Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 03:07:01 UTC

Update Date

2022-03-07 02:57:01 UTC

HMDB ID

HMDB0041430

Secondary Accession Numbers

HMDB41430

Metabolite Identification

Common Name

Gymnodimine

Description

Gymnodimine belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms. The toxicity of gymnodimine has been attributed, at least in part, to the imine functionality as its reduction leads to a non-toxic derivative. Gymnodimine is a very strong basic compound (based on its pKa). Outside of the human body, gymnodimine has been detected, but not quantified in, mollusks. This could make gymnodimine a potential biomarker for the consumption of these foods. No indication of carcinogenicity to humans (not listed by IARC). Gymnodimine is a potentially toxic compound. Gymnodimine exerts its toxic effects via binding to nicotinic acetylcholine receptors with picomolar affinities with no sign of apparent reversibility in short time frames. Gymnodimine and 13-desmethyl spirolide C bound to acetylcholine binding proteins.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 09121203072D          

 37 41  0  0  0  0            999 V2000
   -3.5788    0.2531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2517    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9796    0.3067    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4196    2.2098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0274    1.4819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1881    1.4819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9652    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2372    0.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2372   -0.5311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5108   -0.9219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7830   -0.5311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1186   -1.0911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1186   -1.7626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6701   -2.2098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1114   -1.7062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1114   -0.9219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6150   -0.5311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429   -0.9219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0157   -0.5311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423   -0.9219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423   -1.7626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5108    1.5382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5108    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7830    0.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1114    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6150    0.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429   -0.0825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2530    0.4196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4701    0.6439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0157    0.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    1.5382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9651    0.0839    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4701   -0.5875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2530   -0.3081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9796   -0.6425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  2  3  2  0  0  0  0
  2  5  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 23  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 16  1  0  0  0  0
 11 24  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 35  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 26 32  1  0  0  0  0
 28 29  1  0  0  0  0
 28 36  1  0  0  0  0
 29 30  1  0  0  0  0
 29 34  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
M  END

HMDB0041430
     RDKit          3D
Gymnodimine
 82 86  0  0  0  0  0  0  0  0999 V2000
   -7.9802   -0.8901    1.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8699   -0.0288    0.5246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0274   -0.2196   -0.4684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0827    0.9216   -0.5853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6593    0.4923   -0.5938 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7716    0.8863    0.2830 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1366    1.8102    1.3699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3520    0.3972    0.1867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7498    1.1122   -0.9650 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1990    2.3047   -0.8961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3927    3.3165   -2.0017 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6342    2.7050    0.2629 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1839    3.9321    0.7425 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0694    2.8297   -0.2089 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0273    2.1431    0.7327 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1983    1.6393   -0.0848 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4549    1.5375    0.7271 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9053    0.1283    0.5637 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3303    0.1033    0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9337   -0.4459   -0.4260 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8764    0.3938   -0.5562 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5860   -1.8352   -0.0074 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7799   -2.7526    0.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3610   -2.2627    0.2263 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1826   -2.0572   -0.6550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1665   -1.1741    0.0668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1756   -1.8135    0.0833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2408   -3.0763    0.2467 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3994   -3.8841    0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6236   -3.1569    0.7841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3752   -1.6798    0.9798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4674   -1.0882   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0862   -1.3012   -1.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2531   -0.4370   -1.6805 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4621    1.7627    0.4379 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5415    1.2495    1.1447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1072    1.8116    2.1336 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2133   -1.7253    0.3394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8928   -0.2436    1.0424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7948   -1.2031    2.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0388   -1.0982   -1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3464    1.4277   -1.5591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4702    2.8101    1.0148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8285    1.3614    2.1242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2223    2.0566    1.9904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8737    0.5777    1.1489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7684    0.6186   -1.9290 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5419    3.8416   -2.2057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2360    3.9659   -1.7018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6750    2.7770   -2.9526 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6317    1.9095    1.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8161    4.2364    1.4342 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3502    3.8982   -0.3203 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2022    2.3735   -1.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3904    2.8634    1.5211 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5116    1.2796    1.2364 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3730    2.3638   -0.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2008    2.3047    0.4680 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1759    1.7197    1.7893 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8002   -0.4304    1.5209 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7328    1.1196   -0.1396 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9708   -0.2733    0.9372 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5095   -0.5701   -0.7437 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4544   -0.5438   -1.4144 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4935   -2.2131    0.7926 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1834   -2.8478   -0.9023 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5261   -3.6983    0.6071 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1634   -2.8290    1.1543 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7071   -3.0539   -0.8979 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4203   -1.6041   -1.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5417   -1.0041    1.1219 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1981   -0.1897   -0.3938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5603   -4.4395   -0.6491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1874   -4.6923    1.0585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4443   -3.3563    0.0684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9874   -3.5440    1.7672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3222   -1.1730    1.1207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7867   -1.6104    1.9437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4679   -2.3687   -1.4095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3506   -1.3038   -2.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0093    0.1555   -2.6199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1551   -1.0186   -1.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 22 24  2  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
  4 35  1  0
 35 36  1  0
 36 37  2  0
 36  2  1  0
 34  5  1  0
 32  8  1  0
 21 16  1  0
 32 27  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  3 41  1  0
  4 42  1  0
  7 43  1  0
  7 44  1  0
  7 45  1  0
  8 46  1  0
  9 47  1  0
 11 48  1  0
 11 49  1  0
 11 50  1  0
 12 51  1  0
 13 52  1  0
 14 53  1  0
 14 54  1  0
 15 55  1  0
 15 56  1  0
 16 57  1  0
 17 58  1  0
 17 59  1  0
 18 60  1  0
 19 61  1  0
 19 62  1  0
 19 63  1  0
 20 64  1  0
 23 65  1  0
 23 66  1  0
 23 67  1  0
 24 68  1  0
 25 69  1  0
 25 70  1  0
 26 71  1  0
 26 72  1  0
 29 73  1  0
 29 74  1  0
 30 75  1  0
 30 76  1  0
 31 77  1  0
 31 78  1  0
 33 79  1  0
 33 80  1  0
 34 81  1  0
 34 82  1  0
M  END


