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Showing metabocard for Lc3Cer (HMDB0062485)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-03-23 02:10:29 UTC
Update Date2022-03-07 03:17:55 UTC
HMDB IDHMDB0062485
Secondary Accession Numbers
  • HMDB62485
Metabolite Identification
Common NameLc3Cer
DescriptionN-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid belongs to the class of organic compounds known as glycosyl-n-acylsphingosines. Glycosyl-N-acylsphingosines are compounds containing a sphingosine linked to a simple glucosyl moiety. N-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid is a moderately basic compound (based on its pKa).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0062485 (Lc3Cer)

  Mrv1652303231703102D          

 79 81  0  0  1  0            999 V2000
   -9.2881   -2.8875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2881   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5737   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.2881   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  2  1  1  4  0  0  0
  2  3  1  0  0  0  0
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  4  5  1  0  0  0  0
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  9 10  1  0  0  0  0
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 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  2 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  1  0  0  0
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 21 22  1  1  0  0  0
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 25 26  1  6  0  0  0
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 28 29  1  6  0  0  0
 28 30  1  1  0  0  0
 30 31  1  0  0  0  0
 28 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  6  0  0  0
 35 34  1  6  0  0  0
 35 36  1  1  0  0  0
 35 37  1  0  0  0  0
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 50 51  1  0  0  0  0
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 76 77  2  0  0  0  0
 77 78  1  4  0  0  0
 77 79  1  0  0  0  0
M  END
Download

3D MOL for HMDB0062485 (Lc3Cer)

HMDB0062485
     RDKit          3D
Lc3Cer
132134  0  0  0  0  0  0  0  0999 V2000
   15.1109    1.6063   -1.7810 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4687    2.6748   -0.9794 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9957    2.6745   -0.8602 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3379    1.5174   -0.1846 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5380    0.1825   -0.7979 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8535   -0.9265   -0.1259 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4057   -1.0755   -0.0560 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5223   -0.0679    0.5344 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0921   -0.6289    0.5883 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5079   -0.9879   -0.7190 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3692    0.0854   -1.7263 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5679    1.2713   -1.4123 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1244    1.1573   -1.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2731    0.5565   -2.1451 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5042   -0.4835   -1.8798 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3941   -1.1463   -0.5684 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6493   -0.3751    0.3391 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7520   -2.5125   -0.7476 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2991   -2.3263   -1.1574 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6167   -1.5715   -0.2142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7138   -1.4450   -0.6299 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9470   -0.1109   -0.8068 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2696    0.2728   -0.7557 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2691    1.7536   -1.1626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4857    2.4580   -0.2534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8227    0.1418    0.6536 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1213   -0.3236    0.5773 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0313    0.4886    1.2288 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.6388   -0.1915    2.3082 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0257    0.8634    3.1800 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.4519    0.2827    4.4963 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8292    1.3142    5.3633 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0750    1.7106    2.5208 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.1951    1.6582    3.3739 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3824    1.2021    1.1658 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.3271    0.1846    1.1349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5071    0.5448    0.5252 C   0  0  2  0  0  0  0  0  0  0  0  0
  -10.5363    0.2858    1.4441 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7313    0.8476    1.0035 C   0  0  2  0  0  0  0  0  0  0  0  0
  -12.8045    0.5973    2.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3852    1.1994    3.2078 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0769    0.5170   -0.4040 C   0  0  1  0  0  0  0  0  0  0  0  0
  -12.3756    1.6788   -1.1538 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1649   -0.3829   -1.1432 C   0  0  2  0  0  0  0  0  0  0  0  0
  -11.6810   -1.6850   -1.2674 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7636   -0.4004   -0.6275 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.7779   -0.4011   -1.6434 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3266    0.4780   -2.4078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7976    1.8752   -2.3948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3132    0.1158   -3.3319 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1567    0.9495    0.3571 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.8027    2.0678   -0.4021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0387   -0.9681    1.3679 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9406   -0.4157    2.0089 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6637   -2.0364    0.3584 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8510   -2.4216   -0.2820 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7184   -3.2303    0.5119 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9900   -4.4965    0.5618 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9195   -5.1227    1.9329 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3249   -5.2813   -0.5055 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.4898    1.1286   -2.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.7287    0.8736   -1.1796 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.9312    2.1210   -2.3958 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.7551    3.6871   -1.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.9844    2.6789    0.0208 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5034    2.8695   -1.8643 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0062485 (Lc3Cer)

  Mrv1652303231703102D          

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 55 56  1  6  0  0  0
 55 57  1  1  0  0  0
 55 58  1  0  0  0  0
 58 59  1  1  0  0  0
 58 60  1  6  0  0  0
 58 61  1  0  0  0  0
 48 61  1  0  0  0  0
 61 62  1  6  0  0  0
 61 63  1  6  0  0  0
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 64 65  1  4  0  0  0
 64 66  1  0  0  0  0
 45 67  1  0  0  0  0
 35 67  1  0  0  0  0
 67 68  1  6  0  0  0
 67 69  1  6  0  0  0
 32 70  1  0  0  0  0
 70 71  1  6  0  0  0
 70 72  1  1  0  0  0
 70 73  1  0  0  0  0
 25 73  1  0  0  0  0
 73 74  1  1  0  0  0
 73 75  1  1  0  0  0
 21 76  1  1  0  0  0
 76 77  2  0  0  0  0
 77 78  1  4  0  0  0
 77 79  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0062485

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]C(CCCCCCCCCCCCC)=C([H])[C@@]([H])(O)[C@]([H])(CO[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O[C@]2([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O[C@]3([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])N=C(C)O)[C@@]2([H])O)[C@]([H])(O)[C@@]1([H])O)N=C(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C40H72N2O18/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-25(48)24(41-22(2)46)21-55-39-34(53)33(52)36(28(20-45)58-39)59-40-35(54)37(31(50)27(19-44)57-40)60-38-29(42-23(3)47)32(51)30(49)26(18-43)56-38/h16-17,24-40,43-45,48-54H,4-15,18-21H2,1-3H3,(H,41,46)(H,42,47)/t24-,25+,26+,27+,28+,29+,30+,31-,32+,33+,34+,35+,36+,37-,38-,39+,40-/m0/s1

> <INCHI_KEY>
IZUGJFIVXAZJFA-USLYCZPCSA-N

> <FORMULA>
C40H72N2O18

> <MOLECULAR_WEIGHT>
869.012

> <EXACT_MASS>
868.478013486

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
132

> <JCHEM_AVERAGE_POLARIZABILITY>
94.85006076958385

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid

> <ALOGPS_LOGP>
1.24

> <JCHEM_LOGP>
0.4240927749999987

> <ALOGPS_LOGS>
-3.81

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
6.014007079628412

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.363868802034218

> <JCHEM_PKA_STRONGEST_BASIC>
2.5084474417787184

> <JCHEM_POLAR_SURFACE_AREA>
322.86

> <JCHEM_REFRACTIVITY>
210.72040000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
26

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.35e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0062485 (Lc3Cer)

HMDB0062485
     RDKit          3D
Lc3Cer
132134  0  0  0  0  0  0  0  0999 V2000
   15.1109    1.6063   -1.7810 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4687    2.6748   -0.9794 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9957    2.6745   -0.8602 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3379    1.5174   -0.1846 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5380    0.1825   -0.7979 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8535   -0.9265   -0.1259 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4057   -1.0755   -0.0560 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5223   -0.0679    0.5344 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0921   -0.6289    0.5883 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5079   -0.9879   -0.7190 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3692    0.0854   -1.7263 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5679    1.2713   -1.4123 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1244    1.1573   -1.1019 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2731    0.5565   -2.1451 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5042   -0.4835   -1.8798 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3941   -1.1463   -0.5684 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6493   -0.3751    0.3391 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7520   -2.5125   -0.7476 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2991   -2.3263   -1.1574 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6167   -1.5715   -0.2142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7138   -1.4450   -0.6299 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9470   -0.1109   -0.8068 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2696    0.2728   -0.7557 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2691    1.7536   -1.1626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4857    2.4580   -0.2534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8227    0.1418    0.6536 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1213   -0.3236    0.5773 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0313    0.4886    1.2288 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.6388   -0.1915    2.3082 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0257    0.8634    3.1800 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.4519    0.2827    4.4963 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8292    1.3142    5.3633 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0750    1.7106    2.5208 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.1951    1.6582    3.3739 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3824    1.2021    1.1658 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.3271    0.1846    1.1349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5071    0.5448    0.5252 C   0  0  2  0  0  0  0  0  0  0  0  0
