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Showing metabocard for LacCer(d18:1/25:0) (HMDB0004876)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (72) Show 72 proteinsXML
enzymes (72) Show 72 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-11-30 19:02:45 UTC
HMDB IDHMDB0004876
Secondary Accession Numbers
  • HMDB04876
Metabolite Identification
Common NameLacCer(d18:1/25:0)
DescriptionLacCer(d18:1/25:0) is a lactosylceramide or LacCer. Lactosylceramides are the most important and abundant of the diosylceramides. Lactosylceramides (LacCer) were originally called 'cytolipin H'. It is found in small amounts only in most animal tissues, but it has a number of significant biological functions and it is of great importance as the biosynthetic precursor of most of the neutral oligoglycosylceramides, sulfatides and gangliosides. In animal tissues, biosynthesis of lactosylceramide involves addition of the second monosaccharides unit (galactose) as its nucleotide derivative to monoglucosylceramide, catalysed by a specific beta-1,4-galactosyltransferase on the lumenal side of the Golgi apparatus. The glucosylceramide precursor must first cross from the cytosolic side of the membrane, possibly via the action of a flippase. The lactosylceramide produced can be further glycosylated or transferred to the plasma membrane. Lactosylceramide may assist in stabilizing the plasma membrane and activating receptor molecules in the special micro-domains or rafts, as with the cerebrosides. It may also have its own specialized function in the immunological system in that it is known to bind to specific bacteria. In addition, it is believed that a number of pro-inflammatory factors activate lactosylceramide synthase to generate lactosylceramide, which in turn activates "oxygen-sensitive" signalling pathways that affect such cellular processes as proliferation, adhesion, migration and angiogenesis. Dysfunctions in these pathways can affect several diseases of the cardiovascular system, cancer and inflammatory states, so lactosylceramide metabolism is a potential target for new therapeutic treatments. beta-D-Galactosyl-1,4-beta-D-glucosylceramide is the second to last step in the synthesis of N-Acylsphingosine and is converted. from Glucosylceramide via the enzyme beta-1,4-galactosyltransferase 6(EC:2.4.1.-). It can be converted to Glucosylceramide via the enzyme beta-galactosidase (EC:3.2.1.23).
Structure
Data?1592001279
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0004876 (LacCer(d18:1/25:0))

LacCer(d18:1/25:0)
  Mrv1652306132000302D          

 71 72  0  0  0  0            999 V2000
   -0.1480    0.3572    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5663    0.7697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2643   -0.3572    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5606   -0.3572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1262    2.0035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6976    2.8268    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1262    0.3577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5526    2.8268    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4119    3.2396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6976   -0.4656    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5526   -0.4656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9792    2.0035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2752    0.3577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2649   -0.8773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9792    0.3577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1262    1.1800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6997    0.3588    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9876    0.7699    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9876    1.5921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6997    2.0031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4117    1.5921    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4117    0.7699    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5526    0.3588    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8406    0.7699    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.5526    2.0031    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2647    1.5921    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2647    0.7699    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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  2  1  1  0  0  0  0
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  1 29  1  0  0  0  0
  6  9  1  0  0  0  0
 11 14  1  0  0  0  0
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 69 70  1  0  0  0  0
 70 71  1  0  0  0  0
M  END
Download

3D MOL for HMDB0004876 (LacCer(d18:1/25:0))

HMDB0004876
     RDKit          3D
LacCer(d18:1/25:0)
174175  0  0  0  0  0  0  0  0999 V2000
   -2.5101    2.2185   -6.8566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7096    1.3285   -7.1571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2242   -0.0553   -7.4774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3079   -0.0766   -8.6756 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8394   -1.4985   -8.9693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9218   -1.5304  -10.1532 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3084   -0.7498  -10.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3666   -0.9879   -9.0700 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1072   -2.2637   -9.0618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4107   -3.5081   -8.6739 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9688   -3.4900   -7.2050 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2455   -4.7544   -6.8826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2389   -4.8734   -5.4758 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1757   -3.8275   -5.0597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8909   -3.0243   -4.0353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8103   -1.9530   -3.5827 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.9325   -2.3876   -2.9244 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0275   -1.0219   -2.6837 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7668   -1.7890   -1.4107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0767   -1.0672   -0.5250 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2083   -0.6948   -0.7141 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0660   -1.2216    0.2705 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9474   -0.6109    1.5112 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3043   -1.6850    2.5199 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4497   -2.7813    2.4170 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6737    0.0805    1.7425 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5532    0.7941    2.9210 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6195    0.5657    3.6118 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4596    1.7006    3.5934 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7766    1.2691    3.6498 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -0.7589    1.2722    0.3312 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3432    0.7998   -0.5793 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6981    1.1728   -0.4699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7961    0.1631   -2.3409 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4813    1.4300   -2.8537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5403    1.5499   -3.6687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2231    2.6636   -2.4502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4909    3.8708   -2.9192 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0721    5.1908   -2.4429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0698    5.2223   -0.9229 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4962    6.4962   -0.3122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4809    6.4723    1.1971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1260    6.0647    1.7356 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1087    6.1634    3.2282 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1954    5.6758    3.8291 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2556    5.9207    5.3127 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4842    5.4244    5.9857 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5659    3.8925    5.9946 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8504    3.4479    6.6201 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8387    1.9195    6.7819 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1671    1.4951    7.3336 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2841    0.0912    7.6897 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0043   -0.9727    6.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2926   -2.3447    7.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9926   -3.5080    6.4525 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5020   -3.5998    6.1417 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1520   -4.7852    5.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6749   -4.9005    5.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1021   -5.0626    6.3395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5853   -5.1888    6.0643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6771    1.5999   -6.4597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7736    2.9866   -6.0967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1470    2.7250   -7.7680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3829    1.2914   -6.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2785    1.7169   -8.0023 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0004876 (LacCer(d18:1/25:0))

