NP-MRD: Showing NP-Card for Didemnin B (NP0079887)

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Record Information

Version

2.0

Created at

2022-04-29 00:57:56 UTC

Updated at

2022-04-29 00:57:57 UTC

NP-MRD ID

NP0079887

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Didemnin B

Description

SCHEMBL14618161 belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. Didemnin B is found in Trididemnum solidum. Based on a literature review very few articles have been published on SCHEMBL14618161.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292202582D          

 79 82  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304292202582D          

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   -1.9297   -4.5283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6834   -4.8639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5971   -5.6844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9651   -7.2849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5526   -7.9993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2724   -7.9993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9651   -8.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -8.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9069   -9.4191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0821   -9.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3038  -10.1424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5754   -7.9742    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6347   -7.2669    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.0316   -6.5437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0626   -7.9723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6657   -8.6955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 18 17  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
  1 30  1  0  0  0  0
 27 31  1  6  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
 34 39  1  1  0  0  0
 39 40  1  0  0  0  0
 39 41  1  0  0  0  0
 41 42  2  0  0  0  0
 43 41  1  6  0  0  0
 43 44  1  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 43 47  1  0  0  0  0
 44 48  1  0  0  0  0
 48 49  2  0  0  0  0
 48 50  1  0  0  0  0
 50 51  1  0  0  0  0
 50 52  1  6  0  0  0
 26 53  1  1  0  0  0
 22 54  1  1  0  0  0
 54 55  1  0  0  0  0
 55 56  2  0  0  0  0
 56 57  1  0  0  0  0
 57 58  2  0  0  0  0
 58 59  1  0  0  0  0
 59 60  2  0  0  0  0
 55 60  1  0  0  0  0
 58 61  1  0  0  0  0
 61 62  1  0  0  0  0
 21 63  1  0  0  0  0
 18 64  1  0  0  0  0
 64 65  1  0  0  0  0
 65 66  1  0  0  0  0
 17 66  1  0  0  0  0
 14 67  1  6  0  0  0
 67 68  1  0  0  0  0
 68 69  1  0  0  0  0
 68 70  1  0  0  0  0
 10 71  1  6  0  0  0
  7 72  1  1  0  0  0
 72 73  1  0  0  0  0
 72 74  1  0  0  0  0
  2 75  1  6  0  0  0
  1 76  1  6  0  0  0
 76 77  1  1  0  0  0
 76 78  1  0  0  0  0
 78 79  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0079887

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](C)[C@H]1NC(=O)[C@@H](NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@H]2CCCN2C(=O)[C@H](C)O)[C@@H](C)OC(=O)[C@H](CC2=CC=C(OC)C=C2)N(C)C(=O)[C@@H]2CCCN2C(=O)[C@H](CC(C)C)NC(=O)[C@@H](C)C(=O)[C@@H](OC(=O)C[C@@H]1O)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C57H89N7O15/c1-15-33(8)46-44(66)29-45(67)79-49(32(6)7)48(68)34(9)50(69)58-39(26-30(2)3)54(73)64-25-17-19-41(64)56(75)62(13)43(28-37-20-22-38(77-14)23-21-37)57(76)78-36(11)47(52(71)59-46)60-51(70)42(27-31(4)5)61(12)55(74)40-18-16-24-63(40)53(72)35(10)65/h20-23,30-36,39-44,46-47,49,65-66H,15-19,24-29H2,1-14H3,(H,58,69)(H,59,71)(H,60,70)/t33-,34-,35-,36+,39-,40+,41-,42+,43-,44-,46+,47-,49-/m0/s1

> <INCHI_KEY>
KYHUYMLIVQFXRI-CYJDUVKTSA-N

> <FORMULA>
C57H89N7O15

> <MOLECULAR_WEIGHT>
1112.373

> <EXACT_MASS>
1111.641665194

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
168

> <JCHEM_AVERAGE_POLARIZABILITY>
118.86654255068109

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-N-[(3S,6R,7S,10R,11S,15S,17S,20S,25aS)-10-[(2S)-butan-2-yl]-11-hydroxy-3-[(4-methoxyphenyl)methyl]-2,6,17-trimethyl-20-(2-methylpropyl)-1,4,8,13,16,18,21-heptaoxo-15-(propan-2-yl)-docosahydro-1H-pyrrolo[2,1-f]1,15-dioxa-4,7,10,20-tetraazacyclotricosan-7-yl]-2-{1-[(2R)-1-[(2S)-2-hydroxypropanoyl]pyrrolidin-2-yl]-N-methylformamido}-4-methylpentanamide

> <ALOGPS_LOGP>
3.07

> <JCHEM_LOGP>
3.4377619226666676

> <ALOGPS_LOGS>
-4.47

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.978679216735088

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.882438766525942

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0995749908983656

> <JCHEM_POLAR_SURFACE_AREA>
287.90000000000003

> <JCHEM_REFRACTIVITY>
288.98919999999987

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.77e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-N-[(3S,6R,7S,10R,11S,15S,17S,20S,25aS)-10-[(2S)-butan-2-yl]-11-hydroxy-15-isopropyl-3-[(4-methoxyphenyl)methyl]-2,6,17-trimethyl-20-(2-methylpropyl)-1,4,8,13,16,18,21-heptaoxo-tetradecahydro-3H-pyrrolo[2,1-f]1,15-dioxa-4,7,10,20-tetraazacyclotricosan-7-yl]-2-{1-[(2R)-1-[(2S)-2-hydroxypropanoyl]pyrrolidin-2-yl]-N-methylformamido}-4-methylpentanamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       8.978 -13.598   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.200 -15.093   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.520 -16.599   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.186 -17.369   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       7.025 -18.901   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       6.042 -16.339   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.358 -16.266   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.588 -14.932   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.358 -13.598   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.048 -14.932   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.278 -13.598   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.048 -12.265   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0      -0.262 -13.598   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -1.032 -12.265   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.572 -12.265   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -3.342 -13.598   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0      -3.342 -10.931   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -2.572  -9.597   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.032  -9.597   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.262 -10.931   0.000  0.00  0.00           O+0
HETATM   21  N   UNK     0      -0.262  -8.264   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       1.278  -8.264   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.048  -9.597   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       1.278 -10.931   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       3.588  -9.597   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.358 -10.931   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.898 -10.931   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.668 -12.265   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       5.898 -13.598   0.000  0.00  0.00           O+0
HETATM   30  N   UNK     0       8.208 -12.265   0.000  0.00  0.00           N+0
HETATM   31  N   UNK     0       6.668  -9.597   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       8.208  -9.597   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       8.978 -10.931   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       8.978  -8.264   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.208  -6.930   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       5.898  -8.264   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       5.898  -5.596   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0      10.518  -8.264   0.000  0.00  0.00           N+0
HETATM   40  C   UNK     0      11.288  -9.597   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      11.288  -6.930   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      10.518  -5.596   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      12.828  -6.930   0.000  0.00  0.00           C+0
HETATM   44  N   UNK     0      13.734  -5.684   0.000  0.00  0.00           N+0
HETATM   45  C   UNK     0      15.198  -6.160   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      15.198  -7.700   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      13.734  -8.176   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      13.258  -4.219   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      11.751  -3.899   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0      14.288  -3.075   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      13.812  -1.610   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0      15.795  -3.395   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0       3.588 -12.265   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       2.048  -6.930   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       1.278  -5.596   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -0.262  -5.596   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -1.032  -4.263   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      -0.262  -2.929   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0       1.278  -2.929   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       2.048  -4.263   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0      -1.032  -1.595   0.000  0.00  0.00           O+0
HETATM   62  C   UNK     0      -0.262  -0.262   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      -1.032  -6.930   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      -3.602  -8.453   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      -5.009  -9.079   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      -4.848 -10.611   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      -1.802 -13.598   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      -1.032 -14.932   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0       0.508 -14.932   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      -1.802 -16.266   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0       1.278 -16.266   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0       3.560 -17.582   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0       2.020 -17.549   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0       4.300 -18.932   0.000  0.00  0.00           C+0
HETATM   75  O   UNK     0       6.674 -14.885   0.000  0.00  0.00           O+0
HETATM   76  C   UNK     0      10.518 -13.565   0.000  0.00  0.00           C+0
HETATM   77  C   UNK     0      11.259 -12.215   0.000  0.00  0.00           C+0
HETATM   78  C   UNK     0      11.317 -14.882   0.000  0.00  0.00           C+0
HETATM   79  C   UNK     0      10.576 -16.232   0.000  0.00  0.00           C+0
CONECT    1    2   30   76                                                  
CONECT    2    1    3   75                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   72                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   71                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   67                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   66                                                  
CONECT   18   17   19   64                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   63                                                  
CONECT   22   21   23   54                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27   53                                                  
CONECT   27   26   28   31                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28    1                                                       
CONECT   31   27   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   39                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36                                                            
CONECT   39   34   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41   44   47                                                  
CONECT   44   43   45   48                                                  
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   43                                                       
CONECT   48   44   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50                                                            
CONECT   53   26                                                            
CONECT   54   22   55                                                       
CONECT   55   54   56   60                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59   61                                                  
CONECT   59   58   60                                                       
CONECT   60   59   55                                                       
CONECT   61   58   62                                                       
CONECT   62   61                                                            
CONECT   63   21                                                            
CONECT   64   18   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   17                                                       
CONECT   67   14   68                                                       
CONECT   68   67   69   70                                                  
CONECT   69   68                                                            
CONECT   70   68                                                            
CONECT   71   10                                                            
CONECT   72    7   73   74                                                  
CONECT   73   72                                                            
CONECT   74   72                                                            
CONECT   75    2                                                            
CONECT   76    1   77   78                                                  
CONECT   77   76                                                            
CONECT   78   76   79                                                       
CONECT   79   78                                                            
MASTER        0    0    0    0    0    0    0    0   79    0  164    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅₇H₈₉N₇O₁₅

Average Mass

1112.3730 Da

Monoisotopic Mass

1111.64167 Da

IUPAC Name

(2R)-N-[(3S,6R,7S,10R,11S,15S,17S,20S,25aS)-10-[(2S)-butan-2-yl]-11-hydroxy-3-[(4-methoxyphenyl)methyl]-2,6,17-trimethyl-20-(2-methylpropyl)-1,4,8,13,16,18,21-heptaoxo-15-(propan-2-yl)-docosahydro-1H-pyrrolo[2,1-f]1,15-dioxa-4,7,10,20-tetraazacyclotricosan-7-yl]-2-{1-[(2R)-1-[(2S)-2-hydroxypropanoyl]pyrrolidin-2-yl]-N-methylformamido}-4-methylpentanamide

Traditional Name

(2R)-N-[(3S,6R,7S,10R,11S,15S,17S,20S,25aS)-10-[(2S)-butan-2-yl]-11-hydroxy-15-isopropyl-3-[(4-methoxyphenyl)methyl]-2,6,17-trimethyl-20-(2-methylpropyl)-1,4,8,13,16,18,21-heptaoxo-tetradecahydro-3H-pyrrolo[2,1-f]1,15-dioxa-4,7,10,20-tetraazacyclotricosan-7-yl]-2-{1-[(2R)-1-[(2S)-2-hydroxypropanoyl]pyrrolidin-2-yl]-N-methylformamido}-4-methylpentanamide

CAS Registry Number

Not Available

SMILES

CC[C@H](C)[C@H]1NC(=O)[C@@H](NC(=O)[C@@H](CC(C)C)N(C)C(=O)[C@H]2CCCN2C(=O)[C@H](C)O)[C@@H](C)OC(=O)[C@H](CC2=CC=C(OC)C=C2)N(C)C(=O)[C@@H]2CCCN2C(=O)[C@H](CC(C)C)NC(=O)[C@@H](C)C(=O)[C@@H](OC(=O)C[C@@H]1O)C(C)C

InChI Identifier

InChI=1S/C57H89N7O15/c1-15-33(8)46-44(66)29-45(67)79-49(32(6)7)48(68)34(9)50(69)58-39(26-30(2)3)54(73)64-25-17-19-41(64)56(75)62(13)43(28-37-20-22-38(77-14)23-21-37)57(76)78-36(11)47(52(71)59-46)60-51(70)42(27-31(4)5)61(12)55(74)40-18-16-24-63(40)53(72)35(10)65/h20-23,30-36,39-44,46-47,49,65-66H,15-19,24-29H2,1-14H3,(H,58,69)(H,59,71)(H,60,70)/t33-,34-,35-,36+,39-,40+,41-,42+,43-,44-,46+,47-,49-/m0/s1

InChI Key

KYHUYMLIVQFXRI-CYJDUVKTSA-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
Trididemnum solidum	Animalia	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Depsipeptides

Direct Parent

Cyclic depsipeptides

Alternative Parents

Substituents

Cyclic depsipeptide
Leucine or derivatives
Macrolide lactam
Proline or derivatives
N-acyl-alpha amino acid or derivatives
Macrolactam
Alpha-amino acid ester
Alpha-amino acid amide
Alpha-amino acid or derivatives
Phenoxy compound
Methoxybenzene
Pyrrolidine-2-carboxamide
Pyrrolidine carboxylic acid or derivatives
Phenol ether
N-acylpyrrolidine
Anisole
Alpha-acyloxy ketone
Alkyl aryl ether
Fatty acyl
Benzenoid
1,3-dicarbonyl compound
N-acyl-amine
Fatty amide
Dicarboxylic acid or derivatives
Monocyclic benzene moiety
Tertiary carboxylic acid amide
Pyrrolidine
Cyclic ketone
Secondary carboxylic acid amide
Secondary alcohol
Lactone
Lactam
Ketone
Carboxylic acid ester
Carboxamide group
Oxacycle
Azacycle
Organoheterocyclic compound
Ether
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	3.07	ALOGPS
logP	3.44	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	10.88	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	287.9 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	288.99 m³·mol⁻¹	ChemAxon
Polarizability	118.87 Å³	ChemAxon
Number of Rings	4	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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

89382237

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Didemnin B (NP0079887)

MOL for NP0079887 (Didemnin B)

3D MOL for NP0079887 (Didemnin B)

3D SDF for NP0079887 (Didemnin B)

3D-SDF for NP0079887 (Didemnin B)

PDB for NP0079887 (Didemnin B)

3D PDB for NP0079887 (Didemnin B)

SMILES for NP0079887 (Didemnin B)

INCHI for NP0079887 (Didemnin B)

Structure for NP0079887 (Didemnin B)

3D Structure for NP0079887 (Didemnin B)