  -10.5363    0.2858    1.4441 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7313    0.8476    1.0035 C   0  0  2  0  0  0  0  0  0  0  0  0
  -12.8045    0.5973    2.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3852    1.1994    3.2078 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0769    0.5170   -0.4040 C   0  0  1  0  0  0  0  0  0  0  0  0
  -12.3756    1.6788   -1.1538 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1649   -0.3829   -1.1432 C   0  0  2  0  0  0  0  0  0  0  0  0
  -11.6810   -1.6850   -1.2674 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7636   -0.4004   -0.6275 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.7779   -0.4011   -1.6434 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3266    0.4780   -2.4078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7976    1.8752   -2.3948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3132    0.1158   -3.3319 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1567    0.9495    0.3571 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.8027    2.0678   -0.4021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0387   -0.9681    1.3679 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9406   -0.4157    2.0089 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6637   -2.0364    0.3584 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8510   -2.4216   -0.2820 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7184   -3.2303    0.5119 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9900   -4.4965    0.5618 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9195   -5.1227    1.9329 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3249   -5.2813   -0.5055 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.4898    1.1286   -2.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.7287    0.8736   -1.1796 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.9312    2.1210   -2.3958 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.7551    3.6871   -1.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.9844    2.6789    0.0208 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5034    2.8695   -1.8643 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7180    3.5958   -0.2624 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.8964    1.4442    0.8309 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3252    1.7740    0.1479 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6522   -0.0365   -0.6885 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.4111    0.1867   -1.9103 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2389   -1.8936   -0.6302 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3510   -1.0500    0.9014 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2009   -2.0550    0.4988 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9851   -1.3557   -1.0982 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8059    0.2299    1.5604 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3710    0.8489   -0.1044 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0774   -1.5665    1.2201 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4731    0.0857    1.1799 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5211   -1.4570   -0.5330 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.8944   -0.4075   -2.6415 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3528    0.4331   -2.1390 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0950    1.9351   -0.6414 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6246    1.9518   -2.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9241    0.6124   -0.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7388    2.2261   -0.9995 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.2312   -1.9636   -2.1808 H   0  0  0  0  0  0  0  0  0  0  0  0
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  5 70  1  0
  5 71  1  0
  6 72  1  0
  6 73  1  0
  7 74  1  0
  7 75  1  0
  8 76  1  0
  8 77  1  0
  9 78  1  0
  9 79  1  0
 10 80  1  0
 10 81  1  0
 11 82  1  0
 11 83  1  0
 12 84  1  0
 12 85  1  0
 13 86  1  0
 13 87  1  0
 14 88  1  0
 15 89  1  0
 16 90  1  1
 17 91  1  0
 18 92  1  6
 19 93  1  0
 19 94  1  0
 21 95  1  6
 23 96  1  6
 24 97  1  0
 24 98  1  0
 25 99  1  0
 26100  1  1
 28101  1  1
 30102  1  1
 31103  1  0
 31104  1  0
 32105  1  0
 33106  1  6
 34107  1  0
 35108  1  6
 37109  1  6
 39110  1  6
 40111  1  0
 40112  1  0
 41113  1  0
 42114  1  1
 43115  1  0
 44116  1  6
 45117  1  0
 46118  1  1
 49119  1  0
 49120  1  0
 49121  1  0
 50122  1  0
 51123  1  6
 52124  1  0
 53125  1  1
 54126  1  0
 55127  1  1
 56128  1  0
 59129  1  0
 59130  1  0
 59131  1  0
 60132  1  0
M  END
Download

PDB for HMDB0062485 (Lc3Cer)

HEADER    PROTEIN                                 23-MAR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAR-17         0                                  
HETATM    1  H   UNK     0     -17.338  -5.390   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0     -17.338  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -16.004  -7.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -14.670  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -13.337  -7.700   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -12.003  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -10.669  -7.700   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -18.672  -7.700   0.000  0.00  0.00           C+0
HETATM   17  H   UNK     0     -20.005  -8.470   0.000  0.00  0.00           H+0
HETATM   18  C   UNK     0     -18.672  -9.240   0.000  0.00  0.00           C+0
HETATM   19  H   UNK     0     -17.338  -8.470   0.000  0.00  0.00           H+0
HETATM   20  O   UNK     0     -17.338 -10.010   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0     -20.005 -10.010   0.000  0.00  0.00           C+0
HETATM   22  H   UNK     0     -18.672 -10.780   0.000  0.00  0.00           H+0
HETATM   23  C   UNK     0     -20.005 -11.550   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0     -21.339 -12.320   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0     -21.339 -13.860   0.000  0.00  0.00           C+0
HETATM   26  H   UNK     0     -20.005 -13.090   0.000  0.00  0.00           H+0
HETATM   27  O   UNK     0     -22.673 -14.630   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0     -22.673 -16.170   0.000  0.00  0.00           C+0
HETATM   29  H   UNK     0     -22.673 -17.710   0.000  0.00  0.00           H+0
HETATM   30  C   UNK     0     -24.006 -16.940   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0     -25.340 -16.170   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0     -21.339 -16.940   0.000  0.00  0.00           C+0
HETATM   33  H   UNK     0     -20.005 -17.710   0.000  0.00  0.00           H+0
HETATM   34  O   UNK     0     -21.339 -18.480   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0     -20.005 -19.250   0.000  0.00  0.00           C+0
HETATM   36  H   UNK     0     -21.339 -20.020   0.000  0.00  0.00           H+0
HETATM   37  O   UNK     0     -18.672 -18.480   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0     -17.338 -19.250   0.000  0.00  0.00           C+0
HETATM   39  H   UNK     0     -16.004 -20.020   0.000  0.00  0.00           H+0
HETATM   40  C   UNK     0     -16.004 -18.480   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0     -16.004 -16.940   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0     -17.338 -20.790   0.000  0.00  0.00           C+0
HETATM   43  H   UNK     0     -17.338 -22.330   0.000  0.00  0.00           H+0
HETATM   44  O   UNK     0     -16.004 -21.560   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0     -18.672 -21.560   0.000  0.00  0.00           C+0
HETATM   46  H   UNK     0     -20.005 -22.330   0.000  0.00  0.00           H+0
HETATM   47  O   UNK     0     -18.672 -23.100   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0     -17.338 -23.870   0.000  0.00  0.00           C+0
HETATM   49  H   UNK     0     -18.672 -24.640   0.000  0.00  0.00           H+0
HETATM   50  O   UNK     0     -16.004 -23.100   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0     -14.670 -23.870   0.000  0.00  0.00           C+0
HETATM   52  H   UNK     0     -13.337 -24.640   0.000  0.00  0.00           H+0
HETATM   53  C   UNK     0     -13.337 -23.100   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0     -12.003 -23.870   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0     -14.670 -25.410   0.000  0.00  0.00           C+0
HETATM   56  H   UNK     0     -14.670 -26.950   0.000  0.00  0.00           H+0
HETATM   57  O   UNK     0     -13.337 -26.180   0.000  0.00  0.00           O+0
HETATM   58  C   UNK     0     -16.004 -26.180   0.000  0.00  0.00           C+0
HETATM   59  H   UNK     0     -17.338 -26.950   0.000  0.00  0.00           H+0
HETATM   60  O   UNK     0     -16.004 -27.720   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0     -17.338 -25.410   0.000  0.00  0.00           C+0
HETATM   62  H   UNK     0     -16.004 -24.640   0.000  0.00  0.00           H+0
HETATM   63  N   UNK     0     -18.672 -26.180   0.000  0.00  0.00           N+0
HETATM   64  C   UNK     0     -18.672 -27.720   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -20.005 -28.490   0.000  0.00  0.00           C+0
HETATM   66  O   UNK     0     -17.338 -28.490   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0     -20.005 -20.790   0.000  0.00  0.00           C+0
HETATM   68  H   UNK     0     -18.672 -20.020   0.000  0.00  0.00           H+0
HETATM   69  O   UNK     0     -21.339 -21.560   0.000  0.00  0.00           O+0
HETATM   70  C   UNK     0     -20.005 -16.170   0.000  0.00  0.00           C+0
HETATM   71  H   UNK     0     -18.672 -15.400   0.000  0.00  0.00           H+0
HETATM   72  O   UNK     0     -18.672 -16.940   0.000  0.00  0.00           O+0
HETATM   73  C   UNK     0     -20.005 -14.630   0.000  0.00  0.00           C+0
HETATM   74  H   UNK     0     -21.339 -15.400   0.000  0.00  0.00           H+0
HETATM   75  O   UNK     0     -18.672 -13.860   0.000  0.00  0.00           O+0
HETATM   76  N   UNK     0     -21.339  -9.240   0.000  0.00  0.00           N+0
HETATM   77  C   UNK     0     -21.339  -7.700   0.000  0.00  0.00           C+0
HETATM   78  C   UNK     0     -20.005  -6.930   0.000  0.00  0.00           C+0
HETATM   79  O   UNK     0     -22.673  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16    2   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18   22   23   76                                             
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27   73                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29   30   32                                             
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30                                                            
CONECT   32   28   33   34   70                                             
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   36   37   67                                             
CONECT   36   35                                                            
CONECT   37   35   38                                                       
CONECT   38   37   39   40   42                                             
CONECT   39   38                                                            
CONECT   40   38   41                                                       
CONECT   41   40                                                            
CONECT   42   38   43   44   45                                             
CONECT   43   42                                                            
CONECT   44   42                                                            
CONECT   45   42   46   47   67                                             
CONECT   46   45                                                            
CONECT   47   45   48                                                       
CONECT   48   47   49   50   61                                             
CONECT   49   48                                                            
CONECT   50   48   51                                                       
CONECT   51   50   52   53   55                                             
CONECT   52   51                                                            
CONECT   53   51   54                                                       
CONECT   54   53                                                            
CONECT   55   51   56   57   58                                             
CONECT   56   55                                                            
CONECT   57   55                                                            
CONECT   58   55   59   60   61                                             
CONECT   59   58                                                            
CONECT   60   58                                                            
CONECT   61   58   48   62   63                                             
CONECT   62   61                                                            
CONECT   63   61   64                                                       
CONECT   64   63   65   66                                                  
CONECT   65   64                                                            
CONECT   66   64                                                            
CONECT   67   45   35   68   69                                             
CONECT   68   67                                                            
CONECT   69   67                                                            
CONECT   70   32   71   72   73                                             
CONECT   71   70                                                            
CONECT   72   70                                                            
CONECT   73   70   25   74   75                                             
CONECT   74   73                                                            
CONECT   75   73                                                            
CONECT   76   21   77                                                       
CONECT   77   76   78   79                                                  
CONECT   78   77                                                            
CONECT   79   77                                                            
MASTER        0    0    0    0    0    0    0    0   79    0  162    0
END
Download

3D PDB for HMDB0062485 (Lc3Cer)

COMPND    HMDB0062485
HETATM    1  C1  UNL     1      15.111   1.606  -1.781  1.00  0.00           C  
HETATM    2  C2  UNL     1      14.469   2.675  -0.979  1.00  0.00           C  
HETATM    3  C3  UNL     1      12.996   2.675  -0.860  1.00  0.00           C  
HETATM    4  C4  UNL     1      12.338   1.517  -0.185  1.00  0.00           C  
HETATM    5  C5  UNL     1      12.538   0.183  -0.798  1.00  0.00           C  
HETATM    6  C6  UNL     1      11.853  -0.927  -0.126  1.00  0.00           C  
HETATM    7  C7  UNL     1      10.406  -1.075  -0.056  1.00  0.00           C  
HETATM    8  C8  UNL     1       9.522  -0.068   0.534  1.00  0.00           C  
HETATM    9  C9  UNL     1       8.092  -0.629   0.588  1.00  0.00           C  
HETATM   10  C10 UNL     1       7.508  -0.988  -0.719  1.00  0.00           C  
HETATM   11  C11 UNL     1       7.369   0.085  -1.726  1.00  0.00           C  
HETATM   12  C12 UNL     1       6.568   1.271  -1.412  1.00  0.00           C  
HETATM   13  C13 UNL     1       5.124   1.157  -1.102  1.00  0.00           C  
HETATM   14  C14 UNL     1       4.273   0.557  -2.145  1.00  0.00           C  
HETATM   15  C15 UNL     1       3.504  -0.483  -1.880  1.00  0.00           C  
HETATM   16  C16 UNL     1       3.394  -1.146  -0.568  1.00  0.00           C  
HETATM   17  O1  UNL     1       2.649  -0.375   0.339  1.00  0.00           O  
HETATM   18  C17 UNL     1       2.752  -2.513  -0.748  1.00  0.00           C  
HETATM   19  C18 UNL     1       1.299  -2.326  -1.157  1.00  0.00           C  
HETATM   20  O2  UNL     1       0.617  -1.572  -0.214  1.00  0.00           O  
HETATM   21  C19 UNL     1      -0.714  -1.445  -0.630  1.00  0.00           C  
HETATM   22  O3  UNL     1      -0.947  -0.111  -0.807  1.00  0.00           O  
HETATM   23  C20 UNL     1      -2.270   0.273  -0.756  1.00  0.00           C  
HETATM   24  C21 UNL     1      -2.269   1.754  -1.163  1.00  0.00           C  
HETATM   25  O4  UNL     1      -1.486   2.458  -0.253  1.00  0.00           O  
HETATM   26  C22 UNL     1      -2.823   0.142   0.654  1.00  0.00           C  
HETATM   27  O5  UNL     1      -4.121  -0.324   0.577  1.00  0.00           O  
HETATM   28  C23 UNL     1      -5.031   0.489   1.229  1.00  0.00           C  
HETATM   29  O6  UNL     1      -5.639  -0.192   2.308  1.00  0.00           O  
HETATM   30  C24 UNL     1      -6.026   0.863   3.180  1.00  0.00           C  
HETATM   31  C25 UNL     1      -6.452   0.283   4.496  1.00  0.00           C  
HETATM   32  O7  UNL     1      -6.829   1.314   5.363  1.00  0.00           O  
HETATM   33  C26 UNL     1      -7.075   1.711   2.521  1.00  0.00           C  
HETATM   34  O8  UNL     1      -8.195   1.658   3.374  1.00  0.00           O  
HETATM   35  C27 UNL     1      -7.382   1.202   1.166  1.00  0.00           C  
HETATM   36  O9  UNL     1      -8.327   0.185   1.135  1.00  0.00           O  
HETATM   37  C28 UNL     1      -9.507   0.545   0.525  1.00  0.00           C  
HETATM   38  O10 UNL     1     -10.536   0.286   1.444  1.00  0.00           O  
HETATM   39  C29 UNL     1     -11.731   0.848   1.004  1.00  0.00           C  
HETATM   40  C30 UNL     1     -12.804   0.597   2.006  1.00  0.00           C  
HETATM   41  O11 UNL     1     -12.385   1.199   3.208  1.00  0.00           O  
HETATM   42  C31 UNL     1     -12.077   0.517  -0.404  1.00  0.00           C  
HETATM   43  O12 UNL     1     -12.376   1.679  -1.154  1.00  0.00           O  
HETATM   44  C32 UNL     1     -11.165  -0.383  -1.143  1.00  0.00           C  
HETATM   45  O13 UNL     1     -11.681  -1.685  -1.267  1.00  0.00           O  
HETATM   46  C33 UNL     1      -9.764  -0.400  -0.628  1.00  0.00           C  
HETATM   47  N1  UNL     1      -8.778  -0.401  -1.643  1.00  0.00           N  
HETATM   48  C34 UNL     1      -8.327   0.478  -2.408  1.00  0.00           C  
HETATM   49  C35 UNL     1      -8.798   1.875  -2.395  1.00  0.00           C  
HETATM   50  O14 UNL     1      -7.313   0.116  -3.332  1.00  0.00           O  
HETATM   51  C36 UNL     1      -6.157   0.949   0.357  1.00  0.00           C  
HETATM   52  O15 UNL     1      -5.803   2.068  -0.402  1.00  0.00           O  
HETATM   53  C37 UNL     1      -2.039  -0.968   1.368  1.00  0.00           C  
HETATM   54  O16 UNL     1      -0.941  -0.416   2.009  1.00  0.00           O  
HETATM   55  C38 UNL     1      -1.664  -2.036   0.358  1.00  0.00           C  
HETATM   56  O17 UNL     1      -2.851  -2.422  -0.282  1.00  0.00           O  
HETATM   57  N2  UNL     1       2.718  -3.230   0.512  1.00  0.00           N  
HETATM   58  C39 UNL     1       2.990  -4.496   0.562  1.00  0.00           C  
HETATM   59  C40 UNL     1       2.920  -5.123   1.933  1.00  0.00           C  
HETATM   60  O18 UNL     1       3.325  -5.281  -0.506  1.00  0.00           O  
HETATM   61  H1  UNL     1      14.490   1.129  -2.548  1.00  0.00           H  
HETATM   62  H2  UNL     1      15.729   0.874  -1.180  1.00  0.00           H  
HETATM   63  H3  UNL     1      15.931   2.121  -2.396  1.00  0.00           H  
HETATM   64  H4  UNL     1      14.755   3.687  -1.404  1.00  0.00           H  
HETATM   65  H5  UNL     1      14.984   2.679   0.021  1.00  0.00           H  
HETATM   66  H6  UNL     1      12.503   2.870  -1.864  1.00  0.00           H  
HETATM   67  H7  UNL     1      12.718   3.596  -0.262  1.00  0.00           H  
HETATM   68  H8  UNL     1      12.896   1.444   0.831  1.00  0.00           H  
HETATM   69  H9  UNL     1      11.325   1.774   0.148  1.00  0.00           H  
HETATM   70  H10 UNL     1      13.652  -0.037  -0.688  1.00  0.00           H  
HETATM   71  H11 UNL     1      12.411   0.187  -1.910  1.00  0.00           H  
HETATM   72  H12 UNL     1      12.239  -1.894  -0.630  1.00  0.00           H  
HETATM   73  H13 UNL     1      12.351  -1.050   0.901  1.00  0.00           H  
HETATM   74  H14 UNL     1      10.201  -2.055   0.499  1.00  0.00           H  
HETATM   75  H15 UNL     1       9.985  -1.356  -1.098  1.00  0.00           H  
HETATM   76  H16 UNL     1       9.806   0.230   1.560  1.00  0.00           H  
HETATM   77  H17 UNL     1       9.371   0.849  -0.104  1.00  0.00           H  
HETATM   78  H18 UNL     1       8.077  -1.567   1.220  1.00  0.00           H  
HETATM   79  H19 UNL     1       7.473   0.086   1.180  1.00  0.00           H  
HETATM   80  H20 UNL     1       6.521  -1.457  -0.533  1.00  0.00           H  
HETATM   81  H21 UNL     1       8.116  -1.816  -1.171  1.00  0.00           H  
HETATM   82  H22 UNL     1       6.894  -0.408  -2.641  1.00  0.00           H  
HETATM   83  H23 UNL     1       8.353   0.433  -2.139  1.00  0.00           H  
HETATM   84  H24 UNL     1       7.095   1.935  -0.641  1.00  0.00           H  
HETATM   85  H25 UNL     1       6.625   1.952  -2.335  1.00  0.00           H  
HETATM   86  H26 UNL     1       4.924   0.612  -0.145  1.00  0.00           H  
HETATM   87  H27 UNL     1       4.739   2.226  -1.000  1.00  0.00           H  
HETATM   88  H28 UNL     1       4.249   0.953  -3.174  1.00  0.00           H  
HETATM   89  H29 UNL     1       2.883  -0.908  -2.696  1.00  0.00           H  
HETATM   90  H30 UNL     1       4.375  -1.343  -0.115  1.00  0.00           H  
HETATM   91  H31 UNL     1       2.650  -0.869   1.213  1.00  0.00           H  
HETATM   92  H32 UNL     1       3.253  -3.119  -1.494  1.00  0.00           H  
HETATM   93  H33 UNL     1       0.825  -3.353  -1.139  1.00  0.00           H  
HETATM   94  H34 UNL     1       1.231  -1.964  -2.181  1.00  0.00           H  
HETATM   95  H35 UNL     1      -0.820  -2.022  -1.590  1.00  0.00           H  
HETATM   96  H36 UNL     1      -2.865  -0.263  -1.506  1.00  0.00           H  
HETATM   97  H37 UNL     1      -3.254   2.168  -1.316  1.00  0.00           H  
HETATM   98  H38 UNL     1      -1.733   1.778  -2.141  1.00  0.00           H  
HETATM   99  H39 UNL     1      -1.863   3.369  -0.170  1.00  0.00           H  
HETATM  100  H40 UNL     1      -2.663   1.059   1.195  1.00  0.00           H  
HETATM  101  H41 UNL     1      -4.499   1.379   1.626  1.00  0.00           H  
HETATM  102  H42 UNL     1      -5.094   1.478   3.332  1.00  0.00           H  
HETATM  103  H43 UNL     1      -5.551  -0.195   4.985  1.00  0.00           H  
HETATM  104  H44 UNL     1      -7.217  -0.493   4.438  1.00  0.00           H  
HETATM  105  H45 UNL     1      -6.515   1.124   6.286  1.00  0.00           H  
HETATM  106  H46 UNL     1      -6.675   2.769   2.495  1.00  0.00           H  
HETATM  107  H47 UNL     1      -8.509   0.726   3.431  1.00  0.00           H  
HETATM  108  H48 UNL     1      -7.910   2.070   0.637  1.00  0.00           H  
HETATM  109  H49 UNL     1      -9.533   1.565   0.152  1.00  0.00           H  
HETATM  110  H50 UNL     1     -11.537   1.967   1.034  1.00  0.00           H  
HETATM  111  H51 UNL     1     -13.701   1.205   1.685  1.00  0.00           H  
HETATM  112  H52 UNL     1     -13.034  -0.460   2.147  1.00  0.00           H  
HETATM  113  H53 UNL     1     -11.419   1.398   3.196  1.00  0.00           H  
HETATM  114  H54 UNL     1     -13.089  -0.008  -0.357  1.00  0.00           H  
HETATM  115  H55 UNL     1     -12.573   2.416  -0.501  1.00  0.00           H  
HETATM  116  H56 UNL     1     -11.121  -0.012  -2.209  1.00  0.00           H  
HETATM  117  H57 UNL     1     -12.631  -1.603  -1.538  1.00  0.00           H  
HETATM  118  H58 UNL     1      -9.660  -1.440  -0.128  1.00  0.00           H  
HETATM  119  H59 UNL     1      -8.204   2.496  -1.662  1.00  0.00           H  
HETATM  120  H60 UNL     1      -9.863   1.999  -2.141  1.00  0.00           H  
HETATM  121  H61 UNL     1      -8.572   2.338  -3.397  1.00  0.00           H  
HETATM  122  H62 UNL     1      -7.334   0.498  -4.268  1.00  0.00           H  
HETATM  123  H63 UNL     1      -6.350   0.067  -0.343  1.00  0.00           H  
HETATM  124  H64 UNL     1      -5.611   1.748  -1.326  1.00  0.00           H  
HETATM  125  H65 UNL     1      -2.709  -1.427   2.109  1.00  0.00           H  
HETATM  126  H66 UNL     1      -0.742  -0.983   2.799  1.00  0.00           H  
HETATM  127  H67 UNL     1      -1.215  -2.875   0.939  1.00  0.00           H  
HETATM  128  H68 UNL     1      -3.139  -3.275   0.161  1.00  0.00           H  
HETATM  129  H69 UNL     1       3.369  -4.440   2.675  1.00  0.00           H  
HETATM  130  H70 UNL     1       1.840  -5.334   2.156  1.00  0.00           H  
HETATM  131  H71 UNL     1       3.434  -6.098   1.909  1.00  0.00           H  
HETATM  132  H72 UNL     1       2.872  -5.330  -1.396  1.00  0.00           H  
CONECT    1    2   61   62   63
CONECT    2    3   64   65
CONECT    3    4   66   67
CONECT    4    5   68   69
CONECT    5    6   70   71
CONECT    6    7   72   73
CONECT    7    8   74   75
CONECT    8    9   76   77
CONECT    9   10   78   79
CONECT   10   11   80   81
CONECT   11   12   82   83
CONECT   12   13   84   85
CONECT   13   14   86   87
CONECT   14   15   15   88
CONECT   15   16   89
CONECT   16   17   18   90
CONECT   17   91
CONECT   18   19   57   92
CONECT   19   20   93   94
CONECT   20   21
CONECT   21   22   55   95
CONECT   22   23
CONECT   23   24   26   96
CONECT   24   25   97   98
CONECT   25   99
CONECT   26   27   53  100
CONECT   27   28
CONECT   28   29   51  101
CONECT   29   30
CONECT   30   31   33  102
CONECT   31   32  103  104
CONECT   32  105
CONECT   33   34   35  106
CONECT   34  107
CONECT   35   36   51  108
CONECT   36   37
CONECT   37   38   46  109
CONECT   38   39
CONECT   39   40   42  110
CONECT   40   41  111  112
CONECT   41  113
CONECT   42   43   44  114
CONECT   43  115
CONECT   44   45   46  116
CONECT   45  117
CONECT   46   47  118
CONECT   47   48   48
CONECT   48   49   50
CONECT   49  119  120  121
CONECT   50  122
CONECT   51   52  123
CONECT   52  124
CONECT   53   54   55  125
CONECT   54  126
CONECT   55   56  127
CONECT   56  128
CONECT   57   58   58
CONECT   58   59   60
CONECT   59  129  130  131
CONECT   60  132
END
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SMILES for HMDB0062485 (Lc3Cer)

[H]C(CCCCCCCCCCCCC)=C([H])[C@@]([H])(O)[C@]([H])(CO[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O[C@]2([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O[C@]3([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])N=C(C)O)[C@@]2([H])O)[C@]([H])(O)[C@@]1([H])O)N=C(C)O
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INCHI for HMDB0062485 (Lc3Cer)

InChI=1S/C40H72N2O18/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-25(48)24(41-22(2)46)21-55-39-34(53)33(52)36(28(20-45)58-39)59-40-35(54)37(31(50)27(19-44)57-40)60-38-29(42-23(3)47)32(51)30(49)26(18-43)56-38/h16-17,24-40,43-45,48-54H,4-15,18-21H2,1-3H3,(H,41,46)(H,42,47)/t24-,25+,26+,27+,28+,29+,30+,31-,32+,33+,34+,35+,36+,37-,38-,39+,40-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
N-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidateGenerator
Gal beta 1-4 glcna beta 1-3 gal beta 1-4 GLC-cerHMDB
NeolactotetraosylceramideHMDB
NLC(4)CerHMDB
NLC4CerHMDB
NLTCHMDB
ParaglobosideHMDB
Chemical FormulaC40H72N2O18
Average Molecular Weight869.012
Monoisotopic Molecular Weight868.478013486
IUPAC NameN-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid
Traditional NameN-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid
CAS Registry NumberNot Available
SMILES
[H]C(CCCCCCCCCCCCC)=C([H])[C@@]([H])(O)[C@]([H])(CO[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O[C@]2([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O[C@]3([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])N=C(C)O)[C@@]2([H])O)[C@]([H])(O)[C@@]1([H])O)N=C(C)O
InChI Identifier
InChI=1S/C40H72N2O18/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-25(48)24(41-22(2)46)21-55-39-34(53)33(52)36(28(20-45)58-39)59-40-35(54)37(31(50)27(19-44)57-40)60-38-29(42-23(3)47)32(51)30(49)26(18-43)56-38/h16-17,24-40,43-45,48-54H,4-15,18-21H2,1-3H3,(H,41,46)(H,42,47)/t24-,25+,26+,27+,28+,29+,30+,31-,32+,33+,34+,35+,36+,37-,38-,39+,40-/m0/s1
InChI KeyIZUGJFIVXAZJFA-USLYCZPCSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycosyl-n-acylsphingosines. Glycosyl-N-acylsphingosines are compounds containing a sphingosine linked to a simple glucosyl moiety.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassGlycosphingolipids
Direct ParentGlycosyl-N-acylsphingosines
Alternative Parents
Substituents
  • Glycosyl-n-acylsphingosine
  • Oligosaccharide
  • Fatty acyl glycoside
  • N-acyl-alpha-hexosamine
  • Alkyl glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Oxane
  • Fatty acyl
  • Acetamide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Organoheterocyclic compound
  • Acetal
  • Carboxylic acid derivative
  • Oxacycle
  • Primary alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.39 g/lALOGPS
LogP0.97ALOGPS
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 10V, Positive-QTOFsplash10-0gb9-1026000090-88ab21480528662fd7b42021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 20V, Positive-QTOFsplash10-0fsi-2139100030-abad1b33816cff437f992021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 40V, Positive-QTOFsplash10-000w-4912000000-ea58b1b25df3f04acfb32021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 10V, Negative-QTOFsplash10-01b9-0000110090-f0e56ab5b9c1ba69deab2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 20V, Negative-QTOFsplash10-00b9-1201102290-9de795c7bd35b12e15b02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 40V, Negative-QTOFsplash10-0a4i-9442310140-730ba78b3766c29ce2422021-09-22Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound57041562
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  6. Ghosh S, Strum JC, Bell RM: Lipid biochemistry: functions of glycerolipids and sphingolipids in cellular signaling. FASEB J. 1997 Jan;11(1):45-50. [PubMed:9034165 ]
  7. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  8. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.