LacCer(d18:1/25:0)
  Mrv1652306132000302D          

 71 72  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0004876

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](CO[C@@H]1O[C@H](CO)[C@@H](O[C@]2([H])O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O)(NC(=O)CCCCCCCCCCCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C55H105NO13/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-27-29-31-33-35-37-39-47(60)56-43(44(59)38-36-34-32-30-28-26-16-14-12-10-8-6-4-2)42-66-54-52(65)50(63)53(46(41-58)68-54)69-55-51(64)49(62)48(61)45(40-57)67-55/h36,38,43-46,48-55,57-59,61-65H,3-35,37,39-42H2,1-2H3,(H,56,60)/b38-36+/t43-,44+,45+,46+,48-,49-,50+,51+,52+,53+,54+,55-/m0/s1

> <INCHI_KEY>
WPIHMWBQRSAMDE-WQCHUFMUSA-N

> <FORMULA>
C55H105NO13

> <MOLECULAR_WEIGHT>
988.439

> <EXACT_MASS>
987.758592445

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
174

> <JCHEM_AVERAGE_POLARIZABILITY>
122.69921589949686

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2S,3R,4E)-1-{[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]pentacosanamide

> <ALOGPS_LOGP>
7.55

> <JCHEM_LOGP>
11.324801837333332

> <ALOGPS_LOGS>
-5.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.442514639800741

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.920303071106915

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9813779338405872

> <JCHEM_POLAR_SURFACE_AREA>
227.85999999999996

> <JCHEM_REFRACTIVITY>
272.0113

> <JCHEM_ROTATABLE_BOND_COUNT>
45

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.88e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2S,3R,4E)-1-{[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]pentacosanamide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0004876 (LacCer(d18:1/25:0))

HMDB0004876
     RDKit          3D
LacCer(d18:1/25:0)
174175  0  0  0  0  0  0  0  0999 V2000
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   -3.7096    1.3285   -7.1571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2242   -0.0553   -7.4774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3079   -0.0766   -8.6756 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8394   -1.4985   -8.9693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9218   -1.5304  -10.1532 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3084   -0.7498  -10.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0721    5.1908   -2.4429 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.1260    6.0647    1.7356 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4842    5.4244    5.9857 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8504    3.4479    6.6201 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8387    1.9195    6.7819 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1671    1.4951    7.3336 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2841    0.0912    7.6897 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0043   -0.9727    6.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2926   -2.3447    7.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9926   -3.5080    6.4525 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5020   -3.5998    6.1417 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1520   -4.7852    5.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.1021   -5.0626    6.3395 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.2978    5.8160    1.5994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3997    6.7970    1.3091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8727    5.0271    1.4627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9495    5.7136    3.7503 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.2481    4.6003    3.6724 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2676    7.0451    5.4242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6787    5.6140    5.8254 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4068    5.8417    5.5245 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.5398    3.4838    4.9707 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6989    3.5215    6.5430 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.7177    3.6790    5.9696 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0532    1.6263    7.4923 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.2962    2.1001    8.2880 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.3614   -0.0966    8.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6717   -0.1091    8.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5771   -0.8826    5.7573 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.3729   -2.3123    7.6058 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7453   -2.4298    8.2884 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3874   -4.4502    6.8736 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5316   -3.3727    5.4741 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9864   -3.6613    7.1051 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2671   -2.6687    5.5683 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6336   -4.7136    4.2769 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4921   -5.7345    5.7607 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3081   -3.9829    4.5480 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4127   -5.7598    4.4098 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2294   -5.9508    6.8997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0259   -4.1564    6.9492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8376   -5.2384    5.0039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0202   -6.1107    6.5378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1751   -4.3454    6.5050 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0004876 (LacCer(d18:1/25:0))

