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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-24 10:06:58 UTC

Update Date

2021-09-24 10:06:58 UTC

HMDB ID

HMDB0304482

Secondary Accession Numbers

None

Metabolite Identification

Common Name

secologanin

Description

Secologanin is a member of the class of compounds known as terpene glycosides. Terpene glycosides are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. Thus, secologanin is considered to be an isoprenoid lipid molecule. Secologanin is soluble (in water) and a very weakly acidic compound (based on its pKa). Secologanin can be found in a number of food items such as oyster mushroom, flaxseed, nectarine, and cereals and cereal products, which makes secologanin a potential biomarker for the consumption of these food products. Secologanin is a secoiridoid monoterpene synthesized from geranyl pyrophosphate in the mevalonate pathway. Secologanin then proceeds with dopamine or tryptamine to form ipecac and terpene indole alkaloids, respectively .

Structure

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

  Mrv1652303082006132D          

 27 28  0  0  0  0            999 V2000
   -1.4278   -1.0451    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1415   -0.6313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4282   -1.8651    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8556   -1.0445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1422   -2.2818    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7108   -2.2825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8560   -1.8645    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5622   -0.6307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1426   -3.1018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5630   -2.2811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7128   -0.6335    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0049    0.6090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7107    1.0306    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0049   -0.2194    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7205    1.0162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4293    0.6254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7046    1.8556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7233   -0.6273    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7216    1.8400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4391   -0.2057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1340    1.0445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8527    0.6392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1232    1.8706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5630    1.0590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5603    0.1934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4151    2.2752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4142    3.1018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  6  0  0  0
  4  7  1  0  0  0  0
  4  8  1  1  0  0  0
  5  9  1  1  0  0  0
  7 10  1  6  0  0  0
  5  7  1  0  0  0  0
  1 11  1  1  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  6  0  0  0
 13 16  1  0  0  0  0
 13 17  1  6  0  0  0
 14 18  1  0  0  0  0
 15 19  2  0  0  0  0
 16 20  2  0  0  0  0
 16 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 18 20  1  0  0  0  0
 14 11  1  1  0  0  0
 22 24  1  0  0  0  0
  8 25  1  0  0  0  0
 17 26  1  0  0  0  0
 26 27  2  0  0  0  0
M  END

HMDB0304482
     RDKit          3D
secologanin
 51 52  0  0  0  0  0  0  0  0999 V2000
    1.2885    3.0858   -0.8017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5490    1.8003   -1.0065 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9168    0.7549   -0.1698 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0926   -0.2171   -0.9946 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0683   -0.5533   -0.3148 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197   -0.1702   -0.9888 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9847    0.7261   -0.2775 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1054    0.1875    0.3110 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6415    1.1218    1.3762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6820    1.3341    2.3626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7665   -1.1183    0.9896 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8830   -1.5882    1.6931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4634   -2.1201   -0.0990 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4701   -2.9745    0.4198 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9755   -1.4307   -1.3474 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9816   -1.2087   -2.2553 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546   -1.3695   -1.3458 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2402   -1.1951   -1.5114 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9109   -0.5135   -0.5537 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3165   -0.3303   -0.7220 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8675   -0.8434   -1.7640 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1899    0.3444    0.1010 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5529    0.4157   -0.2470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0319   -0.0572    0.5571 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6514    0.8460    1.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6868    0.2645    2.4015 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9514   -0.9316    2.4522 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6211    3.4388   -0.0376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7719    3.8169   -1.4358 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2212    1.4726   -1.7787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2634    1.1586    0.6177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1672    0.2935   -1.9383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9081    0.3279   -1.9401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8802   -0.0327   -0.4472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5633    0.6758    1.8185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8779    2.1070    0.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7933    2.2201    2.8035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9412   -1.0151    1.7186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5714   -1.8728    1.0352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3393   -2.7660   -0.3278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5997   -2.8575   -0.0588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2156   -2.1204   -1.8051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9687   -1.9262   -2.9366 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7035   -1.6068   -2.3825 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6803    0.7126   -1.2976 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1079   -0.5062    0.0163 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9847    1.2464    0.3749 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5119   -0.9248    0.9942 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9948    1.7663    1.0101 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8375    1.2151    2.2200 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2686    0.9175    3.0398 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  4 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 19 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 24  3  1  0
 15  6  1  0
  1 28  1  0
  1 29  1  0
  2 30  1  0
  3 31  1  1
  4 32  1  6
  6 33  1  6
  8 34  1  6
  9 35  1  0
  9 36  1  0
 10 37  1  0
 11 38  1  1
 12 39  1  0
 13 40  1  6
 14 41  1  0
 15 42  1  6
 16 43  1  0
 18 44  1  0
 23 45  1  0
 23 46  1  0
 23 47  1  0
 24 48  1  1
 25 49  1  0
 25 50  1  0
 26 51  1  0
M  END

