UNL     1       0.189  -7.904  -4.786  1.00  0.00           H  
HETATM   99  H47 UNL     1       2.262  -8.098  -1.933  1.00  0.00           H  
HETATM  100  H48 UNL     1       1.083  -8.089   0.255  1.00  0.00           H  
HETATM  101  H49 UNL     1       1.626  -6.248  -0.390  1.00  0.00           H  
HETATM  102  H50 UNL     1       1.327  -5.163  -2.901  1.00  0.00           H  
HETATM  103  H51 UNL     1      -1.039  -1.233  -2.036  1.00  0.00           H  
HETATM  104  H52 UNL     1      -2.890  -1.739  -2.832  1.00  0.00           H  
HETATM  105  H53 UNL     1      -2.722  -1.825   0.448  1.00  0.00           H  
HETATM  106  H54 UNL     1      -1.291  -0.772   0.507  1.00  0.00           H  
HETATM  107  H55 UNL     1      -2.147   0.657  -1.270  1.00  0.00           H  
HETATM  108  H56 UNL     1      -3.634  -0.282  -1.423  1.00  0.00           H  
HETATM  109  H57 UNL     1      -2.655   1.331   1.040  1.00  0.00           H  
HETATM  110  H58 UNL     1      -3.884   1.843  -0.122  1.00  0.00           H  
HETATM  111  H59 UNL     1      -4.109  -0.399   1.986  1.00  0.00           H  
HETATM  112  H60 UNL     1      -4.903   1.177   1.898  1.00  0.00           H  
HETATM  113  H61 UNL     1      -5.418  -1.075  -0.121  1.00  0.00           H  
HETATM  114  H62 UNL     1      -6.464  -0.506   1.251  1.00  0.00           H  
HETATM  115  H63 UNL     1      -6.391   1.802   0.357  1.00  0.00           H  
HETATM  116  H64 UNL     1      -5.459   1.224  -1.102  1.00  0.00           H  
HETATM  117  H65 UNL     1      -7.753   1.365  -1.852  1.00  0.00           H  
HETATM  118  H66 UNL     1      -7.180  -0.306  -1.744  1.00  0.00           H  
HETATM  119  H67 UNL     1      -9.501   0.044  -0.963  1.00  0.00           H  
HETATM  120  H68 UNL     1      -8.442  -0.696   0.288  1.00  0.00           H  
HETATM  121  H69 UNL     1      -8.249   1.500   1.437  1.00  0.00           H  
HETATM  122  H70 UNL     1      -9.933   0.987   1.172  1.00  0.00           H  
HETATM  123  H71 UNL     1     -10.107   2.427  -0.883  1.00  0.00           H  
HETATM  124  H72 UNL     1      -8.430   2.934  -0.686  1.00  0.00           H  
HETATM  125  H73 UNL     1      -8.771   3.917   1.453  1.00  0.00           H  
HETATM  126  H74 UNL     1      -9.881   4.631   0.183  1.00  0.00           H  
HETATM  127  H75 UNL     1     -10.674   2.499   2.245  1.00  0.00           H  
HETATM  128  H76 UNL     1     -11.750   3.239   0.976  1.00  0.00           H  
HETATM  129  H77 UNL     1     -10.165   4.753   3.108  1.00  0.00           H  
HETATM  130  H78 UNL     1     -11.306   5.449   1.821  1.00  0.00           H  
HETATM  131  H79 UNL     1     -13.193   4.291   2.758  1.00  0.00           H  
HETATM  132  H80 UNL     1     -12.154   3.484   4.048  1.00  0.00           H  
HETATM  133  H81 UNL     1     -12.463   6.489   3.518  1.00  0.00           H  
HETATM  134  H82 UNL     1     -13.387   5.576   4.832  1.00  0.00           H  
HETATM  135  H83 UNL     1     -10.477   6.523   4.660  1.00  0.00           H  
HETATM  136  H84 UNL     1     -10.696   4.783   5.211  1.00  0.00           H  
HETATM  137  H85 UNL     1     -11.475   6.125   6.102  1.00  0.00           H  
CONECT    1    2   53   54   55
CONECT    2    3   56   57
CONECT    3    4   58   59
CONECT    4    5   60   61
CONECT    5    6   62   63
CONECT    6    7   64   65
CONECT    7    8   66   67
CONECT    8    9   68   69
CONECT    9   10   70   71
CONECT   10   11   72   73
CONECT   11   12   74   75
CONECT   12   13   76   77
CONECT   13   14   78   79
CONECT   14   15   80   81
CONECT   15   16   82   83
CONECT   16   17   84   85
CONECT   17   18   86   87
CONECT   18   19   19   20
CONECT   20   21   88
CONECT   21   22   35   89
CONECT   22   23   90   91
CONECT   23   24
CONECT   24   25   33   92
CONECT   25   26
CONECT   26   27   29   93
CONECT   27   28   94   95
CONECT   28   96
CONECT   29   30   31   97
CONECT   30   98
CONECT   31   32   33   99
CONECT   32  100
CONECT   33   34  101
CONECT   34  102
CONECT   35   36   37  103
CONECT   36  104
CONECT   37   38  105  106
CONECT   38   39  107  108
CONECT   39   40  109  110
CONECT   40   41  111  112
CONECT   41   42  113  114
CONECT   42   43  115  116
CONECT   43   44  117  118
CONECT   44   45  119  120
CONECT   45   46  121  122
CONECT   46   47  123  124
CONECT   47   48  125  126
CONECT   48   49  127  128
CONECT   49   50  129  130
CONECT   50   51  131  132
CONECT   51   52  133  134
CONECT   52  135  136  137
END
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SMILES for HMDB0000770 (N-Glycoloylganglioside GM2)

CCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)[C@@H](O)CCCCCCCCCCCCCCCC
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INCHI for HMDB0000770 (N-Glycoloylganglioside GM2)

InChI=1S/C43H85NO8/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-39(47)44-36(35-51-43-42(50)41(49)40(48)38(34-45)52-43)37(46)32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h36-38,40-43,45-46,48-50H,3-35H2,1-2H3,(H,44,47)/t36-,37-,38+,40+,41-,42+,43+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Ganglioside aiiHMDB
N-Glycoloyl-ganglioside GM2HMDB
N-Glycoloyl-GM2HMDB
NeuGc-GM2HMDB
N-[(2S,3S)-3-Hydroxy-1-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}nonadecan-2-yl]octadecanimidateHMDB
Chemical FormulaC43H85NO8
Average Molecular Weight744.1369
Monoisotopic Molecular Weight743.627518701
IUPAC NameN-[(2S,3S)-3-hydroxy-1-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}nonadecan-2-yl]octadecanamide
Traditional NameN-[(2S,3S)-3-hydroxy-1-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}nonadecan-2-yl]octadecanamide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)[C@@H](O)CCCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C43H85NO8/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-39(47)44-36(35-51-43-42(50)41(49)40(48)38(34-45)52-43)37(46)32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h36-38,40-43,45-46,48-50H,3-35H2,1-2H3,(H,44,47)/t36-,37-,38+,40+,41-,42+,43+/m0/s1
InChI KeySYMIJCRAJBNLEL-YPQBUIQASA-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
  • Fatty amide
  • Fatty acyl
  • Monosaccharide
  • N-acyl-amine
  • Oxane
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Organoheterocyclic compound
  • Oxacycle
  • Acetal
  • Carboxylic acid derivative
  • Polyol
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Alcohol
  • Organic oxygen compound
  • Carbonyl group
  • Organic oxide
  • Organooxygen compound
  • Primary alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
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 Solubility0.00051 g/LALOGPS
logP8.25ALOGPS
logP10.63ChemAxon
logS-6.2ALOGPS
pKa (Strongest Acidic)12.19ChemAxon
pKa (Strongest Basic)-1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area148.71 ŲChemAxon
Rotatable Bond Count37ChemAxon
Refractivity211.03 m³·mol⁻¹ChemAxon
Polarizability95.72 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
DarkChem[M+H]+287.49431661259
DarkChem[M-H]-273.8131661259
AllCCS[M+H]+292.95332859911
AllCCS[M-H]-284.86732859911
DeepCCS[M+H]+275.78730932474
DeepCCS[M-H]-273.96230932474
DeepCCS[M-2H]-307.36930932474
DeepCCS[M+Na]+281.39330932474
AllCCS[M+H]+293.032859911
AllCCS[M+H-H2O]+292.932859911
AllCCS[M+NH4]+293.032859911
AllCCS[M+Na]+293.032859911
AllCCS[M-H]-284.932859911
AllCCS[M+Na-2H]-288.632859911
AllCCS[M+HCOO]-292.832859911