  Mrv0541 09121203072D          

 37 41  0  0  0  0            999 V2000
   -3.5788    0.2531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2517    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9796    0.3067    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4196    2.2098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0274    1.4819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1881    1.4819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9652    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2372    0.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2372   -0.5311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5108   -0.9219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7830   -0.5311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1186   -1.0911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1186   -1.7626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6701   -2.2098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1114   -1.7062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1114   -0.9219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6150   -0.5311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429   -0.9219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0157   -0.5311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423   -0.9219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423   -1.7626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5108    1.5382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5108    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7830    0.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1114    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6150    0.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429   -0.0825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2530    0.4196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4701    0.6439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7423    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0157    0.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    0.6989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    1.5382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9651    0.0839    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4701   -0.5875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2530   -0.3081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9796   -0.6425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  2  3  2  0  0  0  0
  2  5  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 23  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 16  1  0  0  0  0
 11 24  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 35  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 26 32  1  0  0  0  0
 28 29  1  0  0  0  0
 28 36  1  0  0  0  0
 29 30  1  0  0  0  0
 29 34  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0041430

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1CC2CCC(O)C(C)=CC3C(C)=C(CCC33CCCN=C3CC\C=C(C)\C1O2)C1OC(=O)C(C)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C32H45NO4/c1-19-8-6-9-29-32(13-7-15-33-29)14-12-25(28-18-22(4)31(35)37-28)23(5)26(32)17-20(2)27(34)11-10-24-16-21(3)30(19)36-24/h8,17-18,21,24,26-28,30,34H,6-7,9-16H2,1-5H3/b19-8+,20-17+

> <INCHI_KEY>
DVXZVCNEGRKLMW-DCJZOFSYSA-N

> <FORMULA>
C32H45NO4

> <MOLECULAR_WEIGHT>
507.704

> <EXACT_MASS>
507.334858933

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
58.05582935848827

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(2E)-19-hydroxy-2,15,18,24-tetramethyl-25-oxa-7-azatetracyclo[20.2.1.0⁶,¹¹.0¹¹,¹⁶]pentacosa-2,6,14,17-tetraen-14-yl]-3-methyl-2,5-dihydrofuran-2-one

> <ALOGPS_LOGP>
5.35

> <JCHEM_LOGP>
5.748440294

> <ALOGPS_LOGS>
-5.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.522930038204485