  Mrv1652303082006132D          

 27 28  0  0  0  0            999 V2000
   -1.4278   -1.0451    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1415   -0.6313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4282   -1.8651    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8556   -1.0445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1422   -2.2818    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7108   -2.2825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8560   -1.8645    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5622   -0.6307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1426   -3.1018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5630   -2.2811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7128   -0.6335    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0049    0.6090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7107    1.0306    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0049   -0.2194    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7205    1.0162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4293    0.6254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7046    1.8556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7233   -0.6273    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7216    1.8400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4391   -0.2057    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1340    1.0445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8527    0.6392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1232    1.8706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5630    1.0590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5603    0.1934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4151    2.2752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4142    3.1018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  6  0  0  0
  4  7  1  0  0  0  0
  4  8  1  1  0  0  0
  5  9  1  1  0  0  0
  7 10  1  6  0  0  0
  5  7  1  0  0  0  0
  1 11  1  1  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 12 15  1  6  0  0  0
 13 16  1  0  0  0  0
 13 17  1  6  0  0  0
 14 18  1  0  0  0  0
 15 19  2  0  0  0  0
 16 20  2  0  0  0  0
 16 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 18 20  1  0  0  0  0
 14 11  1  1  0  0  0
 22 24  1  0  0  0  0
  8 25  1  0  0  0  0
 17 26  1  0  0  0  0
 26 27  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304482

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)C1=CO[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](C=C)[C@@H]1CC=O

> <INCHI_IDENTIFIER>
InChI=1S/C17H24O10/c1-3-8-9(4-5-18)10(15(23)24-2)7-25-16(8)27-17-14(22)13(21)12(20)11(6-19)26-17/h3,5,7-9,11-14,16-17,19-22H,1,4,6H2,2H3/t8-,9+,11-,12-,13+,14-,16+,17+/m1/s1

> <INCHI_KEY>
CSKKDSFETGLMSB-NRZPKYKESA-N

> <FORMULA>
C17H24O10

> <MOLECULAR_WEIGHT>
388.3665

> <EXACT_MASS>
388.136946988

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
37.13961552927309

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (2S,3R,4S)-3-ethenyl-4-(2-oxoethyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-5-carboxylate

> <ALOGPS_LOGP>
-0.83

> <JCHEM_LOGP>
-1.6899511996666665

> <ALOGPS_LOGS>
-1.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.187394981609977

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.205711973943044

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810847615592584

> <JCHEM_POLAR_SURFACE_AREA>
151.98

> <JCHEM_REFRACTIVITY>
88.52059999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.67e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-secologanin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0304482
     RDKit          3D
secologanin
 51 52  0  0  0  0  0  0  0  0999 V2000
    1.2885    3.0858   -0.8017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5490    1.8003   -1.0065 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9168    0.7549   -0.1698 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0926   -0.2171   -0.9946 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0683   -0.5533   -0.3148 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197   -0.1702   -0.9888 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9847    0.7261   -0.2775 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1054    0.1875    0.3110 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6415    1.1218    1.3762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6820    1.3341    2.3626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7665   -1.1183    0.9896 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8830   -1.5882    1.6931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4634   -2.1201   -0.0990 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4701   -2.9745    0.4198 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9755   -1.4307   -1.3474 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9816   -1.2087   -2.2553 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546   -1.3695   -1.3458 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2402   -1.1951   -1.5114 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9109   -0.5135   -0.5537 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3165   -0.3303   -0.7220 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8675   -0.8434   -1.7640 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1899    0.3444    0.1010 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5529    0.4157   -0.2470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0319   -0.0572    0.5571 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6514    0.8460    1.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6868    0.2645    2.4015 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9514   -0.9316    2.4522 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6211    3.4388   -0.0376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7719    3.8169   -1.4358 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2212    1.4726   -1.7787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2634    1.1586    0.6177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1672    0.2935   -1.9383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9081    0.3279   -1.9401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8802   -0.0327   -0.4472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5633    0.6758    1.8185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8779    2.1070    0.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7933    2.2201    2.8035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9412   -1.0151    1.7186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5714   -1.8728    1.0352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3393   -2.7660   -0.3278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5997   -2.8575   -0.0588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2156   -2.1204   -1.8051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9687   -1.9262   -2.9366 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7035   -1.6068   -2.3825 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6803    0.7126   -1.2976 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1079   -0.5062    0.0163 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9847    1.2464    0.3749 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5119   -0.9248    0.9942 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9948    1.7663    1.0101 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8375    1.2151    2.2200 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2686    0.9175    3.0398 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  4 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 19 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 24  3  1  0
 15  6  1  0
  1 28  1  0
  1 29  1  0
  2 30  1  0
  3 31  1  1
  4 32  1  6
  6 33  1  6
  8 34  1  6
  9 35  1  0
  9 36  1  0
 10 37  1  0
 11 38  1  1
 12 39  1  0
 13 40  1  6
 14 41  1  0
 15 42  1  6
 16 43  1  0
 18 44  1  0
 23 45  1  0
 23 46  1  0
 23 47  1  0
 24 48  1  1
 25 49  1  0
 25 50  1  0
 26 51  1  0
M  END

