NP-MRD: Showing NP-Card for (-)-secologanin (NP0277983)

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Record Information

Version

2.0

Created at

2022-09-09 02:51:18 UTC

Updated at

2022-09-09 02:51:19 UTC

NP-MRD ID

NP0277983

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-secologanin

Description

(-)-Secologanin 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. (-)-secologanin is found in Acicarpha tribuloides, Adina pilulifera, Catharanthus roseus, Cinchona calisaya, Cruckshanksia pumila, Cruckshanksia verticillata, Curtia tenuifolia, Desfontainia spinosa, Dipsacus inermis, Gentiana verna, Guettarda speciosa, Hydrangea macrophylla, Lippia graveolens, Lonicera caerulea, Lonicera japonica, Lonicera periclymenum, Lonicera tatarica, Pterocephalus perennis, Sinoadina racemosa, Strychnos nux-vomica and Strychnos spinosa. (-)-secologanin was first documented in 2013 (PMID: 24104568). Thus, (-)-secologanin is considered to be an isoprenoid lipid molecule (-)-Secologanin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 26285573).

Structure

MOL 3D MOL SDF 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

     RDKit          3D

 51 52  0  0  0  0  0  0  0  0999 V2000
   -1.9796    2.5999   -1.7223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9596    1.2986   -1.8476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1541    0.3085   -1.1218 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1955    0.8523   -0.1267 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9554    0.0969    0.0282 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1272    0.7786   -0.1123 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7743    0.3456   -1.2503 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7720   -0.5584   -1.0937 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2228   -1.9807   -0.8995 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2666   -2.8887   -0.7404 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7983   -0.3013   -0.0506 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1068   -0.2328   -0.5799 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4601    1.0133    0.6171 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2980    1.2783    1.6949 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0153    0.8106    1.1046 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7315    1.8807    1.9508 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8121    0.8436    1.1826 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1685    0.9769    1.3444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9241    0.2086    0.5236 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3532    0.2857    0.6201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8946    1.0390    1.4634 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1769   -0.4495   -0.1976 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5874   -0.4079   -0.1463 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1203   -0.6288   -0.3862 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8209   -1.6040   -1.2244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5444   -2.6441   -0.4829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4331   -2.6997    0.7375 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6258    3.2552   -2.3209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3602    3.1117   -1.0143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6523    0.8826   -2.6148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6866   -0.3420   -1.8910 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0026    1.9091   -0.3386 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8729    1.8434   -0.3288 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3213   -0.6110   -2.0760 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6041   -2.0320    0.0096 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6403   -2.2842   -1.8040 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1198   -2.5044   -1.0989 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8068   -1.1093    0.7287 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7779   -0.3100    0.1198 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5269    1.8129   -0.1213 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8287    1.2254    2.5581 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0335   -0.1225    1.6695 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0663    2.4471    1.4835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6809    1.6115    2.0370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9214   -0.3914    0.9175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8983    0.5538   -0.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0037   -1.2679   -0.7113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4168   -1.2047    0.3143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5243   -1.1748   -1.9676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0531   -2.1426   -1.8549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1815   -3.3772   -0.9583 H   0  0  0  0  0  0  0  0  0  0  0  0
 23 22  1  0
 22 20  1  0
 20 21  2  0
 20 19  1  0
 19 18  2  0
 18 17  1  0
 17  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  3  1  0
  3  2  1  0
  2  1  2  3
  3 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 24 19  1  0
 15  6  1  0
 23 45  1  0
 23 46  1  0
 23 47  1  0
 18 44  1  0
  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  1
 16 43  1  0
  3 31  1  6
  2 30  1  0
  1 28  1  0
  1 29  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>
NP0277983

> <DATABASE_NAME>
NP-MRD

> <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

$$$$

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

View in JSmol

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 Mass

388.3665 Da

Monoisotopic Mass

388.13695 Da

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

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Acicarpha tribuloides	LOTUS Database	35616633
Adina pilulifera	LOTUS Database	35616633
Catharanthus roseus	LOTUS Database	35616633
Cinchona calisaya	LOTUS Database	35616633
Cruckshanksia pumila	LOTUS Database	35616633
Cruckshanksia verticillata	LOTUS Database	35616633
Curtia tenuifolia	LOTUS Database	35616633
Desfontainia spinosa	LOTUS Database	35616633
Dipsacus inermis	LOTUS Database	35616633
Gentiana verna	LOTUS Database	35616633
Guettarda speciosa	LOTUS Database	35616633
Hydrangea macrophylla	LOTUS Database	35616633
Lippia graveolens	LOTUS Database	35616633
Lonicera caerulea	LOTUS Database	35616633
Lonicera japonica	LOTUS Database	35616633
Lonicera periclymenum	LOTUS Database	35616633
Lonicera tatarica	LOTUS Database	35616633
Pterocephalus perennis	LOTUS Database	35616633
Sinoadina racemosa	LOTUS Database	35616633
Strychnos nux-vomica	LOTUS Database	35616633
Strychnos spinosa	LOTUS Database	35616633

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 )

Physical Properties

State

Not Available

Experimental 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

Predicted 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB031168

KNApSAcK ID

C00003098

Chemspider ID

Not Available

KEGG Compound ID

C01852

BioCyc ID

SECOLOGANIN-CPD

BiGG ID

Not Available

Wikipedia Link

Secologanin

METLIN ID

Not Available

PubChem Compound

161276

PDB ID

Not Available

ChEBI ID

18002

Good Scents ID

Not Available

References

General References

Asada K, Salim V, Masada-Atsumi S, Edmunds E, Nagatoshi M, Terasaka K, Mizukami H, De Luca V: A 7-deoxyloganetic acid glucosyltransferase contributes a key step in secologanin biosynthesis in Madagascar periwinkle. Plant Cell. 2013 Oct;25(10):4123-34. doi: 10.1105/tpc.113.115154. Epub 2013 Oct 8. [PubMed:24104568 ]
Duge de Bernonville T, Foureau E, Parage C, Lanoue A, Clastre M, Londono MA, Oudin A, Houille B, Papon N, Besseau S, Glevarec G, Atehortua L, Giglioli-Guivarc'h N, St-Pierre B, De Luca V, O'Connor SE, Courdavault V: Characterization of a second secologanin synthase isoform producing both secologanin and secoxyloganin allows enhanced de novo assembly of a Catharanthus roseus transcriptome. BMC Genomics. 2015 Aug 19;16(1):619. doi: 10.1186/s12864-015-1678-y. [PubMed:26285573 ]
LOTUS database [Link]

Showing NP-Card for (-)-secologanin (NP0277983)

MOL for NP0277983 ((-)-secologanin)

3D MOL for NP0277983 ((-)-secologanin)

3D SDF for NP0277983 ((-)-secologanin)

3D-SDF for NP0277983 ((-)-secologanin)

PDB for NP0277983 ((-)-secologanin)

3D PDB for NP0277983 ((-)-secologanin)

SMILES for NP0277983 ((-)-secologanin)

INCHI for NP0277983 ((-)-secologanin)

Structure for NP0277983 ((-)-secologanin)

3D Structure for NP0277983 ((-)-secologanin)