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, 2022.9.71 minutes32390414
Predicted by Siyang on May 30, 202227.586 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.18 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid90.9 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid5352.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid259.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid340.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid183.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid919.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1257.6 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 Acid1182.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)365.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2871.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1036.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2848.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid968.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid694.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate357.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA261.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water9.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
N-Glycoloylganglioside GM2CCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)[C@@H](O)CCCCCCCCCCCCCCCC4205.5Standard polar33892256
N-Glycoloylganglioside GM2CCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)[C@@H](O)CCCCCCCCCCCCCCCC4936.3Standard non polar33892256
N-Glycoloylganglioside GM2CCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)[C@@H](O)CCCCCCCCCCCCCCCC5881.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_1_6) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_7) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_8) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_9) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_10) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_11) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_12) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_13) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_14) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TMS_2_15) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Glycoloylganglioside GM2 GC-MS (TBDMS_1_4) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Glycoloylganglioside GM2 10V, Negative-QTOFsplash10-0006-0000000900-bee4faa9bf515e17d4082021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Glycoloylganglioside GM2 20V, Negative-QTOFsplash10-0006-5110034900-2a1a5346081aa4105b582021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Glycoloylganglioside GM2 40V, Negative-QTOFsplash10-0pk9-9146020000-ab530060298036935dbb2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Glycoloylganglioside GM2 10V, Positive-QTOFsplash10-052f-7000050900-1218e90887b4b8572e2a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Glycoloylganglioside GM2 20V, Positive-QTOFsplash10-06r6-9110081500-7652a75532fc12dd16a02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Glycoloylganglioside GM2 40V, Positive-QTOFsplash10-052f-9032010000-b4d90ec8bb1244b11d2a2021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue Locations
  • Brain
  • Neuron
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022233
KNApSAcK IDNot Available
Chemspider ID393427
KEGG Compound IDC01808
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5737
PubChem Compound445946
PDB IDGM2
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceSchmidt, Richard; Castro-Palomino, Julio C.; Doll, Andreas; Ritter, Gerd; Old, Lloyd J. Preparation of ganglioside GM2. PCT Int. Appl. (1997), 27 pp. CODEN: PIXXD2 WO 9730061 A1 19970821 CAN 127:248363 AN 1997:568133
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Cox EV, Robertson-Smith D, Small M, White AM: The excretion of propionate and acetate in vitamin B12 deficiency. Clin Sci. 1968 Aug;35(1):123-34. [PubMed:5679881 ]
  2. Hanibuchi M, Yano S, Nishioka Y, Yanagawa H, Kawano T, Sone S: Therapeutic efficacy of mouse-human chimeric anti-ganglioside GM2 monoclonal antibody against multiple organ micrometastases of human lung cancer in NK cell-depleted SCID mice. Int J Cancer. 1998 Nov 9;78(4):480-5. [PubMed:9797137 ]

Only showing the first 10 proteins. There are 46 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Alpha-N-acetylneuraminide alpha-2,8-sialyltransferase
General function:
Involved in sialyltransferase activity
Specific function:
Involved in the production of gangliosides GD3 and GT3 from GM3; gangliosides are a subfamily of complex glycosphinglolipds that contain one or more residues of sialic acid.
Gene Name:
ST8SIA1
Uniprot ID:
Q92185
Molecular weight:
40518.655
Enzyme Details
2. Sialidase-3
General function:
Involved in exo-alpha-sialidase activity
Specific function:
Plays a role in modulating the ganglioside content of the lipid bilayer at the level of membrane-bound sialyl glycoconjugates
Gene Name:
NEU3
Uniprot ID:
Q9UQ49
Molecular weight:
48251.5
Enzyme Details
3. Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens
Gene Name:
GBGT1
Uniprot ID:
Q8N5D6
Molecular weight:
40126.9
Enzyme Details
4. N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase
General function:
Involved in N-acetylglucosaminylphosphatidylinositol de
Specific function:
Involved in the second step of GPI biosynthesis. De-N-acetylation of N-acetylglucosaminyl-phosphatidylinositol.
Gene Name:
PIGL
Uniprot ID:
Q9Y2B2
Molecular weight:
28530.965
Enzyme Details
5. Lactosylceramide alpha-2,3-sialyltransferase
General function:
Involved in sialyltransferase activity
Specific function:
Catalyzes the formation of ganglioside GM3 (alpha-N-acetylneuraminyl-2,3-beta-D-galactosyl-1, 4-beta-D-glucosylceramide).
Gene Name:
ST3GAL5
Uniprot ID:
Q9UNP4
Molecular weight:
45584.69
Enzyme Details
6. Beta-1,4 N-acetylgalactosaminyltransferase 1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Involved in the biosynthesis of gangliosides GM2, GD2 and GA2.
Gene Name:
B4GALNT1
Uniprot ID:
Q00973
Molecular weight:
58881.78
Enzyme Details
7. Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGQ
Uniprot ID:
Q9BRB3
Molecular weight:
65343.25
Enzyme Details
8. Phosphatidylinositol N-acetylglucosaminyltransferase subunit A
General function:
Involved in biosynthetic process
Specific function:
Necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, the very early intermediate in GPI-anchor biosynthesis.
Gene Name:
PIGA
Uniprot ID:
P37287
Molecular weight:
54126.065
Enzyme Details
9. Phosphatidylinositol N-acetylglucosaminyltransferase subunit H
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGH
Uniprot ID:
Q14442
Molecular weight:
21080.415
Enzyme Details
10. Phosphatidylinositol N-acetylglucosaminyltransferase subunit P
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGP
Uniprot ID:
P57054
Molecular weight:
18089.055

Only showing the first 10 proteins. There are 46 proteins in total.

Show all enzymes and transporters