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0      -2.665  -1.951   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -3.997  -1.178   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -2.666  -3.482   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.330  -1.950   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.999  -4.259   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.327  -4.261   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -5.331  -3.480   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.649  -1.177   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.000  -5.790   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -6.651  -4.258   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.331  -1.183   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.009   1.137   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.327   1.924   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.009  -0.410   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.345   1.897   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.668   1.167   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.315   3.464   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.350  -1.171   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.347   3.435   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.686  -0.384   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.983   1.950   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       5.325   1.193   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       3.963   3.492   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       6.651   1.977   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -6.646   0.361   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       2.642   4.247   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       2.640   5.790   0.000  0.00  0.00           O+0
CONECT    1    2    3   11                                                  
CONECT    2    1    4                                                       
CONECT    3    1    5    6                                                  
CONECT    4    2    7    8                                                  
CONECT    5    3    9    7                                                  
CONECT    6    3                                                            
CONECT    7    4   10    5                                                  
CONECT    8    4   25                                                       
CONECT    9    5                                                            
CONECT   10    7                                                            
CONECT   11    1   14                                                       
CONECT   12   13   14   15                                                  
CONECT   13   12   16   17                                                  
CONECT   14   12   18   11                                                  
CONECT   15   12   19                                                       
CONECT   16   13   20   21                                                  
CONECT   17   13   26                                                       
CONECT   18   14   20                                                       
CONECT   19   15                                                            
CONECT   20   16   18                                                       
CONECT   21   16   22   23                                                  
CONECT   22   21   24                                                       
CONECT   23   21                                                            
CONECT   24   22                                                            
CONECT   25    8                                                            
CONECT   26   17   27                                                       
CONECT   27   26                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END