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.562223129315775

> <JCHEM_PKA_STRONGEST_BASIC>
7.190035433246869

> <JCHEM_POLAR_SURFACE_AREA>
68.12

> <JCHEM_REFRACTIVITY>
150.0324

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.32e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(2E)-19-hydroxy-2,15,18,24-tetramethyl-25-oxa-7-azatetracyclo[20.2.1.0⁶,¹¹.0¹¹,¹⁶]pentacosa-2,6,14,17-tetraen-14-yl]-3-methyl-5H-furan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0041430
     RDKit          3D
Gymnodimine
 82 86  0  0  0  0  0  0  0  0999 V2000
   -7.9802   -0.8901    1.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8699   -0.0288    0.5246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0274   -0.2196   -0.4684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0827    0.9216   -0.5853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6593    0.4923   -0.5938 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7716    0.8863    0.2830 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1366    1.8102    1.3699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3520    0.3972    0.1867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7498    1.1122   -0.9650 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1990    2.3047   -0.8961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3927    3.3165   -2.0017 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6342    2.7050    0.2629 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1839    3.9321    0.7425 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0694    2.8297   -0.2089 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0273    2.1431    0.7327 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1983    1.6393   -0.0848 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4549    1.5375    0.7271 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9053    0.1283    0.5637 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3303    0.1033    0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9337   -0.4459   -0.4260 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8764    0.3938   -0.5562 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5860   -1.8352   -0.0074 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7799   -2.7526    0.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3610   -2.2627    0.2263 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1826   -2.0572   -0.6550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1665   -1.1741    0.0668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1756   -1.8135    0.0833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2408   -3.0763    0.2467 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3994   -3.8841    0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6236   -3.1569    0.7841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3752   -1.6798    0.9798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4674   -1.0882   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0862   -1.3012   -1.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2531   -0.4370   -1.6805 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4621    1.7627    0.4379 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5415    1.2495    1.1447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1072    1.8116    2.1336 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2133   -1.7253    0.3394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8928   -0.2436    1.0424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7948   -1.2031    2.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0388   -1.0982   -1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3464    1.4277   -1.5591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4702    2.8101    1.0148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8285    1.3614    2.1242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2223    2.0566    1.9904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8737    0.5777    1.1489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7684    0.6186   -1.9290 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5419    3.8416   -2.2057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2360    3.9659   -1.7018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6750    2.7770   -2.9526 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6317    1.9095    1.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8161    4.2364    1.4342 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3502    3.8982   -0.3203 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2022    2.3735   -1.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3904    2.8634    1.5211 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5116    1.2796    1.2364 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3730    2.3638   -0.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2008    2.3047    0.4680 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1759    1.7197    1.7893 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8002   -0.4304    1.5209 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7328    1.1196   -0.1396 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9708   -0.2733    0.9372 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5095   -0.5701   -0.7437 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4544   -0.5438   -1.4144 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4935   -2.2131    0.7926 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1834   -2.8478   -0.9023 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5261   -3.6983    0.6071 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1634   -2.8290    1.1543 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7071   -3.0539   -0.8979 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4203   -1.6041   -1.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5417   -1.0041    1.1219 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1981   -0.1897   -0.3938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5603   -4.4395   -0.6491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1874   -4.6923    1.0585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4443   -3.3563    0.0684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9874   -3.5440    1.7672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3222   -1.1730    1.1207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7867   -1.6104    1.9437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4679   -2.3687   -1.4095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3506   -1.3038   -2.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0093    0.1555   -2.6199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1551   -1.0186   -1.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 22 24  2  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
  4 35  1  0
 35 36  1  0
 36 37  2  0
 36  2  1  0
 34  5  1  0
 32  8  1  0
 21 16  1  0
 32 27  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  3 41  1  0
  4 42  1  0
  7 43  1  0
  7 44  1  0
  7 45  1  0
  8 46  1  0
  9 47  1  0
 11 48  1  0
 11 49  1  0
 11 50  1  0
 12 51  1  0
 13 52  1  0
 14 53  1  0
 14 54  1  0
 15 55  1  0
 15 56  1  0
 16 57  1  0
 17 58  1  0
 17 59  1  0
 18 60  1  0
 19 61  1  0
 19 62  1  0
 19 63  1  0
 20 64  1  0
 23 65  1  0
 23 66  1  0
 23 67  1  0
 24 68  1  0
 25 69  1  0
 25 70  1  0
 26 71  1  0
 26 72  1  0
 29 73  1  0
 29 74  1  0
 30 75  1  0
 30 76  1  0
 31 77  1  0
 31 78  1  0
 33 79  1  0
 33 80  1  0
 34 81  1  0
 34 82  1  0
M  END

HEADER    PROTEIN                                 12-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-12         0                                  
HETATM    1  O   UNK     0      -6.680   0.472   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -7.937   1.305   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -9.295   0.573   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -8.250   4.125   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -7.518   2.766   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.951   2.766   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.535   1.305   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.176   0.573   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.176  -0.991   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.820  -1.721   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.462  -0.991   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.088  -2.037   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.088  -3.290   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.251  -4.125   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -0.208  -3.185   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      -0.208  -1.721   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.148  -0.991   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.507  -1.721   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.763  -0.991   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.119  -1.721   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.119  -3.290   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.820   2.871   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -2.820   1.305   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.462   0.573   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.208   1.305   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.148   0.573   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.507  -0.154   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.939   0.783   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.478   1.202   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.119   1.305   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.763   0.573   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.507   1.305   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.507   2.871   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       5.535   0.157   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       6.478  -1.097   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.939  -0.575   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       9.295  -1.199   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    3    5                                                  
CONECT    3    2                                                            
CONECT    4    5                                                            
CONECT    5    2    4    6                                                  
CONECT    6    5    7                                                       
CONECT    7    1    6    8                                                  
CONECT    8    7    9   23                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16   24                                             
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   11   15   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   35                                                  
CONECT   21   20                                                            
CONECT   22   23                                                            
CONECT   23    8   22   24                                                  
CONECT   24   11   23   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   32                                                  
CONECT   27   26                                                            
CONECT   28   29   36                                                       
CONECT   29   28   30   34                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   26   31   33                                                  
CONECT   33   32                                                            
CONECT   34   29   35                                                       
CONECT   35   20   34   36                                                  
CONECT   36   28   35   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

COMPND    HMDB0041430
HETATM    1  C1  UNL     1      -7.980  -0.890   1.014  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.870  -0.029   0.525  1.00  0.00           C  
HETATM    3  C3  UNL     1      -6.027  -0.220  -0.468  1.00  0.00           C  
HETATM    4  C4  UNL     1      -5.083   0.922  -0.585  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.659   0.492  -0.594  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.772   0.886   0.283  1.00  0.00           C  
HETATM    7  C7  UNL     1      -3.137   1.810   1.370  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.352   0.397   0.187  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.750   1.112  -0.965  1.00  0.00           C  
HETATM   10  C10 UNL     1      -0.199   2.305  -0.896  1.00  0.00           C  
HETATM   11  C11 UNL     1      -0.393   3.316  -2.002  1.00  0.00           C  
HETATM   12  C12 UNL     1       0.634   2.705   0.263  1.00  0.00           C  
HETATM   13  O1  UNL     1       0.184   3.932   0.742  1.00  0.00           O  
HETATM   14  C13 UNL     1       2.069   2.830  -0.209  1.00  0.00           C  
HETATM   15  C14 UNL     1       3.027   2.143   0.733  1.00  0.00           C  
HETATM   16  C15 UNL     1       4.198   1.639  -0.085  1.00  0.00           C  
HETATM   17  C16 UNL     1       5.455   1.537   0.727  1.00  0.00           C  
HETATM   18  C17 UNL     1       5.905   0.128   0.564  1.00  0.00           C  
HETATM   19  C18 UNL     1       7.330   0.103   0.102  1.00  0.00           C  
HETATM   20  C19 UNL     1       4.934  -0.446  -0.426  1.00  0.00           C  
HETATM   21  O2  UNL     1       3.876   0.394  -0.556  1.00  0.00           O  
HETATM   22  C20 UNL     1       4.586  -1.835  -0.007  1.00  0.00           C  
HETATM   23  C21 UNL     1       5.780  -2.753   0.136  1.00  0.00           C  
HETATM   24  C22 UNL     1       3.361  -2.263   0.226  1.00  0.00           C  
HETATM   25  C23 UNL     1       2.183  -2.057  -0.655  1.00  0.00           C  
HETATM   26  C24 UNL     1       1.166  -1.174   0.067  1.00  0.00           C  
HETATM   27  C25 UNL     1      -0.176  -1.813   0.083  1.00  0.00           C  
HETATM   28  N1  UNL     1      -0.241  -3.076   0.247  1.00  0.00           N  
HETATM   29  C26 UNL     1      -1.399  -3.884   0.295  1.00  0.00           C  
HETATM   30  C27 UNL     1      -2.624  -3.157   0.784  1.00  0.00           C  
HETATM   31  C28 UNL     1      -2.375  -1.680   0.980  1.00  0.00           C  
HETATM   32  C29 UNL     1      -1.467  -1.088  -0.078  1.00  0.00           C  
HETATM   33  C30 UNL     1      -2.086  -1.301  -1.411  1.00  0.00           C  
HETATM   34  C31 UNL     1      -3.253  -0.437  -1.681  1.00  0.00           C  
HETATM   35  O3  UNL     1      -5.462   1.763   0.438  1.00  0.00           O  
HETATM   36  C32 UNL     1      -6.542   1.250   1.145  1.00  0.00           C  
HETATM   37  O4  UNL     1      -7.107   1.812   2.134  1.00  0.00           O  
HETATM   38  H1  UNL     1      -8.213  -1.725   0.339  1.00  0.00           H  
HETATM   39  H2  UNL     1      -8.893  -0.244   1.042  1.00  0.00           H  
HETATM   40  H3  UNL     1      -7.795  -1.203   2.060  1.00  0.00           H  
HETATM   41  H4  UNL     1      -6.039  -1.098  -1.103  1.00  0.00           H  
HETATM   42  H5  UNL     1      -5.346   1.428  -1.559  1.00  0.00           H  
HETATM   43  H6  UNL     1      -3.470   2.810   1.015  1.00  0.00           H  
HETATM   44  H7  UNL     1      -3.829   1.361   2.124  1.00  0.00           H  
HETATM   45  H8  UNL     1      -2.222   2.057   1.990  1.00  0.00           H  
HETATM   46  H9  UNL     1      -0.874   0.578   1.149  1.00  0.00           H  
HETATM   47  H10 UNL     1      -0.768   0.619  -1.929  1.00  0.00           H  
HETATM   48  H11 UNL     1       0.542   3.842  -2.206  1.00  0.00           H  
HETATM   49  H12 UNL     1      -1.236   3.966  -1.702  1.00  0.00           H  
HETATM   50  H13 UNL     1      -0.675   2.777  -2.953  1.00  0.00           H  
HETATM   51  H14 UNL     1       0.632   1.910   1.029  1.00  0.00           H  
HETATM   52  H15 UNL     1       0.816   4.236   1.434  1.00  0.00           H  
HETATM   53  H16 UNL     1       2.350   3.898  -0.320  1.00  0.00           H  
HETATM   54  H17 UNL     1       2.202   2.373  -1.221  1.00  0.00           H  
HETATM   55  H18 UNL     1       3.390   2.863   1.521  1.00  0.00           H  
HETATM   56  H19 UNL     1       2.512   1.280   1.236  1.00  0.00           H  
HETATM   57  H20 UNL     1       4.373   2.364  -0.899  1.00  0.00           H  
HETATM   58  H21 UNL     1       6.201   2.305   0.468  1.00  0.00           H  
HETATM   59  H22 UNL     1       5.176   1.720   1.789  1.00  0.00           H  
HETATM   60  H23 UNL     1       5.800  -0.430   1.521  1.00  0.00           H  
HETATM   61  H24 UNL     1       7.733   1.120  -0.140  1.00  0.00           H  
HETATM   62  H25 UNL     1       7.971  -0.273   0.937  1.00  0.00           H  
HETATM   63  H26 UNL     1       7.510  -0.570  -0.744  1.00  0.00           H  
HETATM   64  H27 UNL     1       5.454  -0.544  -1.414  1.00  0.00           H  
HETATM   65  H28 UNL     1       6.494  -2.213   0.793  1.00  0.00           H  
HETATM   66  H29 UNL     1       6.183  -2.848  -0.902  1.00  0.00           H  
HETATM   67  H30 UNL     1       5.526  -3.698   0.607  1.00  0.00           H  
HETATM   68  H31 UNL     1       3.163  -2.829   1.154  1.00  0.00           H  
HETATM   69  H32 UNL     1       1.707  -3.054  -0.898  1.00  0.00           H  
HETATM   70  H33 UNL     1       2.420  -1.604  -1.613  1.00  0.00           H  
HETATM   71  H34 UNL     1       1.542  -1.004   1.122  1.00  0.00           H  
HETATM   72  H35 UNL     1       1.198  -0.190  -0.394  1.00  0.00           H  
HETATM   73  H36 UNL     1      -1.560  -4.440  -0.649  1.00  0.00           H  
HETATM   74  H37 UNL     1      -1.187  -4.692   1.059  1.00  0.00           H  
HETATM   75  H38 UNL     1      -3.444  -3.356   0.068  1.00  0.00           H  
HETATM   76  H39 UNL     1      -2.987  -3.544   1.767  1.00  0.00           H  
HETATM   77  H40 UNL     1      -3.322  -1.173   1.121  1.00  0.00           H  
HETATM   78  H41 UNL     1      -1.787  -1.610   1.944  1.00  0.00           H  
HETATM   79  H42 UNL     1      -2.468  -2.369  -1.409  1.00  0.00           H  
HETATM   80  H43 UNL     1      -1.351  -1.304  -2.248  1.00  0.00           H  
HETATM   81  H44 UNL     1      -3.009   0.155  -2.620  1.00  0.00           H  
HETATM   82  H45 UNL     1      -4.155  -1.019  -1.990  1.00  0.00           H  
CONECT    1    2   38   39   40
CONECT    2    3    3   36
CONECT    3    4   41
CONECT    4    5   35   42
CONECT    5    6    6   34
CONECT    6    7    8
CONECT    7   43   44   45
CONECT    8    9   32   46
CONECT    9   10   10   47
CONECT   10   11   12
CONECT   11   48   49   50
CONECT   12   13   14   51
CONECT   13   52
CONECT   14   15   53   54
CONECT   15   16   55   56
CONECT   16   17   21   57
CONECT   17   18   58   59
CONECT   18   19   20   60
CONECT   19   61   62   63
CONECT   20   21   22   64
CONECT   22   23   24   24
CONECT   23   65   66   67
CONECT   24   25   68
CONECT   25   26   69   70
CONECT   26   27   71   72
CONECT   27   28   28   32
CONECT   28   29
CONECT   29   30   73   74
CONECT   30   31   75   76
CONECT   31   32   77   78
CONECT   32   33
CONECT   33   34   79   80
CONECT   34   81   82
CONECT   35   36
CONECT   36   37   37
END

HMDB0041430
     RDKit          3D
Gymnodimine
 82 86  0  0  0  0  0  0  0  0999 V2000
   -7.9802   -0.8901    1.0139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8699   -0.0288    0.5246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0274   -0.2196   -0.4684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0827    0.9216   -0.5853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6593    0.4923   -0.5938 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7716    0.8863    0.2830 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1366    1.8102    1.3699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3520    0.3972    0.1867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7498    1.1122   -0.9650 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1990    2.3047   -0.8961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3927    3.3165   -2.0017 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6342    2.7050    0.2629 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1839    3.9321    0.7425 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0694    2.8297   -0.2089 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0273    2.1431    0.7327 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1983    1.6393   -0.0848 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4549    1.5375    0.7271 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9053    0.1283    0.5637 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3303    0.1033    0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9337   -0.4459   -0.4260 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8764    0.3938   -0.5562 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5860   -1.8352   -0.0074 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7799   -2.7526    0.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3610   -2.2627    0.2263 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1826   -2.0572   -0.6550 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1665   -1.1741    0.0668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1756   -1.8135    0.0833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2408   -3.0763    0.2467 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3994   -3.8841    0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6236   -3.1569    0.7841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3752   -1.6798    0.9798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4674   -1.0882   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0862   -1.3012   -1.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2531   -0.4370   -1.6805 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4621    1.7627    0.4379 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5415    1.2495    1.1447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1072    1.8116    2.1336 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2133   -1.7253    0.3394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8928   -0.2436    1.0424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7948   -1.2031    2.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0388   -1.0982   -1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3464    1.4277   -1.5591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4702    2.8101    1.0148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8285    1.3614    2.1242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2223    2.0566    1.9904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8737    0.5777    1.1489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7684    0.6186   -1.9290 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5419    3.8416   -2.2057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2360    3.9659   -1.7018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6750    2.7770   -2.9526 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6317    1.9095    1.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8161    4.2364    1.4342 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3502    3.8982   -0.3203 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2022    2.3735   -1.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3904    2.8634    1.5211 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5116    1.2796    1.2364 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3730    2.3638   -0.8994 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2008    2.3047    0.4680 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1759    1.7197    1.7893 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8002   -0.4304    1.5209 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7328    1.1196   -0.1396 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9708   -0.2733    0.9372 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5095   -0.5701   -0.7437 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4544   -0.5438   -1.4144 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4935   -2.2131    0.7926 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1834   -2.8478   -0.9023 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5261   -3.6983    0.6071 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1634   -2.8290    1.1543 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7071   -3.0539   -0.8979 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4203   -1.6041   -1.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5417   -1.0041    1.1219 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1981   -0.1897   -0.3938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5603   -4.4395   -0.6491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1874   -4.6923    1.0585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4443   -3.3563    0.0684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9874   -3.5440    1.7672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3222   -1.1730    1.1207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7867   -1.6104    1.9437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4679   -2.3687   -1.4095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3506   -1.3038   -2.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0093    0.1555   -2.6199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1551   -1.0186   -1.9896 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 22 24  2  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
  4 35  1  0
 35 36  1  0
 36 37  2  0
 36  2  1  0
 34  5  1  0
 32  8  1  0
 21 16  1  0
 32 27  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  3 41  1  0
  4 42  1  0
  7 43  1  0
  7 44  1  0
  7 45  1  0
  8 46  1  0
  9 47  1  0
 11 48  1  0
 11 49  1  0
 11 50  1  0
 12 51  1  0
 13 52  1  0
 14 53  1  0
 14 54  1  0
 15 55  1  0
 15 56  1  0
 16 57  1  0
 17 58  1  0
 17 59  1  0
 18 60  1  0
 19 61  1  0
 19 62  1  0
 19 63  1  0
 20 64  1  0
 23 65  1  0
 23 66  1  0
 23 67  1  0
 24 68  1  0
 25 69  1  0
 25 70  1  0
 26 71  1  0
 26 72  1  0
 29 73  1  0
 29 74  1  0
 30 75  1  0
 30 76  1  0
 31 77  1  0
 31 78  1  0
 33 79  1  0
 33 80  1  0
 34 81  1  0
 34 82  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₃₂H₄₅NO₄

Average Molecular Weight

507.704

Monoisotopic Molecular Weight

507.334858933

IUPAC Name

5-[(2E)-19-hydroxy-2,15,18,24-tetramethyl-25-oxa-7-azatetracyclo[20.2.1.0⁶,¹¹.0¹¹,¹⁶]pentacosa-2,6,14,17-tetraen-14-yl]-3-methyl-2,5-dihydrofuran-2-one

Traditional Name

5-[(2E)-19-hydroxy-2,15,18,24-tetramethyl-25-oxa-7-azatetracyclo[20.2.1.0⁶,¹¹.0¹¹,¹⁶]pentacosa-2,6,14,17-tetraen-14-yl]-3-methyl-5H-furan-2-one

CAS Registry Number

173792-58-0

SMILES

CC1CC2CCC(O)C(C)=CC3C(C)=C(CCC33CCCN=C3CC\C=C(C)\C1O2)C1OC(=O)C(C)=C1

InChI Identifier

InChI=1S/C32H45NO4/c1-19-8-6-9-29-32(13-7-15-33-29)14-12-25(28-18-22(4)31(35)37-28)23(5)26(32)17-20(2)27(34)11-10-24-16-21(3)30(19)36-24/h8,17-18,21,24,26-28,30,34H,6-7,9-16H2,1-5H3/b19-8+,20-17+

InChI Key

DVXZVCNEGRKLMW-DCJZOFSYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Hydropyridines

Direct Parent

Tetrahydropyridines

Alternative Parents

Substituents

Tetrahydropyridine
2-furanone
Dihydrofuran
Tetrahydrofuran
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Carboxylic acid ester
Ketimine
Lactone
Secondary alcohol
Carboxylic acid derivative
Dialkyl ether
Ether
Monocarboxylic acid or derivatives
Oxacycle
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organic oxide
Imine
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Organonitrogen compound
Organooxygen compound
Alcohol
Organic oxygen compound
Organopnictogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

extracellular (HMDB: HMDB0041430)
Membrane (HMDB: HMDB0041430)

Mollusks (FooDB: FOOD00868)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0023 g/L	ALOGPS
logP	5.35	ALOGPS
logP	5.75	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	14.56	ChemAxon
pKa (Strongest Basic)	7.19	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	68.12 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	150.03 m³·mol⁻¹	ChemAxon
Polarizability	58.06 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	218.477	31661259
DarkChem	[M-H]-	216.74	31661259
DeepCCS	[M-2H]-	257.842	30932474
DeepCCS	[M+Na]+	233.267	30932474
AllCCS	[M+H]+	225.4	32859911
AllCCS	[M+H-H2O]+	223.7	32859911
AllCCS	[M+NH4]+	227.0	32859911
AllCCS	[M+Na]+	227.5	32859911
AllCCS	[M-H]-	222.3	32859911
AllCCS	[M+Na-2H]-	224.8	32859911
AllCCS	[M+HCOO]-	227.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Gymnodimine	CC1CC2CCC(O)C(C)=CC3C(C)=C(CCC33CCCN=C3CC\C=C(C)\C1O2)C1OC(=O)C(C)=C1	4246.0	Standard polar	33892256
Gymnodimine	CC1CC2CCC(O)C(C)=CC3C(C)=C(CCC33CCCN=C3CC\C=C(C)\C1O2)C1OC(=O)C(C)=C1	4139.7	Standard non polar	33892256
Gymnodimine	CC1CC2CCC(O)C(C)=CC3C(C)=C(CCC33CCCN=C3CC\C=C(C)\C1O2)C1OC(=O)C(C)=C1	4060.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Gymnodimine,1TMS,isomer #1	CC1=CC(C2=C(C)C3C=C(C)C(O[Si](C)(C)C)CCC4CC(C)C(O4)/C(C)=C/CCC4=NCCCC43CC2)OC1=O	4152.3	Semi standard non polar	33892256
Gymnodimine,1TBDMS,isomer #1	CC1=CC(C2=C(C)C3C=C(C)C(O[Si](C)(C)C(C)(C)C)CCC4CC(C)C(O4)/C(C)=C/CCC4=NCCCC43CC2)OC1=O	4346.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Gymnodimine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-1000900000-b82637757d6a83477790	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Gymnodimine GC-MS (1 TMS) - 70eV, Positive	splash10-0hb9-5000390000-fee203e839b6cb58df1b	2017-10-06	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 10V, Positive-QTOF	splash10-0536-0000920000-a3f628705e2e6a0e2a46	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 20V, Positive-QTOF	splash10-00yu-0000900000-9df5c5e06bee3a748b6c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 40V, Positive-QTOF	splash10-004r-7109700000-10d898778adbd4ed830c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 10V, Negative-QTOF	splash10-0a4i-0000790000-47d22a5a77d06aeed9a0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 20V, Negative-QTOF	splash10-0bt9-2000940000-56e4a3edbcde7f3df501	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 40V, Negative-QTOF	splash10-000x-2015900000-843815d7349a6995ca31	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 10V, Positive-QTOF	splash10-0a4l-0002980000-04328292a60ad2c1c5aa	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 20V, Positive-QTOF	splash10-0bt9-0000940000-ccbf9796bdaa2ac405d4	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 40V, Positive-QTOF	splash10-0006-1004900000-ed2558f11fcccc20e1c2	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 10V, Negative-QTOF	splash10-0a4i-0000290000-f29567e802fbf48154c8	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 20V, Negative-QTOF	splash10-000i-0000910000-9376a4fbf77032e3293a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gymnodimine 40V, Negative-QTOF	splash10-0udr-5001940000-ee51e656106fa49d7058	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021381

KNApSAcK ID

Not Available

Chemspider ID

8611700

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10436276

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Gymnodimine (HMDB0041430)

MOL for HMDB0041430 (Gymnodimine)

3D MOL for HMDB0041430 (Gymnodimine)

3D SDF for HMDB0041430 (Gymnodimine)

3D-SDF for HMDB0041430 (Gymnodimine)

PDB for HMDB0041430 (Gymnodimine)

3D PDB for HMDB0041430 (Gymnodimine)

SMILES for HMDB0041430 (Gymnodimine)

INCHI for HMDB0041430 (Gymnodimine)

Structure for HMDB0041430 (Gymnodimine)

3D Structure for HMDB0041430 (Gymnodimine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra