NP-MRD: Showing NP-Card for Methyl protogracillin (NP0071495)

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Record Information

Version

2.0

Created at

2022-04-28 16:52:20 UTC

Updated at

2022-04-28 16:52:20 UTC

NP-MRD ID

NP0071495

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Methyl protogracillin

Description

Methyl protogracillin belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative. Thus, methyl protogracillin is considered to be a sterol. Methyl protogracillin is found in Dioscorea collettii var.hypoglauca, Dioscorea futschauensis , Dioscorea pseudojaponica, Dioscorea spongiosa, Dracaena concinna, Dracaena draco and Lilium regale. Methyl protogracillin was first documented in 2003 (PMID: 14558759). Based on a literature review a small amount of articles have been published on Methyl protogracillin (PMID: 28814124) (PMID: 25712888) (PMID: 12820229).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282218522D          

 75 83  0  0  1  0            999 V2000
    8.1476    0.4152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.6816    2.4093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8616    2.3185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   12.2310   -2.7265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

161169  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652304282218522D          

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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
  9 11  1  1  0  0  0
  8 12  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  7 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 18 17  1  1  0  0  0
 14 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 17 21  1  1  0  0  0
 20 22  1  1  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  1  0  0  0  0
 27 26  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 27 32  1  0  0  0  0
 32 33  1  6  0  0  0
 31 34  1  1  0  0  0
 30 35  1  6  0  0  0
 29 36  1  1  0  0  0
 36 37  1  0  0  0  0
 24 38  1  6  0  0  0
 20 39  1  6  0  0  0
 39 40  1  0  0  0  0
 19 41  1  6  0  0  0
 14 42  1  1  0  0  0
  2 43  1  1  0  0  0
 44 43  1  1  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 44 49  1  0  0  0  0
 49 50  1  6  0  0  0
 51 50  1  6  0  0  0
 51 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 51 56  1  0  0  0  0
 55 57  1  1  0  0  0
 54 58  1  6  0  0  0
 53 59  1  1  0  0  0
 52 60  1  1  0  0  0
 48 61  1  1  0  0  0
 62 61  1  1  0  0  0
 62 63  1  0  0  0  0
 63 64  1  0  0  0  0
 64 65  1  0  0  0  0
 65 66  1  0  0  0  0
 66 67  1  0  0  0  0
 62 67  1  0  0  0  0
 66 68  1  1  0  0  0
 68 69  1  0  0  0  0
 65 70  1  6  0  0  0
 64 71  1  1  0  0  0
 63 72  1  6  0  0  0
 47 73  1  6  0  0  0
 46 74  1  1  0  0  0
 74 75  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0071495

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@]1(CC[C@@H](C)CO[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)O[C@H]2C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]3(C)[C@H]2[C@@H]1C)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]1O[C@@H]1O[C@@H](C)[C@H](O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C52H86O23/c1-21(20-67-46-41(63)39(61)35(57)30(17-53)70-46)9-14-52(66-6)22(2)33-29(75-52)16-28-26-8-7-24-15-25(10-12-50(24,4)27(26)11-13-51(28,33)5)69-49-45(74-47-42(64)38(60)34(56)23(3)68-47)44(37(59)32(19-55)72-49)73-48-43(65)40(62)36(58)31(18-54)71-48/h7,21-23,25-49,53-65H,8-20H2,1-6H3/t21-,22+,23+,25+,26-,27+,28+,29+,30-,31-,32-,33+,34+,35-,36-,37-,38-,39+,40+,41-,42-,43-,44+,45-,46-,47+,48+,49-,50+,51+,52-/m1/s1

> <INCHI_KEY>
LOSNTJHBTWBJCC-QTGARSGCSA-N

> <FORMULA>
C52H86O23

> <MOLECULAR_WEIGHT>
1079.237

> <EXACT_MASS>
1078.555989029

> <JCHEM_ACCEPTOR_COUNT>
23

> <JCHEM_ATOM_COUNT>
161

> <JCHEM_AVERAGE_POLARIZABILITY>
114.08954533277517

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
13

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-2-[(2R)-4-[(1S,2S,4S,6R,7S,8R,9S,12S,13R,16S)-16-{[(2R,3R,4S,5R,6R)-5-hydroxy-6-(hydroxymethyl)-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-2-yl]oxy}-6-methoxy-7,9,13-trimethyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-en-6-yl]-2-methylbutoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.18

> <JCHEM_LOGP>
-1.6277042306666647

> <ALOGPS_LOGS>
-3.14

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.19445947777967

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.75592140577752

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483775752817795

> <JCHEM_POLAR_SURFACE_AREA>
355.29

> <JCHEM_REFRACTIVITY>
256.6367000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.85e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6R)-2-[(2R)-4-[(1S,2S,4S,6R,7S,8R,9S,12S,13R,16S)-16-{[(2R,3R,4S,5R,6R)-5-hydroxy-6-(hydroxymethyl)-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-2-yl]oxy}-6-methoxy-7,9,13-trimethyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-en-6-yl]-2-methylbutoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      15.209   0.775   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      15.827   2.185   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.915   3.426   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.384   3.257   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.472   4.497   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.942   4.328   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.323   2.917   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.235   1.677   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.766   1.846   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.678   0.606   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.148   0.436   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.617   0.266   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.086   0.097   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.174   1.337   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.793   2.748   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.642   3.772   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.313   2.994   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.642   1.490   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.312   0.712   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.162   1.736   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.781   3.147   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.690   2.189   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.562   1.140   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.090   1.592   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.037   0.543   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -2.510   0.995   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -3.637  -0.053   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -5.109   0.399   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -6.237  -0.650   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -5.893  -2.151   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.421  -2.603   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.293  -1.554   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -1.821  -2.007   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -4.076  -4.104   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -7.020  -3.200   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -7.709  -0.198   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -8.837  -1.246   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -0.254   3.093   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       3.013   0.711   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       3.326  -0.796   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       5.160  -0.820   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       7.412  -0.001   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      17.358   2.355   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      18.270   1.114   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      17.652  -0.296   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      18.564  -1.537   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      20.095  -1.367   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      20.713   0.043   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      19.801   1.284   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0      20.419   2.694   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      19.507   3.935   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      20.125   5.345   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      19.213   6.586   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      17.683   6.417   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      17.064   5.006   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      17.976   3.765   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0      15.534   4.837   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      16.770   7.657   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      19.832   7.997   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      21.656   5.515   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      22.244   0.213   0.000  0.00  0.00           O+0
HETATM   62  C   UNK     0      23.156  -1.028   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      24.686  -0.858   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      25.599  -2.099   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      24.980  -3.510   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      23.450  -3.679   0.000  0.00  0.00           C+0
HETATM   67  O   UNK     0      22.537  -2.438   0.000  0.00  0.00           O+0
HETATM   68  C   UNK     0      22.831  -5.089   0.000  0.00  0.00           C+0
HETATM   69  O   UNK     0      23.743  -6.330   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0      25.892  -4.750   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0      27.129  -1.930   0.000  0.00  0.00           O+0
HETATM   72  O   UNK     0      25.305   0.552   0.000  0.00  0.00           O+0
HETATM   73  O   UNK     0      21.007  -2.608   0.000  0.00  0.00           O+0
HETATM   74  C   UNK     0      17.945  -2.947   0.000  0.00  0.00           C+0
HETATM   75  O   UNK     0      16.415  -3.117   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3   43                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8    4   10   11                                             
CONECT   10    9    1                                                       
CONECT   11    9                                                            
CONECT   12    8   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   18   42                                             
CONECT   15   14    7   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   21                                                  
CONECT   18   17   14   19                                                  
CONECT   19   18   20   41                                                  
CONECT   20   19   21   22   39                                             
CONECT   21   20   17                                                       
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   38                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   36                                                  
CONECT   30   29   31   35                                                  
CONECT   31   30   32   34                                                  
CONECT   32   31   27   33                                                  
CONECT   33   32                                                            
CONECT   34   31                                                            
CONECT   35   30                                                            
CONECT   36   29   37                                                       
CONECT   37   36                                                            
CONECT   38   24                                                            
CONECT   39   20   40                                                       
CONECT   40   39                                                            
CONECT   41   19                                                            
CONECT   42   14                                                            
CONECT   43    2   44                                                       
CONECT   44   43   45   49                                                  
CONECT   45   44   46                                                       
CONECT   46   45   47   74                                                  
CONECT   47   46   48   73                                                  
CONECT   48   47   49   61                                                  
CONECT   49   48   44   50                                                  
CONECT   50   49   51                                                       
CONECT   51   50   52   56                                                  
CONECT   52   51   53   60                                                  
CONECT   53   52   54   59                                                  
CONECT   54   53   55   58                                                  
CONECT   55   54   56   57                                                  
CONECT   56   55   51                                                       
CONECT   57   55                                                            
CONECT   58   54                                                            
CONECT   59   53                                                            
CONECT   60   52                                                            
CONECT   61   48   62                                                       
CONECT   62   61   63   67                                                  
CONECT   63   62   64   72                                                  
CONECT   64   63   65   71                                                  
CONECT   65   64   66   70                                                  
CONECT   66   65   67   68                                                  
CONECT   67   66   62                                                       
CONECT   68   66   69                                                       
CONECT   69   68                                                            
CONECT   70   65                                                            
CONECT   71   64                                                            
CONECT   72   63                                                            
CONECT   73   47                                                            
CONECT   74   46   75                                                       
CONECT   75   74                                                            
MASTER        0    0    0    0    0    0    0    0   75    0  166    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅₂H₈₆O₂₃

Average Mass

1079.2370 Da

Monoisotopic Mass

1078.55599 Da

IUPAC Name

(2R,3R,4S,5S,6R)-2-[(2R)-4-[(1S,2S,4S,6R,7S,8R,9S,12S,13R,16S)-16-{[(2R,3R,4S,5R,6R)-5-hydroxy-6-(hydroxymethyl)-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-2-yl]oxy}-6-methoxy-7,9,13-trimethyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-en-6-yl]-2-methylbutoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

CAS Registry Number

Not Available

SMILES

CO[C@]1(CC[C@@H](C)CO[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)O[C@H]2C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]3(C)[C@H]2[C@@H]1C)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]1O[C@@H]1O[C@@H](C)[C@H](O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C52H86O23/c1-21(20-67-46-41(63)39(61)35(57)30(17-53)70-46)9-14-52(66-6)22(2)33-29(75-52)16-28-26-8-7-24-15-25(10-12-50(24,4)27(26)11-13-51(28,33)5)69-49-45(74-47-42(64)38(60)34(56)23(3)68-47)44(37(59)32(19-55)72-49)73-48-43(65)40(62)36(58)31(18-54)71-48/h7,21-23,25-49,53-65H,8-20H2,1-6H3/t21-,22+,23+,25+,26-,27+,28+,29+,30-,31-,32-,33+,34+,35-,36-,37-,38-,39+,40+,41-,42-,43-,44+,45-,46-,47+,48+,49-,50+,51+,52-/m1/s1

InChI Key

LOSNTJHBTWBJCC-QTGARSGCSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Dioscorea collettii var.hypoglauca	Plant	KNApSAcK
Dioscorea futschauensis	Plant	KNApSAcK
Dioscorea pseudojaponica	Plant	KNApSAcK
Dioscorea spongiosa	LOTUS Database	35616633
Dracaena concinna	LOTUS Database	35616633
Dracaena draco	LOTUS Database	35616633
Lilium regale	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal glycosides

Direct Parent

Steroidal saponins

Alternative Parents

Substituents

Steroidal saponin
Diterpene glycoside
Furostane-skeleton
Oligosaccharide
Diterpenoid
Delta-5-steroid
Terpene glycoside
Fatty acyl glycoside
Alkyl glycoside
Glycosyl compound
O-glycosyl compound
Ketal
Fatty acyl
Oxane
Oxolane
Secondary alcohol
Oxacycle
Polyol
Acetal
Organoheterocyclic compound
Hydrocarbon derivative
Primary alcohol
Organic oxygen compound
Organooxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

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	-0.18	ALOGPS
logP	-1.6	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	11.76	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	23	ChemAxon
Hydrogen Donor Count	13	ChemAxon
Polar Surface Area	355.29 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	256.64 m³·mol⁻¹	ChemAxon
Polarizability	114.09 Å³	ChemAxon
Number of Rings	9	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00030765

Chemspider ID

23339557

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44566783

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kumar A, Maurya AK, Chand G, Agnihotri VK: Comparative metabolic profiling of Costus speciosus leaves and rhizomes using NMR, GC-MS and UPLC/ESI-MS/MS. Nat Prod Res. 2018 Apr;32(7):826-833. doi: 10.1080/14786419.2017.1365069. Epub 2017 Aug 17. [PubMed:28814124 ]
Lim H, Min DS, Kang Y, Kim HW, Son KH, Kim HP: Inhibition of matrix metalloproteinase-13 expression in IL-1beta-treated articular chondrocytes by a steroidal saponin, spicatoside A, and its cellular mechanisms of action. Arch Pharm Res. 2015 Jun;38(6):1108-16. doi: 10.1007/s12272-015-0581-z. Epub 2015 Feb 25. [PubMed:25712888 ]
Yang DJ, Lu TJ, Hwang LS: Isolation and identification of steroidal saponins in Taiwanese yam cultivar (Dioscorea pseudojaponica Yamamoto). J Agric Food Chem. 2003 Oct 22;51(22):6438-44. doi: 10.1021/jf030390j. [PubMed:14558759 ]
Hu K, Yao X: The cytotoxicity of methyl protoneogracillin (NSC-698793) and gracillin (NSC-698787), two steroidal saponins from the rhizomes of Dioscorea collettii var. hypoglauca, against human cancer cells in vitro. Phytother Res. 2003 Jun;17(6):620-6. doi: 10.1002/ptr.1211. [PubMed:12820229 ]

Showing NP-Card for Methyl protogracillin (NP0071495)

MOL for NP0071495 (Methyl protogracillin)

3D MOL for NP0071495 (Methyl protogracillin)

3D SDF for NP0071495 (Methyl protogracillin)

3D-SDF for NP0071495 (Methyl protogracillin)

PDB for NP0071495 (Methyl protogracillin)

3D PDB for NP0071495 (Methyl protogracillin)

SMILES for NP0071495 (Methyl protogracillin)

INCHI for NP0071495 (Methyl protogracillin)

Structure for NP0071495 (Methyl protogracillin)

3D Structure for NP0071495 (Methyl protogracillin)