Np mrd loader

Showing NP-Card for (2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol (NP0003424)

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Record Information
Version1.0
Created at2020-12-09 00:41:02 UTC
Updated at2021-07-15 16:46:23 UTC
NP-MRD IDNP0003424
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol
Provided ByNPAtlasNPAtlas Logo
Description(2R)-2-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tricosanimidic acid belongs to the class of organic compounds known as phytoceramides. These are n-acylated 4-hydroxysphinganine. (2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol is found in Grifola and Grifola frondosa. It was first documented in 2000 (PMID: 10993238). Based on a literature review very few articles have been published on (2R)-2-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tricosanimidic acid.
Structure
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MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0003424 ((2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol)


  Mrv1652307012117093D          

130129  0  0  0  0            999 V2000
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M  END
Download

3D MOL for NP0003424 ((2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol)

     RDKit          3D

130129  0  0  0  0  0  0  0  0999 V2000
  -15.3965    1.2537   -1.9726 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3583    1.5201   -0.9048 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for NP0003424 ((2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol)


  Mrv1652307012117093D          

130129  0  0  0  0            999 V2000
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    3.2453    0.3734    3.0415 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0357    1.3182    3.6533 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5837   -1.0509    3.3186 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3578   -1.2681    4.7432 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9853   -1.5014    3.0368 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3753   -1.3404    1.6254 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.7707   -1.8945    1.3423 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.8550   -1.2237    2.1298 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.0337    0.2057    1.8516 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.3469    0.5997    0.4846 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.5842    0.2429   -0.2204 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.8979   -1.1793   -0.4546 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.1348   -1.4785   -1.2142 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.3178   -1.0856   -2.6045 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.3045    0.3181   -3.0412 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.3289    1.1919   -2.3608 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2171    2.6108   -2.9067 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.2352    3.5201   -2.2489 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.4202    1.4505   -1.6056 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.1416    1.8555   -2.8470 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2940    0.1683   -2.2576 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.5358    2.5770   -0.5632 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.5405    0.8617   -0.0387 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.8478    2.1580   -2.2617 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7862    0.4049   -1.9195 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1929    2.7175    0.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2522    1.0323    0.5666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9668    1.8603    0.2163 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3457    2.3967   -1.4392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1007    0.3314   -1.5362 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8083   -0.0186   -2.0875 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1399   -0.4640    0.8539 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5817   -0.8560   -0.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4710   -2.8554    0.3174 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6973   -2.4871   -1.4004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2567   -2.1830   -1.7284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6979   -3.7276   -1.0115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0952   -3.0282    1.2333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7166   -3.0750    0.0882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9317   -0.4422    1.1512 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4317   -1.3331    1.5684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5470   -1.0733   -0.5213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9744   -0.3810   -1.2698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5947    0.7993    1.2558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1292    1.3780    0.5728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8699    2.0671   -1.5528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4023    2.8667   -0.0406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6008    2.6072   -1.3907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3371    1.7566    0.1227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9646    0.2631   -2.5552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6061   -0.4644   -0.9521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7928    1.5468   -2.3385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5744   -0.2051   -2.5156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5123    1.5808   -0.0166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1581    0.7856   -0.7705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9498   -0.3032    1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5984   -0.4107    0.7620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7769   -2.2131   -0.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7223   -2.5482    0.7727 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0951   -3.4785   -0.4295 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5143   -2.5732    1.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0996   -2.6459   -0.8542 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2811   -2.2983   -2.4890 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4225   -0.9124    1.6977 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6176    1.1030    1.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1033    1.6980    2.5601 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5118    2.3010    0.8708 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8813    3.6961    1.7738 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2160    0.4732    3.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0282    1.1445    4.6259 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8197   -1.7065    2.8700 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6473   -2.2308    4.8269 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6455   -0.8784    3.6914 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0322   -2.5768    3.3464 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6441   -1.8121    0.9584 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3747   -0.2385    1.3895 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9430   -1.6891    0.2683 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7683   -2.9940    1.4683 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7616   -1.8079    2.1179 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5643   -1.2753    3.2561 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.4785    0.3508   -0.2310 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3071    1.7560    0.4654 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6048    0.8670   -1.1566 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4766    0.6422    0.4068 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0157   -1.7727   -0.8222 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1047   -1.6254    0.5805 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2474   -2.6235   -1.1891 H   0  0  0  0  0  0  0  0  0  0  0  0
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   12.2428   -1.5762   -3.0575 H   0  0  0  0  0  0  0  0  0  0  0  0
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   12.2610    1.1521   -1.2628 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2296    3.0433   -2.7629 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3921    2.5209   -4.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.1517    2.9765   -1.9329 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4492    4.3425   -2.9546 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7777    3.9852   -1.3371 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
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 47129  1  0  0  0  0
 47130  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0003424