HEADER    PROTEIN                                 13-JUN-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: LacCer(d18:1/25:0)                                
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUN-20         0                                  
HETATM    1  C   UNK     0      -0.276   0.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.057   1.437   0.000  0.00  0.00           C+0
HETATM    3  H   UNK     0       0.493  -0.667   0.000  0.00  0.00           H+0
HETATM    4  N   UNK     0      -1.046  -0.667   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0       7.702   3.740   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.036   5.277   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.702   0.668   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      10.365   5.277   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       6.369   6.047   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       5.036  -0.869   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      10.365  -0.869   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      13.028   3.740   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.380   0.668   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      11.694  -1.638   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      13.028   0.668   0.000  0.00  0.00           O+0
HETATM   16  H   UNK     0       7.702   2.203   0.000  0.00  0.00           H+0
HETATM   17  C   UNK     0       5.039   0.670   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.710   1.437   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.710   2.972   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.039   3.739   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.369   2.972   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.369   1.437   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.365   0.670   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       9.036   1.437   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       9.036   2.972   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.365   3.739   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      11.694   2.972   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.694   1.437   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -1.610   1.437   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -1.610   2.877   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -2.943   0.666   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -4.276   1.437   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.609   0.666   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -6.942   1.437   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -8.275   0.666   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -9.608   1.437   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -10.941   0.666   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -12.274   1.437   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -13.607   0.666   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -14.940   1.437   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -16.273   0.666   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -17.606   1.437   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -18.939   0.666   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -20.273   1.437   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -21.606   0.666   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -2.380  -1.437   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0      -2.380  -2.877   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0      -3.713  -0.666   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -5.046  -1.437   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -6.379  -0.666   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      -7.712  -1.437   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -9.045  -0.666   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -10.378  -1.437   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -11.711  -0.666   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -13.044  -1.437   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0     -14.377  -0.666   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -15.711  -1.437   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -17.044  -0.666   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -18.377  -1.437   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -19.710  -0.666   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -21.043  -1.437   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -22.376  -0.666   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -23.709  -1.437   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -25.042  -0.666   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -26.375  -1.437   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0     -27.708  -0.666   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0     -29.041  -1.437   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0     -30.374  -0.666   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0     -31.707  -1.437   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0     -33.040  -0.666   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0     -34.373  -1.437   0.000  0.00  0.00           C+0
CONECT    1    2    3    4   29                                             
CONECT    2    1   13                                                       
CONECT    3    1                                                            
CONECT    4    1   46                                                       
CONECT    5   21   25                                                       
CONECT    6    9   20                                                       
CONECT    7   22                                                            
CONECT    8   26                                                            
CONECT    9    6                                                            
CONECT   10   17                                                            
CONECT   11   14   23                                                       
CONECT   12   27                                                            
CONECT   13   18    2                                                       
CONECT   14   11                                                            
CONECT   15   28                                                            
CONECT   16   25                                                            
CONECT   17   18   22   10                                                  
CONECT   18   17   19   13                                                  
CONECT   19   18   20                                                       
CONECT   20   21   19    6                                                  
CONECT   21   20   22    5                                                  
CONECT   22   17   21    7                                                  
CONECT   23   28   24   11                                                  
CONECT   24   23   25                                                       
CONECT   25   26   24    5   16                                             
CONECT   26   25   27    8                                                  
CONECT   27   26   28   12                                                  
CONECT   28   23   27   15                                                  
CONECT   29    1   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44                                                            
CONECT   46    4   47   48                                                  
CONECT   47   46                                                            
CONECT   48   46   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   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69                                                       
CONECT   69   68   70                                                       
CONECT   70   69   71                                                       
CONECT   71   70                                                            
MASTER        0    0    0    0    0    0    0    0   71    0  144    0
END
Download

3D PDB for HMDB0004876 (LacCer(d18:1/25:0))