COMPND    HMDB0304482
HETATM    1  C1  UNL     1       1.289   3.086  -0.802  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.549   1.800  -1.006  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.917   0.755  -0.170  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.093  -0.217  -0.995  1.00  0.00           C  
HETATM    5  O1  UNL     1      -1.068  -0.553  -0.315  1.00  0.00           O  
HETATM    6  C5  UNL     1      -2.220  -0.170  -0.989  1.00  0.00           C  
HETATM    7  O2  UNL     1      -2.985   0.726  -0.278  1.00  0.00           O  
HETATM    8  C6  UNL     1      -4.105   0.187   0.311  1.00  0.00           C  
HETATM    9  C7  UNL     1      -4.641   1.122   1.376  1.00  0.00           C  
HETATM   10  O3  UNL     1      -3.682   1.334   2.363  1.00  0.00           O  
HETATM   11  C8  UNL     1      -3.766  -1.118   0.990  1.00  0.00           C  
HETATM   12  O4  UNL     1      -4.883  -1.588   1.693  1.00  0.00           O  
HETATM   13  C9  UNL     1      -3.463  -2.120  -0.099  1.00  0.00           C  
HETATM   14  O5  UNL     1      -2.470  -2.975   0.420  1.00  0.00           O  
HETATM   15  C10 UNL     1      -2.976  -1.431  -1.347  1.00  0.00           C  
HETATM   16  O6  UNL     1      -3.982  -1.209  -2.255  1.00  0.00           O  
HETATM   17  O7  UNL     1       0.855  -1.369  -1.346  1.00  0.00           O  
HETATM   18  C11 UNL     1       2.240  -1.195  -1.511  1.00  0.00           C  
HETATM   19  C12 UNL     1       2.911  -0.514  -0.554  1.00  0.00           C  
HETATM   20  C13 UNL     1       4.316  -0.330  -0.722  1.00  0.00           C  
HETATM   21  O8  UNL     1       4.867  -0.843  -1.764  1.00  0.00           O  
HETATM   22  O9  UNL     1       5.190   0.344   0.101  1.00  0.00           O  
HETATM   23  C14 UNL     1       6.553   0.416  -0.247  1.00  0.00           C  
HETATM   24  C15 UNL     1       2.032  -0.057   0.557  1.00  0.00           C  
HETATM   25  C16 UNL     1       2.651   0.846   1.545  1.00  0.00           C  
HETATM   26  C17 UNL     1       3.687   0.264   2.401  1.00  0.00           C  
HETATM   27  O10 UNL     1       3.951  -0.932   2.452  1.00  0.00           O  
HETATM   28  H1  UNL     1       0.621   3.439  -0.038  1.00  0.00           H  
HETATM   29  H2  UNL     1       1.772   3.817  -1.436  1.00  0.00           H  
HETATM   30  H3  UNL     1       2.221   1.473  -1.779  1.00  0.00           H  
HETATM   31  H4  UNL     1       0.263   1.159   0.618  1.00  0.00           H  
HETATM   32  H5  UNL     1      -0.167   0.294  -1.938  1.00  0.00           H  
HETATM   33  H6  UNL     1      -1.908   0.328  -1.940  1.00  0.00           H  
HETATM   34  H7  UNL     1      -4.880  -0.033  -0.447  1.00  0.00           H  
HETATM   35  H8  UNL     1      -5.563   0.676   1.819  1.00  0.00           H  
HETATM   36  H9  UNL     1      -4.878   2.107   0.927  1.00  0.00           H  
HETATM   37  H10 UNL     1      -3.793   2.220   2.803  1.00  0.00           H  
HETATM   38  H11 UNL     1      -2.941  -1.015   1.719  1.00  0.00           H  
HETATM   39  H12 UNL     1      -5.571  -1.873   1.035  1.00  0.00           H  
HETATM   40  H13 UNL     1      -4.339  -2.766  -0.328  1.00  0.00           H  
HETATM   41  H14 UNL     1      -1.600  -2.857  -0.059  1.00  0.00           H  
HETATM   42  H15 UNL     1      -2.216  -2.120  -1.805  1.00  0.00           H  
HETATM   43  H16 UNL     1      -3.969  -1.926  -2.937  1.00  0.00           H  
HETATM   44  H17 UNL     1       2.704  -1.607  -2.383  1.00  0.00           H  
HETATM   45  H18 UNL     1       6.680   0.713  -1.298  1.00  0.00           H  
HETATM   46  H19 UNL     1       7.108  -0.506   0.016  1.00  0.00           H  
HETATM   47  H20 UNL     1       6.985   1.246   0.375  1.00  0.00           H  
HETATM   48  H21 UNL     1       1.512  -0.925   0.994  1.00  0.00           H  
HETATM   49  H22 UNL     1       2.995   1.766   1.010  1.00  0.00           H  
HETATM   50  H23 UNL     1       1.837   1.215   2.220  1.00  0.00           H  
HETATM   51  H24 UNL     1       4.269   0.917   3.040  1.00  0.00           H  
CONECT    1    2    2   28   29
CONECT    2    3   30
CONECT    3    4   24   31
CONECT    4    5   17   32
CONECT    5    6
CONECT    6    7   15   33
CONECT    7    8
CONECT    8    9   11   34
CONECT    9   10   35   36
CONECT   10   37
CONECT   11   12   13   38
CONECT   12   39
CONECT   13   14   15   40
CONECT   14   41
CONECT   15   16   42
CONECT   16   43
CONECT   17   18
CONECT   18   19   19   44
CONECT   19   20   24
CONECT   20   21   21   22
CONECT   22   23
CONECT   23   45   46   47
CONECT   24   25   48
CONECT   25   26   49   50
CONECT   26   27   27   51
END