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@]([H])(N([H])C(=O)[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])[C@]([H])(O[H])[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C41H83NO5/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-25-27-29-31-33-35-39(45)41(47)42-37(36-43)40(46)38(44)34-32-30-28-26-24-16-14-12-10-8-6-4-2/h37-40,43-46H,3-36H2,1-2H3,(H,42,47)/t37-,38+,39+,40-/m0/s1

> <INCHI_KEY>
LXCDJSOYWPJYDC-KQQMQGIYSA-N

> <FORMULA>
C41H83NO5

> <MOLECULAR_WEIGHT>
670.117

> <EXACT_MASS>
669.627124777

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
130

> <JCHEM_AVERAGE_POLARIZABILITY>
85.39300654513193

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tricosanamide

> <ALOGPS_LOGP>
9.30

> <JCHEM_LOGP>
12.23738046766667

> <ALOGPS_LOGS>
-6.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.42438895494546

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.696305495085273

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7917255790393964

> <JCHEM_POLAR_SURFACE_AREA>
110.02000000000001

> <JCHEM_REFRACTIVITY>
199.8738

> <JCHEM_ROTATABLE_BOND_COUNT>
38

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.52e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tricosanamide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0003424 ((2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol)

     RDKit          3D

130129  0  0  0  0  0  0  0  0999 V2000
  -15.3965    1.2537   -1.9726 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3583    1.5201   -0.9048 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.9482    1.3936   -1.4626 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0112    1.6669   -0.3271 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5635    1.5936   -0.6791 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1334    0.2339   -1.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4166   -0.8071   -0.1747 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0390   -2.1861   -0.5090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6568   -2.6120   -0.7558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6688   -2.4900    0.3329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2392   -1.1645    0.7767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4152   -0.4262   -0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1343    0.9124    0.2604 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.9262    1.6357   -0.8629 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for NP0003424 ((2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol)

HEADER    PROTEIN                                 01-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-JUL-21         0                                  
HETATM    1  C   UNK     0     -15.396   1.254  -1.973  0.00  0.00           C+0
HETATM    2  C   UNK     0     -14.358   1.520  -0.905  0.00  0.00           C+0
HETATM    3  C   UNK     0     -12.948   1.394  -1.463  0.00  0.00           C+0
HETATM    4  C   UNK     0     -12.011   1.667  -0.327  0.00  0.00           C+0
HETATM    5  C   UNK     0     -10.563   1.594  -0.679  0.00  0.00           C+0
HETATM    6  C   UNK     0     -10.133   0.234  -1.213  0.00  0.00           C+0
HETATM    7  C   UNK     0     -10.417  -0.807  -0.175  0.00  0.00           C+0
HETATM    8  C   UNK     0     -10.039  -2.186  -0.509  0.00  0.00           C+0
HETATM    9  C   UNK     0      -8.657  -2.612  -0.756  0.00  0.00           C+0
HETATM   10  C   UNK     0      -7.669  -2.490   0.333  0.00  0.00           C+0
HETATM   11  C   UNK     0      -7.239  -1.165   0.777  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.415  -0.426  -0.331  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.134   0.912   0.260  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.356   1.835  -0.550  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.926   1.636  -0.863  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.456   0.449  -1.606  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.944   0.563  -1.843  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.231   0.634  -0.508  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.536  -0.508   0.371  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.202  -1.879  -0.013  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.182  -2.369  -0.065  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.241  -1.784  -0.870  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.034  -1.725  -2.223  0.00  0.00           O+0
HETATM   24  C   UNK     0       2.036  -0.679  -0.311  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.756   0.028  -1.051  0.00  0.00           O+0
HETATM   26  N   UNK     0       2.035  -0.350   1.077  0.00  0.00           N+0
HETATM   27  C   UNK     0       2.813   0.711   1.658  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.892   1.960   1.829  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.654   2.984   2.393  0.00  0.00           O+0
HETATM   30  C   UNK     0       3.245   0.373   3.042  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.036   1.318   3.653  0.00  0.00           O+0
HETATM   32  C   UNK     0       3.584  -1.051   3.319  0.00  0.00           C+0
HETATM   33  O   UNK     0       3.358  -1.268   4.743  0.00  0.00           O+0
HETATM   34  C   UNK     0       4.985  -1.501   3.037  0.00  0.00           C+0
HETATM   35  C   UNK     0       5.375  -1.340   1.625  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.771  -1.895   1.342  0.00  0.00           C+0
HETATM   37  C   UNK     0       7.855  -1.224   2.130  0.00  0.00           C+0
HETATM   38  C   UNK     0       8.034   0.206   1.852  0.00  0.00           C+0
HETATM   39  C   UNK     0       8.347   0.600   0.485  0.00  0.00           C+0
HETATM   40  C   UNK     0       9.584   0.243  -0.220  0.00  0.00           C+0
HETATM   41  C   UNK     0       9.898  -1.179  -0.455  0.00  0.00           C+0
HETATM   42  C   UNK     0      11.135  -1.478  -1.214  0.00  0.00           C+0
HETATM   43  C   UNK     0      11.318  -1.086  -2.604  0.00  0.00           C+0
HETATM   44  C   UNK     0      11.305   0.318  -3.041  0.00  0.00           C+0
HETATM   45  C   UNK     0      12.329   1.192  -2.361  0.00  0.00           C+0
HETATM   46  C   UNK     0      12.217   2.611  -2.907  0.00  0.00           C+0
HETATM   47  C   UNK     0      13.235   3.520  -2.249  0.00  0.00           C+0
HETATM   48  H   UNK     0     -16.420   1.450  -1.606  0.00  0.00           H+0
HETATM   49  H   UNK     0     -15.142   1.855  -2.847  0.00  0.00           H+0
HETATM   50  H   UNK     0     -15.294   0.168  -2.258  0.00  0.00           H+0
HETATM   51  H   UNK     0     -14.536   2.577  -0.563  0.00  0.00           H+0
HETATM   52  H   UNK     0     -14.540   0.862  -0.039  0.00  0.00           H+0
HETATM   53  H   UNK     0     -12.848   2.158  -2.262  0.00  0.00           H+0
HETATM   54  H   UNK     0     -12.786   0.405  -1.920  0.00  0.00           H+0
HETATM   55  H   UNK     0     -12.193   2.717   0.029  0.00  0.00           H+0
HETATM   56  H   UNK     0     -12.252   1.032   0.567  0.00  0.00           H+0
HETATM   57  H   UNK     0      -9.967   1.860   0.216  0.00  0.00           H+0
HETATM   58  H   UNK     0     -10.346   2.397  -1.439  0.00  0.00           H+0
HETATM   59  H   UNK     0      -9.101   0.331  -1.536  0.00  0.00           H+0
HETATM   60  H   UNK     0     -10.808  -0.019  -2.087  0.00  0.00           H+0
HETATM   61  H   UNK     0     -10.140  -0.464   0.854  0.00  0.00           H+0
HETATM   62  H   UNK     0     -11.582  -0.856  -0.049  0.00  0.00           H+0
HETATM   63  H   UNK     0     -10.471  -2.855   0.317  0.00  0.00           H+0
HETATM   64  H   UNK     0     -10.697  -2.487  -1.400  0.00  0.00           H+0
HETATM   65  H   UNK     0      -8.257  -2.183  -1.728  0.00  0.00           H+0
HETATM   66  H   UNK     0      -8.698  -3.728  -1.012  0.00  0.00           H+0
HETATM   67  H   UNK     0      -8.095  -3.028   1.233  0.00  0.00           H+0
HETATM   68  H   UNK     0      -6.717  -3.075   0.088  0.00  0.00           H+0
HETATM   69  H   UNK     0      -7.932  -0.442   1.151  0.00  0.00           H+0
HETATM   70  H   UNK     0      -6.432  -1.333   1.568  0.00  0.00           H+0
HETATM   71  H   UNK     0      -5.547  -1.073  -0.521  0.00  0.00           H+0
HETATM   72  H   UNK     0      -6.974  -0.381  -1.270  0.00  0.00           H+0
HETATM   73  H   UNK     0      -5.595   0.799   1.256  0.00  0.00           H+0
HETATM   74  H   UNK     0      -7.129   1.378   0.573  0.00  0.00           H+0
HETATM   75  H   UNK     0      -5.870   2.067  -1.553  0.00  0.00           H+0
HETATM   76  H   UNK     0      -5.402   2.867  -0.041  0.00  0.00           H+0
HETATM   77  H   UNK     0      -3.601   2.607  -1.391  0.00  0.00           H+0
HETATM   78  H   UNK     0      -3.337   1.757   0.123  0.00  0.00           H+0
HETATM   79  H   UNK     0      -3.965   0.263  -2.555  0.00  0.00           H+0
HETATM   80  H   UNK     0      -3.606  -0.464  -0.952  0.00  0.00           H+0
HETATM   81  H   UNK     0      -1.793   1.547  -2.338  0.00  0.00           H+0
HETATM   82  H   UNK     0      -1.574  -0.205  -2.516  0.00  0.00           H+0
HETATM   83  H   UNK     0      -1.512   1.581  -0.017  0.00  0.00           H+0
HETATM   84  H   UNK     0      -0.158   0.786  -0.771  0.00  0.00           H+0
HETATM   85  H   UNK     0      -0.950  -0.303   1.351  0.00  0.00           H+0
HETATM   86  H   UNK     0      -2.598  -0.411   0.762  0.00  0.00           H+0
HETATM   87  H   UNK     0      -1.777  -2.213  -0.943  0.00  0.00           H+0
HETATM   88  H   UNK     0      -1.722  -2.548   0.773  0.00  0.00           H+0
HETATM   89  H   UNK     0       0.095  -3.478  -0.430  0.00  0.00           H+0
HETATM   90  H   UNK     0       0.514  -2.573   1.010  0.00  0.00           H+0
HETATM   91  H   UNK     0       2.100  -2.646  -0.854  0.00  0.00           H+0
HETATM   92  H   UNK     0       0.281  -2.298  -2.489  0.00  0.00           H+0
HETATM   93  H   UNK     0       1.423  -0.912   1.698  0.00  0.00           H+0
HETATM   94  H   UNK     0       3.618   1.103   1.035  0.00  0.00           H+0
HETATM   95  H   UNK     0       1.103   1.698   2.560  0.00  0.00           H+0
HETATM   96  H   UNK     0       1.512   2.301   0.871  0.00  0.00           H+0
HETATM   97  H   UNK     0       2.881   3.696   1.774  0.00  0.00           H+0
HETATM   98  H   UNK     0       2.216   0.473   3.664  0.00  0.00           H+0
HETATM   99  H   UNK     0       4.028   1.145   4.626  0.00  0.00           H+0
HETATM  100  H   UNK     0       2.820  -1.706   2.870  0.00  0.00           H+0
HETATM  101  H   UNK     0       3.647  -2.231   4.827  0.00  0.00           H+0
HETATM  102  H   UNK     0       5.646  -0.878   3.691  0.00  0.00           H+0
HETATM  103  H   UNK     0       5.032  -2.577   3.346  0.00  0.00           H+0
HETATM  104  H   UNK     0       4.644  -1.812   0.958  0.00  0.00           H+0
HETATM  105  H   UNK     0       5.375  -0.239   1.389  0.00  0.00           H+0
HETATM  106  H   UNK     0       6.943  -1.689   0.268  0.00  0.00           H+0
HETATM  107  H   UNK     0       6.768  -2.994   1.468  0.00  0.00           H+0
HETATM  108  H   UNK     0       8.762  -1.808   2.118  0.00  0.00           H+0
HETATM  109  H   UNK     0       7.564  -1.275   3.256  0.00  0.00           H+0
HETATM  110  H   UNK     0       7.218   0.846   2.315  0.00  0.00           H+0
HETATM  111  H   UNK     0       8.939   0.530   2.491  0.00  0.00           H+0
HETATM  112  H   UNK     0       7.479   0.351  -0.231  0.00  0.00           H+0
HETATM  113  H   UNK     0       8.307   1.756   0.465  0.00  0.00           H+0
HETATM  114  H   UNK     0       9.605   0.867  -1.157  0.00  0.00           H+0
HETATM  115  H   UNK     0      10.477   0.642   0.407  0.00  0.00           H+0
HETATM  116  H   UNK     0       9.016  -1.773  -0.822  0.00  0.00           H+0
HETATM  117  H   UNK     0      10.105  -1.625   0.581  0.00  0.00           H+0
HETATM  118  H   UNK     0      11.247  -2.624  -1.189  0.00  0.00           H+0
HETATM  119  H   UNK     0      11.995  -1.173  -0.542  0.00  0.00           H+0
HETATM  120  H   UNK     0      10.492  -1.614  -3.204  0.00  0.00           H+0
HETATM  121  H   UNK     0      12.243  -1.576  -3.058  0.00  0.00           H+0
HETATM  122  H   UNK     0      10.342   0.818  -3.191  0.00  0.00           H+0
HETATM  123  H   UNK     0      11.688   0.272  -4.151  0.00  0.00           H+0
HETATM  124  H   UNK     0      13.358   0.837  -2.626  0.00  0.00           H+0
HETATM  125  H   UNK     0      12.261   1.152  -1.263  0.00  0.00           H+0
HETATM  126  H   UNK     0      11.230   3.043  -2.763  0.00  0.00           H+0
HETATM  127  H   UNK     0      12.392   2.521  -4.013  0.00  0.00           H+0
HETATM  128  H   UNK     0      14.152   2.977  -1.933  0.00  0.00           H+0
HETATM  129  H   UNK     0      13.449   4.343  -2.955  0.00  0.00           H+0
HETATM  130  H   UNK     0      12.778   3.985  -1.337  0.00  0.00           H+0
CONECT    1    2   48   49   50                                             
CONECT    2    1    3   51   52                                             
CONECT    3    2    4   53   54                                             
CONECT    4    3    5   55   56                                             
CONECT    5    4    6   57   58                                             
CONECT    6    5    7   59   60                                             
CONECT    7    6    8   61   62                                             
CONECT    8    7    9   63   64                                             
CONECT    9    8   10   65   66                                             
CONECT   10    9   11   67   68                                             
CONECT   11   10   12   69   70                                             
CONECT   12   11   13   71   72                                             
CONECT   13   12   14   73   74                                             
CONECT   14   13   15   75   76                                             
CONECT   15   14   16   77   78                                             
CONECT   16   15   17   79   80                                             
CONECT   17   16   18   81   82                                             
CONECT   18   17   19   83   84                                             
CONECT   19   18   20   85   86                                             
CONECT   20   19   21   87   88                                             
CONECT   21   20   22   89   90                                             
CONECT   22   21   23   24   91                                             
CONECT   23   22   92                                                       
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27   93                                                  
CONECT   27   26   28   30   94                                             
CONECT   28   27   29   95   96                                             
CONECT   29   28   97                                                       
CONECT   30   27   31   32   98                                             
CONECT   31   30   99                                                       
CONECT   32   30   33   34  100                                             
CONECT   33   32  101                                                       
CONECT   34   32   35  102  103                                             
CONECT   35   34   36  104  105                                             
CONECT   36   35   37  106  107                                             
CONECT   37   36   38  108  109                                             
CONECT   38   37   39  110  111                                             
CONECT   39   38   40  112  113                                             
CONECT   40   39   41  114  115                                             
CONECT   41   40   42  116  117                                             
CONECT   42   41   43  118  119                                             
CONECT   43   42   44  120  121                                             
CONECT   44   43   45  122  123                                             
CONECT   45   44   46  124  125                                             
CONECT   46   45   47  126  127                                             
CONECT   47   46  128  129  130                                             
CONECT   48    1                                                            
CONECT   49    1                                                            
CONECT   50    1                                                            
CONECT   51    2                                                            
CONECT   52    2                                                            
CONECT   53    3                                                            
CONECT   54    3                                                            
CONECT   55    4                                                            
CONECT   56    4                                                            
CONECT   57    5                                                            
CONECT   58    5                                                            
CONECT   59    6                                                            
CONECT   60    6                                                            
CONECT   61    7                                                            
CONECT   62    7                                                            
CONECT   63    8                                                            
CONECT   64    8                                                            
CONECT   65    9                                                            
CONECT   66    9                                                            
CONECT   67   10                                                            
CONECT   68   10                                                            
CONECT   69   11                                                            
CONECT   70   11                                                            
CONECT   71   12                                                            
CONECT   72   12                                                            
CONECT   73   13                                                            
CONECT   74   13                                                            
CONECT   75   14                                                            
CONECT   76   14                                                            
CONECT   77   15                                                            
CONECT   78   15                                                            
CONECT   79   16                                                            
CONECT   80   16                                                            
CONECT   81   17                                                            
CONECT   82   17                                                            
CONECT   83   18                                                            
CONECT   84   18                                                            
CONECT   85   19                                                            
CONECT   86   19                                                            
CONECT   87   20                                                            
CONECT   88   20                                                            
CONECT   89   21                                                            
CONECT   90   21                                                            
CONECT   91   22                                                            
CONECT   92   23                                                            
CONECT   93   26                                                            
CONECT   94   27                                                            
CONECT   95   28                                                            
CONECT   96   28                                                            
CONECT   97   29                                                            
CONECT   98   30                                                            
CONECT   99   31                                                            
CONECT  100   32                                                            
CONECT  101   33                                                            
CONECT  102   34                                                            
CONECT  103   34                                                            
CONECT  104   35                                                            
CONECT  105   35                                                            
CONECT  106   36                                                            
CONECT  107   36                                                            
CONECT  108   37                                                            
CONECT  109   37                                                            
CONECT  110   38                                                            
CONECT  111   38                                                            
CONECT  112   39                                                            
CONECT  113   39                                                            
CONECT  114   40                                                            
CONECT  115   40                                                            
CONECT  116   41                                                            
CONECT  117   41                                                            
CONECT  118   42                                                            
CONECT  119   42                                                            
CONECT  120   43                                                            
CONECT  121   43                                                            
CONECT  122   44                                                            
CONECT  123   44                                                            
CONECT  124   45                                                            
CONECT  125   45                                                            
CONECT  126   46                                                            
CONECT  127   46                                                            
CONECT  128   47                                                            
CONECT  129   47                                                            
CONECT  130   47                                                            
MASTER        0    0    0    0    0    0    0    0  130    0  258    0
END
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3D PDB for NP0003424 ((2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol)

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SMILES for NP0003424 ((2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol)
[H]OC([H])([H])[C@]([H])(N([H])C(=O)[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])[C@]([H])(O[H])[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]
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INCHI for NP0003424 ((2S, 3S, 4R)-2-[(2'R)-2'-hydroxytricosanoylamino]-1, 3, 4-octadecanetriol)
InChI=1S/C41H83NO5/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-25-27-29-31-33-35-39(45)41(47)42-37(36-43)40(46)38(44)34-32-30-28-26-24-16-14-12-10-8-6-4-2/h37-40,43-46H,3-36H2,1-2H3,(H,42,47)/t37-,38+,39+,40-/m0/s1
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View in JSmolView NMR Assignments
Synonyms
ValueSource
(2R)-2-Hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tricosanimidateGenerator
Chemical FormulaC41H83NO5
Average Mass670.1170 Da
Monoisotopic Mass669.62712 Da
IUPAC Name2-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tricosanamide
Traditional Name2-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tricosanamide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCCCCCCC[C@@H](O)C(=O)N[C@@H](CO)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C41H83NO5/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-25-27-29-31-33-35-39(45)41(47)42-37(36-43)40(46)38(44)34-32-30-28-26-24-16-14-12-10-8-6-4-2/h37-40,43-46H,3-36H2,1-2H3,(H,42,47)/t37-,38+,39+,40-/m0/s1
InChI KeyLXCDJSOYWPJYDC-KQQMQGIYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
GrifolaNPAtlas
Grifola frondosaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phytoceramides. These are n-acylated 4-hydroxysphinganine.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassSphingolipids  
Sub ClassCeramides  
Direct ParentPhytoceramides  
Alternative Parents
Substituents
  • N-acyl-4-hydroxysphinganine
    • 

  • Fatty amide
    • 

  • Monosaccharide
    • 

  • Fatty acyl
    • 

  • N-acyl-amine
    • 

  • 1,2-diol
    • 

  • Carboxamide group
    • 

  • Secondary carboxylic acid amide
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Polyol
    • 

  • Organonitrogen compound
    • 

  • Primary alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP9.3ALOGPS
logP12.24ChemAxon
logS-6.8ALOGPS
pKa (Strongest Acidic)12.7ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area110.02 ŲChemAxon
Rotatable Bond Count38ChemAxon
Refractivity199.87 m³·mol⁻¹ChemAxon
Polarizability85.39 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
NPAtlas IDNPA013210  
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID8874980  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10699639  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Yaoita Y, Ishizuka T, Kakuda R, Machida K, Kikuchi M: Structures of new ceramides from the fruit bodies of Grifola frondosa. Chem Pharm Bull (Tokyo). 2000 Sep;48(9):1356-8. doi: 10.1248/cpb.48.1356. [PubMed:10993238  ]