COMPND    HMDB0004876
HETATM    1  C1  UNL     1      -2.510   2.219  -6.857  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.710   1.329  -7.157  1.00  0.00           C  
HETATM    3  C3  UNL     1      -3.224  -0.055  -7.477  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.308  -0.077  -8.676  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.839  -1.498  -8.969  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.922  -1.530 -10.153  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.308  -0.750 -10.054  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.367  -0.988  -9.070  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.107  -2.264  -9.062  1.00  0.00           C  
HETATM   10  C10 UNL     1       1.411  -3.508  -8.674  1.00  0.00           C  
HETATM   11  C11 UNL     1       0.969  -3.490  -7.205  1.00  0.00           C  
HETATM   12  C12 UNL     1       0.245  -4.754  -6.883  1.00  0.00           C  
HETATM   13  C13 UNL     1      -0.239  -4.873  -5.476  1.00  0.00           C  
HETATM   14  C14 UNL     1      -1.176  -3.827  -5.060  1.00  0.00           C  
HETATM   15  C15 UNL     1      -0.891  -3.024  -4.035  1.00  0.00           C  
HETATM   16  C16 UNL     1      -1.810  -1.953  -3.583  1.00  0.00           C  
HETATM   17  O1  UNL     1      -2.932  -2.388  -2.924  1.00  0.00           O  
HETATM   18  C17 UNL     1      -1.028  -1.022  -2.684  1.00  0.00           C  
HETATM   19  C18 UNL     1      -0.767  -1.789  -1.411  1.00  0.00           C  
HETATM   20  O2  UNL     1      -0.077  -1.067  -0.525  1.00  0.00           O  
HETATM   21  C19 UNL     1       1.208  -0.695  -0.714  1.00  0.00           C  
HETATM   22  O3  UNL     1       2.066  -1.222   0.271  1.00  0.00           O  
HETATM   23  C20 UNL     1       1.947  -0.611   1.511  1.00  0.00           C  
HETATM   24  C21 UNL     1       2.304  -1.685   2.520  1.00  0.00           C  
HETATM   25  O4  UNL     1       1.450  -2.781   2.417  1.00  0.00           O  
HETATM   26  C22 UNL     1       0.674   0.080   1.742  1.00  0.00           C  
HETATM   27  O5  UNL     1       0.553   0.794   2.921  1.00  0.00           O  
HETATM   28  C23 UNL     1      -0.620   0.566   3.612  1.00  0.00           C  
HETATM   29  O6  UNL     1      -1.460   1.701   3.593  1.00  0.00           O  
HETATM   30  C24 UNL     1      -2.777   1.269   3.650  1.00  0.00           C  
HETATM   31  C25 UNL     1      -3.619   2.404   4.180  1.00  0.00           C  
HETATM   32  O7  UNL     1      -3.548   3.523   3.355  1.00  0.00           O  
HETATM   33  C26 UNL     1      -2.957   0.012   4.444  1.00  0.00           C  
HETATM   34  O8  UNL     1      -4.190   0.154   5.126  1.00  0.00           O  
HETATM   35  C27 UNL     1      -1.924  -0.162   5.523  1.00  0.00           C  
HETATM   36  O9  UNL     1      -2.260   0.574   6.636  1.00  0.00           O  
HETATM   37  C28 UNL     1      -0.508   0.192   5.037  1.00  0.00           C  
HETATM   38  O10 UNL     1       0.391  -0.781   5.360  1.00  0.00           O  
HETATM   39  C29 UNL     1       0.579   1.189   0.658  1.00  0.00           C  
HETATM   40  O11 UNL     1      -0.759   1.272   0.331  1.00  0.00           O  
HETATM   41  C30 UNL     1       1.343   0.800  -0.579  1.00  0.00           C  
HETATM   42  O12 UNL     1       2.698   1.173  -0.470  1.00  0.00           O  
HETATM   43  N1  UNL     1      -1.796   0.163  -2.341  1.00  0.00           N  
HETATM   44  C31 UNL     1      -1.481   1.430  -2.854  1.00  0.00           C  
HETATM   45  O13 UNL     1      -0.540   1.550  -3.669  1.00  0.00           O  
HETATM   46  C32 UNL     1      -2.223   2.664  -2.450  1.00  0.00           C  
HETATM   47  C33 UNL     1      -1.491   3.871  -2.919  1.00  0.00           C  
HETATM   48  C34 UNL     1      -2.072   5.191  -2.443  1.00  0.00           C  
HETATM   49  C35 UNL     1      -2.070   5.222  -0.923  1.00  0.00           C  
HETATM   50  C36 UNL     1      -2.496   6.496  -0.312  1.00  0.00           C  
HETATM   51  C37 UNL     1      -2.481   6.472   1.197  1.00  0.00           C  
HETATM   52  C38 UNL     1      -1.126   6.065   1.736  1.00  0.00           C  
HETATM   53  C39 UNL     1      -1.109   6.163   3.228  1.00  0.00           C  
HETATM   54  C40 UNL     1       0.195   5.676   3.829  1.00  0.00           C  
HETATM   55  C41 UNL     1       0.256   5.921   5.313  1.00  0.00           C  
HETATM   56  C42 UNL     1       1.484   5.424   5.986  1.00  0.00           C  
HETATM   57  C43 UNL     1       1.566   3.893   5.995  1.00  0.00           C  
HETATM   58  C44 UNL     1       2.850   3.448   6.620  1.00  0.00           C  
HETATM   59  C45 UNL     1       2.839   1.920   6.782  1.00  0.00           C  
HETATM   60  C46 UNL     1       4.167   1.495   7.334  1.00  0.00           C  
HETATM   61  C47 UNL     1       4.284   0.091   7.690  1.00  0.00           C  
HETATM   62  C48 UNL     1       4.004  -0.973   6.678  1.00  0.00           C  
HETATM   63  C49 UNL     1       4.293  -2.345   7.309  1.00  0.00           C  
HETATM   64  C50 UNL     1       3.993  -3.508   6.453  1.00  0.00           C  
HETATM   65  C51 UNL     1       2.502  -3.600   6.142  1.00  0.00           C  
HETATM   66  C52 UNL     1       2.152  -4.785   5.298  1.00  0.00           C  
HETATM   67  C53 UNL     1       0.675  -4.901   5.039  1.00  0.00           C  
HETATM   68  C54 UNL     1      -0.102  -5.063   6.339  1.00  0.00           C  
HETATM   69  C55 UNL     1      -1.585  -5.189   6.064  1.00  0.00           C  
HETATM   70  H1  UNL     1      -1.677   1.600  -6.460  1.00  0.00           H  
HETATM   71  H2  UNL     1      -2.774   2.987  -6.097  1.00  0.00           H  
HETATM   72  H3  UNL     1      -2.147   2.725  -7.768  1.00  0.00           H  
HETATM   73  H4  UNL     1      -4.383   1.291  -6.264  1.00  0.00           H  
HETATM   74  H5  UNL     1      -4.278   1.717  -8.002  1.00  0.00           H  
HETATM   75  H6  UNL     1      -4.076  -0.750  -7.607  1.00  0.00           H  
HETATM   76  H7  UNL     1      -2.630  -0.472  -6.616  1.00  0.00           H  
HETATM   77  H8  UNL     1      -2.903   0.259  -9.565  1.00  0.00           H  
HETATM   78  H9  UNL     1      -1.430   0.556  -8.509  1.00  0.00           H  
HETATM   79  H10 UNL     1      -1.333  -1.875  -8.086  1.00  0.00           H  
HETATM   80  H11 UNL     1      -2.739  -2.143  -9.191  1.00  0.00           H  
HETATM   81  H12 UNL     1      -0.837  -2.575 -10.519  1.00  0.00           H  
HETATM   82  H13 UNL     1      -1.520  -1.045 -11.024  1.00  0.00           H  
HETATM   83  H14 UNL     1       0.782  -0.754 -11.100  1.00  0.00           H  
HETATM   84  H15 UNL     1      -0.022   0.354  -9.979  1.00  0.00           H  
HETATM   85  H16 UNL     1       1.011  -0.822  -8.006  1.00  0.00           H  
HETATM   86  H17 UNL     1       2.111  -0.122  -9.179  1.00  0.00           H  
HETATM   87  H18 UNL     1       2.966  -2.138  -8.313  1.00  0.00           H  
HETATM   88  H19 UNL     1       2.588  -2.389 -10.087  1.00  0.00           H  
HETATM   89  H20 UNL     1       0.537  -3.799  -9.243  1.00  0.00           H  
HETATM   90  H21 UNL     1       2.188  -4.332  -8.703  1.00  0.00           H  
HETATM   91  H22 UNL     1       0.502  -2.557  -6.964  1.00  0.00           H  
HETATM   92  H23 UNL     1       1.971  -3.461  -6.649  1.00  0.00           H  
HETATM   93  H24 UNL     1       1.000  -5.587  -7.018  1.00  0.00           H  
HETATM   94  H25 UNL     1      -0.546  -4.986  -7.622  1.00  0.00           H  
HETATM   95  H26 UNL     1       0.635  -4.982  -4.805  1.00  0.00           H  
HETATM   96  H27 UNL     1      -0.770  -5.869  -5.411  1.00  0.00           H  
HETATM   97  H28 UNL     1      -2.119  -3.675  -5.565  1.00  0.00           H  
HETATM   98  H29 UNL     1       0.080  -3.216  -3.549  1.00  0.00           H  
HETATM   99  H30 UNL     1      -2.179  -1.372  -4.470  1.00  0.00           H  
HETATM  100  H31 UNL     1      -3.452  -3.069  -3.382  1.00  0.00           H  
HETATM  101  H32 UNL     1      -0.105  -0.747  -3.180  1.00  0.00           H  
HETATM  102  H33 UNL     1      -1.800  -1.987  -0.979  1.00  0.00           H  
HETATM  103  H34 UNL     1      -0.359  -2.809  -1.619  1.00  0.00           H  
HETATM  104  H35 UNL     1       1.643  -1.032  -1.681  1.00  0.00           H  
HETATM  105  H36 UNL     1       2.771   0.163   1.640  1.00  0.00           H  
HETATM  106  H37 UNL     1       2.319  -1.352   3.553  1.00  0.00           H  
HETATM  107  H38 UNL     1       3.328  -2.093   2.320  1.00  0.00           H  
HETATM  108  H39 UNL     1       1.857  -3.509   1.883  1.00  0.00           H  
HETATM  109  H40 UNL     1      -0.186  -0.579   1.676  1.00  0.00           H  
HETATM  110  H41 UNL     1      -1.194  -0.201   3.055  1.00  0.00           H  
HETATM  111  H42 UNL     1      -3.088   1.048   2.594  1.00  0.00           H  
HETATM  112  H43 UNL     1      -4.654   2.061   4.295  1.00  0.00           H  
HETATM  113  H44 UNL     1      -3.161   2.714   5.164  1.00  0.00           H  
HETATM  114  H45 UNL     1      -4.258   3.520   2.652  1.00  0.00           H  
HETATM  115  H46 UNL     1      -3.090  -0.902   3.822  1.00  0.00           H  
HETATM  116  H47 UNL     1      -4.279  -0.470   5.866  1.00  0.00           H  
HETATM  117  H48 UNL     1      -1.884  -1.260   5.753  1.00  0.00           H  
HETATM  118  H49 UNL     1      -1.697   1.390   6.641  1.00  0.00           H  
HETATM  119  H50 UNL     1      -0.219   1.113   5.617  1.00  0.00           H  
HETATM  120  H51 UNL     1       0.050  -1.259   6.174  1.00  0.00           H  
HETATM  121  H52 UNL     1       0.994   2.140   1.044  1.00  0.00           H  
HETATM  122  H53 UNL     1      -1.281   1.886   0.871  1.00  0.00           H  
HETATM  123  H54 UNL     1       0.923   1.324  -1.444  1.00  0.00           H  
HETATM  124  H55 UNL     1       2.701   2.159  -0.572  1.00  0.00           H  
HETATM  125  H56 UNL     1      -2.594   0.067  -1.703  1.00  0.00           H  
HETATM  126  H57 UNL     1      -2.428   2.605  -1.382  1.00  0.00           H  
HETATM  127  H58 UNL     1      -3.209   2.592  -2.995  1.00  0.00           H  
HETATM  128  H59 UNL     1      -1.600   3.893  -4.044  1.00  0.00           H  
HETATM  129  H60 UNL     1      -0.393   3.829  -2.755  1.00  0.00           H  
HETATM  130  H61 UNL     1      -1.517   6.053  -2.805  1.00  0.00           H  
HETATM  131  H62 UNL     1      -3.104   5.252  -2.845  1.00  0.00           H  
HETATM  132  H63 UNL     1      -2.825   4.438  -0.612  1.00  0.00           H  
HETATM  133  H64 UNL     1      -1.077   4.878  -0.595  1.00  0.00           H  
HETATM  134  H65 UNL     1      -3.500   6.821  -0.622  1.00  0.00           H  
HETATM  135  H66 UNL     1      -1.761   7.293  -0.617  1.00  0.00           H  
HETATM  136  H67 UNL     1      -2.693   7.495   1.561  1.00  0.00           H  
HETATM  137  H68 UNL     1      -3.298   5.816   1.599  1.00  0.00           H  
HETATM  138  H69 UNL     1      -0.400   6.797   1.309  1.00  0.00           H  
HETATM  139  H70 UNL     1      -0.873   5.027   1.463  1.00  0.00           H  
HETATM  140  H71 UNL     1      -1.949   5.714   3.750  1.00  0.00           H  
HETATM  141  H72 UNL     1      -1.145   7.266   3.474  1.00  0.00           H  
HETATM  142  H73 UNL     1       1.067   6.120   3.304  1.00  0.00           H  
HETATM  143  H74 UNL     1       0.248   4.600   3.672  1.00  0.00           H  
HETATM  144  H75 UNL     1       0.268   7.045   5.424  1.00  0.00           H  
HETATM  145  H76 UNL     1      -0.679   5.614   5.825  1.00  0.00           H  
HETATM  146  H77 UNL     1       2.407   5.842   5.524  1.00  0.00           H  
HETATM  147  H78 UNL     1       1.538   5.728   7.052  1.00  0.00           H  
HETATM  148  H79 UNL     1       1.540   3.484   4.971  1.00  0.00           H  
HETATM  149  H80 UNL     1       0.699   3.521   6.543  1.00  0.00           H  
HETATM  150  H81 UNL     1       2.962   3.863   7.644  1.00  0.00           H  
HETATM  151  H82 UNL     1       3.718   3.679   5.970  1.00  0.00           H  
HETATM  152  H83 UNL     1       2.053   1.626   7.492  1.00  0.00           H  
HETATM  153  H84 UNL     1       2.630   1.453   5.817  1.00  0.00           H  
HETATM  154  H85 UNL     1       4.296   2.100   8.288  1.00  0.00           H  
HETATM  155  H86 UNL     1       5.007   1.884   6.694  1.00  0.00           H  
HETATM  156  H87 UNL     1       5.361  -0.097   8.022  1.00  0.00           H  
HETATM  157  H88 UNL     1       3.672  -0.109   8.617  1.00  0.00           H  
HETATM  158  H89 UNL     1       4.577  -0.883   5.757  1.00  0.00           H  
HETATM  159  H90 UNL     1       2.915  -0.965   6.473  1.00  0.00           H  
HETATM  160  H91 UNL     1       5.373  -2.312   7.606  1.00  0.00           H  
HETATM  161  H92 UNL     1       3.745  -2.430   8.288  1.00  0.00           H  
HETATM  162  H93 UNL     1       4.387  -4.450   6.874  1.00  0.00           H  
HETATM  163  H94 UNL     1       4.532  -3.373   5.474  1.00  0.00           H  
HETATM  164  H95 UNL     1       1.986  -3.661   7.105  1.00  0.00           H  
HETATM  165  H96 UNL     1       2.267  -2.669   5.568  1.00  0.00           H  
HETATM  166  H97 UNL     1       2.634  -4.714   4.277  1.00  0.00           H  
HETATM  167  H98 UNL     1       2.492  -5.735   5.761  1.00  0.00           H  
HETATM  168  H99 UNL     1       0.308  -3.983   4.548  1.00  0.00           H  
HETATM  169  HA0 UNL     1       0.413  -5.760   4.410  1.00  0.00           H  
HETATM  170  HA1 UNL     1       0.229  -5.951   6.900  1.00  0.00           H  
HETATM  171  HA2 UNL     1       0.026  -4.156   6.949  1.00  0.00           H  
HETATM  172  HA3 UNL     1      -1.838  -5.238   5.004  1.00  0.00           H  
HETATM  173  HA4 UNL     1      -2.020  -6.111   6.538  1.00  0.00           H  
HETATM  174  HA5 UNL     1      -2.175  -4.345   6.505  1.00  0.00           H  
CONECT    1    2   70   71   72
CONECT    2    3   73   74
CONECT    3    4   75   76
CONECT    4    5   77   78
CONECT    5    6   79   80
CONECT    6    7   81   82
CONECT    7    8   83   84
CONECT    8    9   85   86
CONECT    9   10   87   88
CONECT   10   11   89   90
CONECT   11   12   91   92
CONECT   12   13   93   94
CONECT   13   14   95   96
CONECT   14   15   15   97
CONECT   15   16   98
CONECT   16   17   18   99
CONECT   17  100
CONECT   18   19   43  101
CONECT   19   20  102  103
CONECT   20   21
CONECT   21   22   41  104
CONECT   22   23
CONECT   23   24   26  105
CONECT   24   25  106  107
CONECT   25  108
CONECT   26   27   39  109
CONECT   27   28
CONECT   28   29   37  110
CONECT   29   30
CONECT   30   31   33  111
CONECT   31   32  112  113
CONECT   32  114
CONECT   33   34   35  115
CONECT   34  116
CONECT   35   36   37  117
CONECT   36  118
CONECT   37   38  119
CONECT   38  120
CONECT   39   40   41  121
CONECT   40  122
CONECT   41   42  123
CONECT   42  124
CONECT   43   44  125
CONECT   44   45   45   46
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   58  148  149
CONECT   58   59  150  151
CONECT   59   60  152  153
CONECT   60   61  154  155
CONECT   61   62  156  157
CONECT   62   63  158  159
CONECT   63   64  160  161
CONECT   64   65  162  163
CONECT   65   66  164  165
CONECT   66   67  166  167
CONECT   67   68  168  169
CONECT   68   69  170  171
CONECT   69  172  173  174
END
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SMILES for HMDB0004876 (LacCer(d18:1/25:0))

[H][C@@](CO[C@@H]1O[C@H](CO)[C@@H](O[C@]2([H])O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O)(NC(=O)CCCCCCCCCCCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCC
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INCHI for HMDB0004876 (LacCer(d18:1/25:0))

InChI=1S/C55H105NO13/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-27-29-31-33-35-37-39-47(60)56-43(44(59)38-36-34-32-30-28-26-16-14-12-10-8-6-4-2)42-66-54-52(65)50(63)53(46(41-58)68-54)69-55-51(64)49(62)48(61)45(40-57)67-55/h36,38,43-46,48-55,57-59,61-65H,3-35,37,39-42H2,1-2H3,(H,56,60)/b38-36+/t43-,44+,45+,46+,48-,49-,50+,51+,52+,53+,54+,55-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
N-[(2S,3R,4E)-1-{[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]pentacosanimidateGenerator
LacCer d18:1/25:0HMDB
LacCer(d18:1/25:0)HMDB
Lactosylceramide (d18:1,C25:0)HMDB
Lactosylceramide (d18:1/25:0)HMDB
Lactosylceramide(d18:1/25:0)HMDB
Chemical FormulaC55H105NO13
Average Molecular Weight988.439
Monoisotopic Molecular Weight987.758592445
IUPAC NameN-[(2S,3R,4E)-1-{[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]pentacosanamide
Traditional NameN-[(2S,3R,4E)-1-{[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]pentacosanamide
CAS Registry Number2066483-64-3
SMILES
[H][C@@](CO[C@@H]1O[C@H](CO)[C@@H](O[C@]2([H])O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O)(NC(=O)CCCCCCCCCCCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCC
InChI Identifier
InChI=1S/C55H105NO13/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-27-29-31-33-35-37-39-47(60)56-43(44(59)38-36-34-32-30-28-26-16-14-12-10-8-6-4-2)42-66-54-52(65)50(63)53(46(41-58)68-54)69-55-51(64)49(62)48(61)45(40-57)67-55/h36,38,43-46,48-55,57-59,61-65H,3-35,37,39-42H2,1-2H3,(H,56,60)/b38-36+/t43-,44+,45+,46+,48-,49-,50+,51+,52+,53+,54+,55-/m0/s1
InChI KeyWPIHMWBQRSAMDE-WQCHUFMUSA-N
Chemical Taxonomy
ClassificationNot classified
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 Solubility0Not Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0019 g/LALOGPS
logP7.55ALOGPS
logP11.32ChemAxon
logS-5.7ALOGPS
pKa (Strongest Acidic)11.92ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area227.86 ŲChemAxon
Rotatable Bond Count45ChemAxon
Refractivity272.01 m³·mol⁻¹ChemAxon
Polarizability122.7 ųChemAxon
Number of Rings2ChemAxon
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]+313.49730932474
DeepCCS[M-H]-311.77330932474
DeepCCS[M-2H]-345.81730932474
DeepCCS[M+Na]+319.82730932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LacCer(d18:1/25:0) 10V, Positive-QTOFsplash10-01tj-2400009084-8d6fd9e1d6bcdaee88442021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LacCer(d18:1/25:0) 20V, Positive-QTOFsplash10-052b-3900004031-e8cdae7f1fa1cdcfdf882021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LacCer(d18:1/25:0) 40V, Positive-QTOFsplash10-02al-4910004100-aded64227ecbf9c783d62021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LacCer(d18:1/25:0) 10V, Negative-QTOFsplash10-000i-0101000019-840f7c89eb04778842782021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LacCer(d18:1/25:0) 20V, Negative-QTOFsplash10-0ap3-7591202036-619d77d564943dff3a532021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LacCer(d18:1/25:0) 40V, Negative-QTOFsplash10-0ab9-4323903000-c446fda1cadbbf991cb72021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue Locations
  • Adrenal Gland
  • Brain
  • Fibroblasts
  • 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 IDFDB023469
KNApSAcK IDNot Available
Chemspider ID59651474
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNicolaou, K. C.; Caulfield, T.; Kataoka, H.; Kumazawa, T. A practical and enantioselective synthesis of glycosphingolipids and related compounds. Total synthesis of globotriaosylceramide (Gb3). Journal of the American Chemical Society (1988), 110(23), 791
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Takizawa M, Nomura T, Wakisaka E, Yoshizuka N, Aoki J, Arai H, Inoue K, Hattori M, Matsuo N: cDNA cloning and expression of human lactosylceramide synthase. Biochim Biophys Acta. 1999 May 18;1438(2):301-4. [PubMed:10320813 ]
  2. Ohdoi C, Nyhan WL, Kuhara T: Chemical diagnosis of Lesch-Nyhan syndrome using gas chromatography-mass spectrometry detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 15;792(1):123-30. [PubMed:12829005 ]
  3. Ledvinova J, Poupetova H, Hanackova A, Pisacka M, Elleder M: Blood group B glycosphingolipids in alpha-galactosidase deficiency (Fabry disease): influence of secretor status. Biochim Biophys Acta. 1997 Apr 1;1345(2):180-7. [PubMed:9106497 ]
  4. Choudhury A, Dominguez M, Puri V, Sharma DK, Narita K, Wheatley CL, Marks DL, Pagano RE: Rab proteins mediate Golgi transport of caveola-internalized glycosphingolipids and correct lipid trafficking in Niemann-Pick C cells. J Clin Invest. 2002 Jun;109(12):1541-50. [PubMed:12070301 ]
  5. Sala G, Dupre T, Seta N, Codogno P, Ghidoni R: Increased biosynthesis of glycosphingolipids in congenital disorder of glycosylation Ia (CDG-Ia) fibroblasts. Pediatr Res. 2002 Nov;52(5):645-51. [PubMed:12409508 ]
  6. Furukawa K, Takamiya K, Furukawa K: Beta1,4-N-acetylgalactosaminyltransferase--GM2/GD2 synthase: a key enzyme to control the synthesis of brain-enriched complex gangliosides. Biochim Biophys Acta. 2002 Dec 19;1573(3):356-62. [PubMed:12417418 ]
  7. Komagome R, Sawa H, Suzuki T, Suzuki Y, Tanaka S, Atwood WJ, Nagashima K: Oligosaccharides as receptors for JC virus. J Virol. 2002 Dec;76(24):12992-3000. [PubMed:12438625 ]
  8. Prinetti A, Basso L, Appierto V, Villani MG, Valsecchi M, Loberto N, Prioni S, Chigorno V, Cavadini E, Formelli F, Sonnino S: Altered sphingolipid metabolism in N-(4-hydroxyphenyl)-retinamide-resistant A2780 human ovarian carcinoma cells. J Biol Chem. 2003 Feb 21;278(8):5574-83. Epub 2002 Dec 16. [PubMed:12486134 ]
  9. Moore RM, Silver RJ, Moore JJ: Physiological apoptotic agents have different effects upon human amnion epithelial and mesenchymal cells. Placenta. 2003 Feb-Mar;24(2-3):173-80. [PubMed:12566244 ]
  10. Hulkova H, Ledvinova J, Asfaw B, Koubek K, Kopriva K, Elleder M: Lactosylceramide in lysosomal storage disorders: a comparative immunohistochemical and biochemical study. Virchows Arch. 2005 Jul;447(1):31-44. Epub 2005 May 26. [PubMed:15918012 ]
  11. Sharma DK, Brown JC, Cheng Z, Holicky EL, Marks DL, Pagano RE: The glycosphingolipid, lactosylceramide, regulates beta1-integrin clustering and endocytosis. Cancer Res. 2005 Sep 15;65(18):8233-41. [PubMed:16166299 ]

Only showing the first 10 proteins. There are 72 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Galactocerebrosidase
General function:
Involved in galactosylceramidase activity
Specific function:
Hydrolyzes the galactose ester bonds of galactosylceramide, galactosylsphingosine, lactosylceramide, and monogalactosyldiglyceride. Enzyme with very low activity responsible for the lysosomal catabolism of galactosylceramide, a major lipid in myelin, kidney and epithelial cells of small intestine and colon.
Gene Name:
GALC
Uniprot ID:
P54803
Molecular weight:
77062.86
Enzyme Details
2. Sialidase-2
General function:
Involved in exo-alpha-sialidase activity
Specific function:
Hydrolyzes sialylated compounds.
Gene Name:
NEU2
Uniprot ID:
Q9Y3R4
Molecular weight:
Not Available
Enzyme Details
3. Sialidase-4
General function:
Involved in exo-alpha-sialidase activity
Specific function:
May function in lysosomal catabolism of sialylated glycoconjugates. Has sialidase activity towards synthetic substrates, such as 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid (4-MU-NANA or 4MU-NeuAc). Has a broad substrate specificity being active on glycoproteins, oligosaccharides and sialylated glycolipids.
Gene Name:
NEU4
Uniprot ID:
Q8WWR8
Molecular weight:
Not Available
Enzyme Details
4. Sialidase-1
General function:
Involved in exo-alpha-sialidase activity
Specific function:
Catalyzes the removal of sialic acid (N-acetylneuramic acid) moities from glycoproteins and glycolipids. To be active, it is strictly dependent on its presence in the multienzyme complex. Appears to have a preference for alpha 2-3 and alpha 2-6 sialyl linkage.
Gene Name:
NEU1
Uniprot ID:
Q99519
Molecular weight:
Not Available
Enzyme Details
5. Lactase-phlorizin hydrolase
General function:
Involved in hydrolase activity, hydrolyzing O-glycosyl compounds
Specific function:
LPH splits lactose in the small intestine.
Gene Name:
LCT
Uniprot ID:
P09848
Molecular weight:
218584.77
Enzyme Details
6. 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
7. 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
8. Alpha-galactosidase A
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
GLA
Uniprot ID:
P06280
Molecular weight:
Not Available
Enzyme Details
9. 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
10. Sphingomyelin phosphodiesterase
General function:
Involved in hydrolase activity
Specific function:
Converts sphingomyelin to ceramide. Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost catalytic activity.
Gene Name:
SMPD1
Uniprot ID:
P17405
Molecular weight:
69935.53

Only showing the first 10 proteins. There are 72 proteins in total.

Show all enzymes and transporters