HMDB0304482
     RDKit          3D
secologanin
 51 52  0  0  0  0  0  0  0  0999 V2000
    1.2885    3.0858   -0.8017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5490    1.8003   -1.0065 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9168    0.7549   -0.1698 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0926   -0.2171   -0.9946 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0683   -0.5533   -0.3148 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197   -0.1702   -0.9888 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9847    0.7261   -0.2775 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1054    0.1875    0.3110 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6415    1.1218    1.3762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6820    1.3341    2.3626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7665   -1.1183    0.9896 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8830   -1.5882    1.6931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4634   -2.1201   -0.0990 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4701   -2.9745    0.4198 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9755   -1.4307   -1.3474 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9816   -1.2087   -2.2553 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546   -1.3695   -1.3458 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2402   -1.1951   -1.5114 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9109   -0.5135   -0.5537 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3165   -0.3303   -0.7220 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8675   -0.8434   -1.7640 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1899    0.3444    0.1010 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5529    0.4157   -0.2470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0319   -0.0572    0.5571 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6514    0.8460    1.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6868    0.2645    2.4015 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9514   -0.9316    2.4522 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6211    3.4388   -0.0376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7719    3.8169   -1.4358 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2212    1.4726   -1.7787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2634    1.1586    0.6177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1672    0.2935   -1.9383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9081    0.3279   -1.9401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8802   -0.0327   -0.4472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5633    0.6758    1.8185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8779    2.1070    0.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7933    2.2201    2.8035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9412   -1.0151    1.7186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5714   -1.8728    1.0352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3393   -2.7660   -0.3278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5997   -2.8575   -0.0588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2156   -2.1204   -1.8051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9687   -1.9262   -2.9366 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7035   -1.6068   -2.3825 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6803    0.7126   -1.2976 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1079   -0.5062    0.0163 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9847    1.2464    0.3749 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5119   -0.9248    0.9942 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9948    1.7663    1.0101 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8375    1.2151    2.2200 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2686    0.9175    3.0398 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  4 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 19 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 24  3  1  0
 15  6  1  0
  1 28  1  0
  1 29  1  0
  2 30  1  0
  3 31  1  1
  4 32  1  6
  6 33  1  6
  8 34  1  6
  9 35  1  0
  9 36  1  0
 10 37  1  0
 11 38  1  1
 12 39  1  0
 13 40  1  6
 14 41  1  0
 15 42  1  6
 16 43  1  0
 18 44  1  0
 23 45  1  0
 23 46  1  0
 23 47  1  0
 24 48  1  1
 25 49  1  0
 25 50  1  0
 26 51  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Ethenyl-2-(beta-D-glucopyranosyloxy)-3,4-dihydro-4-(2-oxoethyl)-2H-pyran-5-carboxylic acid, methyl ester	ChEBI
METHYL (2S,3R,4S)-2-(BETA-D-glucopyranosyloxy)-4-(2-oxoethyl)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylATE	ChEBI
Methyl (2S,3R,4S)-4-(formylmethyl)-2-(beta-D-glucopyranosyloxy)-3,4-dihydro-3-vinyl-2H-pyran-5-carboxylate	ChEBI
Secologanin	ChEBI
3-Ethenyl-2-(b-D-glucopyranosyloxy)-3,4-dihydro-4-(2-oxoethyl)-2H-pyran-5-carboxylate, methyl ester	Generator
3-Ethenyl-2-(b-D-glucopyranosyloxy)-3,4-dihydro-4-(2-oxoethyl)-2H-pyran-5-carboxylic acid, methyl ester	Generator
3-Ethenyl-2-(beta-D-glucopyranosyloxy)-3,4-dihydro-4-(2-oxoethyl)-2H-pyran-5-carboxylate, methyl ester	Generator
3-Ethenyl-2-(β-D-glucopyranosyloxy)-3,4-dihydro-4-(2-oxoethyl)-2H-pyran-5-carboxylate, methyl ester	Generator
3-Ethenyl-2-(β-D-glucopyranosyloxy)-3,4-dihydro-4-(2-oxoethyl)-2H-pyran-5-carboxylic acid, methyl ester	Generator
METHYL (2S,3R,4S)-2-(b-D-glucopyranosyloxy)-4-(2-oxoethyl)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylate	Generator
METHYL (2S,3R,4S)-2-(b-D-glucopyranosyloxy)-4-(2-oxoethyl)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylic acid	Generator
METHYL (2S,3R,4S)-2-(beta-D-glucopyranosyloxy)-4-(2-oxoethyl)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylic acid	Generator
METHYL (2S,3R,4S)-2-(β-D-glucopyranosyloxy)-4-(2-oxoethyl)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylate	Generator
METHYL (2S,3R,4S)-2-(β-D-glucopyranosyloxy)-4-(2-oxoethyl)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylic acid	Generator
Methyl (2S,3R,4S)-4-(formylmethyl)-2-(b-D-glucopyranosyloxy)-3,4-dihydro-3-vinyl-2H-pyran-5-carboxylate	Generator
Methyl (2S,3R,4S)-4-(formylmethyl)-2-(b-D-glucopyranosyloxy)-3,4-dihydro-3-vinyl-2H-pyran-5-carboxylic acid	Generator
Methyl (2S,3R,4S)-4-(formylmethyl)-2-(beta-D-glucopyranosyloxy)-3,4-dihydro-3-vinyl-2H-pyran-5-carboxylic acid	Generator
Methyl (2S,3R,4S)-4-(formylmethyl)-2-(β-D-glucopyranosyloxy)-3,4-dihydro-3-vinyl-2H-pyran-5-carboxylate	Generator
Methyl (2S,3R,4S)-4-(formylmethyl)-2-(β-D-glucopyranosyloxy)-3,4-dihydro-3-vinyl-2H-pyran-5-carboxylic acid	Generator

Chemical Formula

C₁₇H₂₄O₁₀

Average Molecular Weight

388.3665

Monoisotopic Molecular Weight

388.136946988

IUPAC Name

methyl (2S,3R,4S)-3-ethenyl-4-(2-oxoethyl)-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-5-carboxylate

Traditional Name

(-)-secologanin

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CO[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](C=C)[C@@H]1CC=O

InChI Identifier

InChI=1S/C17H24O10/c1-3-8-9(4-5-18)10(15(23)24-2)7-25-16(8)27-17-14(22)13(21)12(20)11(6-19)26-17/h3,5,7-9,11-14,16-17,19-22H,1,4,6H2,2H3/t8-,9+,11-,12-,13+,14-,16+,17+/m1/s1

InChI Key

CSKKDSFETGLMSB-NRZPKYKESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Glycosyl compound
Secoiridoid-skeleton
O-glycosyl compound
Monocyclic monoterpenoid
Monoterpenoid
Sugar acid
Monosaccharide
Oxane
Alpha-hydrogen aldehyde
Vinylogous ester
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Methyl ester
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Monocarboxylic acid or derivatives
Acetal
Carboxylic acid derivative
Polyol
Primary alcohol
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Aldehyde
Organooxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

carboxylic ester (CHEBI:18002 )
beta-D-glucoside (CHEBI:18002 )
pyrans (CHEBI:18002 )
iridoid monoterpenoid (CHEBI:18002 )
Iridoid, 10-alkyliridoid and secoiridoid monoterpenoids (C01852 )
Secoiridoids (C01852 )
Iridoid, 10-alkyliridoid and secoiridoid monoterpenoids (LMPR0102070002 )

Ontology

Not Available

Exogenous (HMDB: HMDB0304482)

Herbs and Spices (FooDB: FOOD00866)

Nut

Almond (FooDB: FOOD00148)
Brazil nut (FooDB: FOOD00024)
Cashew nut (FooDB: FOOD00011)
Chestnut (FooDB: FOOD00045)
Hazelnut (FooDB: FOOD00376)
Peanut (FooDB: FOOD00016)
Pecan nut (FooDB: FOOD00044)
Pine nut (FooDB: FOOD00138)
Pistachio (FooDB: FOOD00140)
Walnut (FooDB: FOOD00608)
Acorn (FooDB: FOOD00282)
Beech nut (FooDB: FOOD00299)
Butternut (FooDB: FOOD00316)
Chinese chestnut (FooDB: FOOD00331)
European chestnut (FooDB: FOOD00363)
Hickory nut (FooDB: FOOD00377)
Macadamia nut (FooDB: FOOD00525)
Mixed nuts (FooDB: FOOD00771)
Pili nut (FooDB: FOOD00432)
Colorado pinyon (FooDB: FOOD00433)
Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)
Japanese chestnut (FooDB: FOOD00385)
Common hazelnut (FooDB: FOOD00062)
Macadamia nut (M. tetraphylla) (FooDB: FOOD00225)
Japanese walnut (FooDB: FOOD00240)
Nuts (FooDB: FOOD00869)

Fruit

Pome

Drupe

Apricot (FooDB: FOOD00144)
Prunus (Cherry, Plum) (FooDB: FOOD00143)
Nectarine (FooDB: FOOD00229)
Peach (FooDB: FOOD00149)
European plum (FooDB: FOOD00147)
Sour cherry (FooDB: FOOD00146)
Sweet cherry (FooDB: FOOD00145)
Common chokecherry (FooDB: FOOD00562)
Peach (var.) (FooDB: FOOD00230)

Tropical fruit

Berry

Bilberry (FooDB: FOOD00193)
Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Elderberry (FooDB: FOOD00358)
Gooseberry (FooDB: FOOD00157)
Grape (FooDB: FOOD00369)
Lingonberry (FooDB: FOOD00194)
Loganberry (FooDB: FOOD00400)
Strawberry (FooDB: FOOD00083)
Boysenberry (FooDB: FOOD00542)
American cranberry (FooDB: FOOD00192)
Common grape (FooDB: FOOD00204)
Strawberry guava (FooDB: FOOD00482)
Black mulberry (FooDB: FOOD00117)
Red raspberry (FooDB: FOOD00162)
Muscadine grape (FooDB: FOOD00203)
Salmonberry (FooDB: FOOD00456)
Alaska blueberry (FooDB: FOOD00380)
Sea-buckthornberry (FooDB: FOOD00087)
Black elderberry (FooDB: FOOD00166)
Black crowberry (FooDB: FOOD00075)
Black huckleberry (FooDB: FOOD00084)
Mulberry (FooDB: FOOD00116)
Black chokeberry (FooDB: FOOD00136)
Cloudberry (FooDB: FOOD00161)
Black raspberry (FooDB: FOOD00163)
Rowanberry (FooDB: FOOD00176)
Lowbush blueberry (FooDB: FOOD00189)
Sparkleberry (FooDB: FOOD00190)
Highbush blueberry (FooDB: FOOD00191)
Arctic blackberry (FooDB: FOOD00207)
Bayberry (FooDB: FOOD00209)
Elliott's blueberry (FooDB: FOOD00210)
Canada blueberry (FooDB: FOOD00211)
Bog bilberry (FooDB: FOOD00212)
Buffalo currant (FooDB: FOOD00213)
European cranberry (FooDB: FOOD00217)
Deerberry (FooDB: FOOD00218)
Cascade huckleberry (FooDB: FOOD00220)
Oval-leaf huckleberry (FooDB: FOOD00221)
Evergreen huckleberry (FooDB: FOOD00222)
Red huckleberry (FooDB: FOOD00223)
Summer grape (FooDB: FOOD00227)
Fox grape (FooDB: FOOD00228)
Half-highbush blueberry (FooDB: FOOD00248)
Jostaberry (FooDB: FOOD00257)
Sweet rowanberry (FooDB: FOOD00265)
Skunk currant (FooDB: FOOD00267)
Squashberry (FooDB: FOOD00344)
Ohelo berry (FooDB: FOOD00419)
Chinese bayberry (FooDB: FOOD00852)
Saskatoon berry (FooDB: FOOD00884)
Nanking cherry (FooDB: FOOD00885)

Other fruit

Date (FooDB: FOOD00135)
Fig (FooDB: FOOD00081)
Jujube (FooDB: FOOD00388)

Citrus

Grapefruit (FooDB: FOOD00256)
Lemon (FooDB: FOOD00054)
Lime (FooDB: FOOD00053)
Sweet orange (FooDB: FOOD00057)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Persian lime (FooDB: FOOD00543)
Pummelo (FooDB: FOOD00055)
Grapefruit/Pummelo hybrid (FooDB: FOOD00255)
Citrus (FooDB: FOOD00859)

Fruits (FooDB: FOOD00871)

Vegetable

Shoot vegetable

Fruit vegetable

Eggplant (FooDB: FOOD00174)
Avocado (FooDB: FOOD00130)
Groundcherry (FooDB: FOOD00371)
Olive (FooDB: FOOD00121)
Pepper (FooDB: FOOD00040)
Garden tomato (FooDB: FOOD00171)
Mexican groundcherry (FooDB: FOOD00491)
Green bell pepper (FooDB: FOOD00877)
Yellow bell pepper (FooDB: FOOD00878)
Red bell pepper (FooDB: FOOD00880)
Italian sweet red pepper (FooDB: FOOD00881)
Garden tomato (var.) (FooDB: FOOD00173)
Cherry tomato (FooDB: FOOD00172)
Pepper (C. baccatum) (FooDB: FOOD00231)
Pepper (C. chinense) (FooDB: FOOD00232)
Pepper (Capsicum) (FooDB: FOOD00233)
Pepper (C. frutescens) (FooDB: FOOD00428)
Pepper (C. pubescens) (FooDB: FOOD00849)
Orange bell pepper (FooDB: FOOD00879)

Root vegetable

Cabbage

Leaf vegetable

Lettuce (FooDB: FOOD00095)
Swiss chard (FooDB: FOOD00237)
Garden cress (FooDB: FOOD00099)
Endive (FooDB: FOOD00048)
Spinach (FooDB: FOOD00178)
Common beet (FooDB: FOOD00025)
Garland chrysanthemum (FooDB: FOOD00333)
Jute (FooDB: FOOD00389)
Lambsquarters (FooDB: FOOD00394)
New Zealand spinach (FooDB: FOOD00415)
Swamp cabbage (FooDB: FOOD00091)
Rocket salad (ssp.) (FooDB: FOOD00077)
Yautia (FooDB: FOOD00510)
Romaine lettuce (FooDB: FOOD00888)
Rocket salad (FooDB: FOOD00244)
Chicory leaves (FooDB: FOOD00250)
Corn salad (FooDB: FOOD00340)
Malabar spinach (FooDB: FOOD00404)
Ostrich fern (FooDB: FOOD00556)
Green vegetables (FooDB: FOOD00872)

Mushroom

Tuber

Onion-family vegetable

Leek (FooDB: FOOD00007)
Allium (FooDB: FOOD00005)
Wild leek (FooDB: FOOD00396)
Shallot (FooDB: FOOD00243)
Garden onion (FooDB: FOOD00006)
Garden onion (var.) (FooDB: FOOD00226)
Onion-family vegetables (FooDB: FOOD00855)
Green onion (FooDB: FOOD00963)
Red onion (FooDB: FOOD00962)

Other vegetable

Okra (FooDB: FOOD00420)
Horseradish tree (FooDB: FOOD00379)
Sacred lotus (FooDB: FOOD00402)
Tree fern (FooDB: FOOD00797)
Chinese water chestnut (FooDB: FOOD00332)
Nopal (FooDB: FOOD00416)
Carob (FooDB: FOOD00321)
Agave (FooDB: FOOD00563)
Narrowleaf cattail (FooDB: FOOD00564)
Giant butterbur (FooDB: FOOD00314)
Sesbania flower (FooDB: FOOD00469)

Stalk vegetable

Brassica

Brassicas (FooDB: FOOD00857)

Cereal and cereal product

Other bread

Other bread (FooDB: FOOD00269)

Cereal

Cereal product

Dough

Sourdough (FooDB: FOOD00275)

Cereals and cereal products (FooDB: FOOD00858)

Pulse

Bean

Lentil

Lentils (FooDB: FOOD00098)

Pea

Other pulse

White lupine (FooDB: FOOD00403)
Lupine (FooDB: FOOD00104)

Pulses (FooDB: FOOD00867)

Soy

Soy bean (FooDB: FOOD00085)

Soy product

Other soy product (FooDB: FOOD00271)

Abalone (FooDB: FOOD00279)
Conch (FooDB: FOOD00611)

Gourd

Chayote (FooDB: FOOD00325)
Cucumber (FooDB: FOOD00065)
Muskmelon (FooDB: FOOD00064)
Cucurbita (FooDB: FOOD00066)
Watermelon (FooDB: FOOD00052)
Bitter gourd (FooDB: FOOD00115)
Calabash (FooDB: FOOD00318)
Towel gourd (FooDB: FOOD00492)
Winter squash (FooDB: FOOD00283)
Butternut squash (FooDB: FOOD00317)
Wax gourd (FooDB: FOOD00499)
Green zucchini (FooDB: FOOD00875)
Yellow zucchini (FooDB: FOOD00876)
Japanese pumpkin (FooDB: FOOD00886)
Sunburst squash (pattypan squash) (FooDB: FOOD00874)
Tinda (FooDB: FOOD00559)
Horned melon (FooDB: FOOD00761)

Tea

Herbal tea

Greenthread tea (FooDB: FOOD00820)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Indole Alkaloid Biosynthesis (PathBank: SMP0063467)

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
logP	-0.83	ALOGPS
logP	-1.7	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	151.98 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	88.52 m³·mol⁻¹	ChemAxon
Polarizability	37.14 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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
AllCCS	[M+H]+	190.296	32859911
AllCCS	[M+H-H2O]+	187.723	32859911
AllCCS	[M+Na]+	193.343	32859911
AllCCS	[M+NH4]+	192.665	32859911
AllCCS	[M-H]-	186.938	32859911
AllCCS	[M+Na-2H]-	187.178	32859911
AllCCS	[M+HCOO]-	187.579	32859911
DeepCCS	[M+H]+	185.352	30932474
DeepCCS	[M-H]-	183.457	30932474
DeepCCS	[M-2H]-	216.698	30932474
DeepCCS	[M+Na]+	190.959	30932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
secologanin,5TMS,isomer #1	C=C[C@H]1[C@H](O[C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)OC=C(C(=O)OC)[C@H]1C=CO[Si](C)(C)C	2750.2	Semi standard non polar	33892256
secologanin,5TMS,isomer #1	C=C[C@H]1[C@H](O[C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)OC=C(C(=O)OC)[C@H]1C=CO[Si](C)(C)C	2910.1	Standard non polar	33892256
secologanin,5TMS,isomer #1	C=C[C@H]1[C@H](O[C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)OC=C(C(=O)OC)[C@H]1C=CO[Si](C)(C)C	3437.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - secologanin GC-MS (Non-derivatized)	splash10-0gb9-2941000000-d1989e58bf06ee4cf380	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - secologanin GC-MS (Non-derivatized)	splash10-0gdr-2931000000-c41c7965ee5f98595452	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - secologanin GC-MS (Non-derivatized)	splash10-0gb9-2931000000-c7d5b403f8c624e91877	2014-06-16	HMDB team, MONA, MassBank	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 10V, Positive-QTOF	splash10-070i-0955000000-d2599f28cf7a95703756	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 20V, Positive-QTOF	splash10-06vs-1931000000-a09d52f1f1cf62ee287d	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 40V, Positive-QTOF	splash10-052r-9700000000-d0e2b29a1c685fcd4c86	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 10V, Negative-QTOF	splash10-004r-1569000000-626e940a7c2b3725a4b0	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 20V, Negative-QTOF	splash10-02di-3945000000-5047d0b9654c59e24afc	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 40V, Negative-QTOF	splash10-002f-4920000000-79158472c746f9f83e9f	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 10V, Positive-QTOF	splash10-009i-0849000000-559ffea33d0bf7fe8f95	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 20V, Positive-QTOF	splash10-001i-0910000000-daf99a97c8d320310dda	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 40V, Positive-QTOF	splash10-0mpp-8940000000-d1c75f2aaecb96f2cb03	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 10V, Negative-QTOF	splash10-0002-0911000000-2bfe9ec0a38a1fbfb058	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 20V, Negative-QTOF	splash10-03y0-3739000000-808031158bd3414bf3fd	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - secologanin 40V, Negative-QTOF	splash10-0apm-4911000000-03618a6e12c1993b6821	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Secologanin

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

18002

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

Not Available

Showing metabocard for secologanin (HMDB0304482)

MOL for HMDB0304482 (secologanin)

3D MOL for HMDB0304482 (secologanin)

3D SDF for HMDB0304482 (secologanin)

3D-SDF for HMDB0304482 (secologanin)

PDB for HMDB0304482 (secologanin)

3D PDB for HMDB0304482 (secologanin)

SMILES for HMDB0304482 (secologanin)

INCHI for HMDB0304482 (secologanin)

Structure for HMDB0304482 (secologanin)

3D Structure for HMDB0304482 (secologanin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra