NP-MRD: Showing NP-Card for Oridamycin B (NP0009106)

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Record Information

Version

2.0

Created at

2020-12-09 06:33:25 UTC

Updated at

2021-07-15 17:02:19 UTC

NP-MRD ID

NP0009106

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Oridamycin B

Provided By

NPAtlas

Description

Oridamycin B belongs to the class of organic compounds known as steroid acids. Steroid acids are compounds containing a carboxyl group attached to a steroid backbone. Oridamycin B is found in Streptomyces sp. KS84. Oridamycin B was first documented in 2015 (PMID: 26069989). Based on a literature review very few articles have been published on Oridamycin B (PMID: 29171266) (PMID: 25648883).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242106323D          

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   -2.4804   -0.8016    2.5913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3267   -0.6516    3.4433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0663   -2.2659    2.8170 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2023   -2.1344    2.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7949   -2.1089    1.3487 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9919   -1.4042   -0.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6681    0.0806   -2.1418 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9790    1.5833   -3.0818 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6367    1.6279   -2.1984 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3711    1.2887   -0.9339 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7 10  1  1  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  7 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 13  2  1  0  0  0  0
 28 16  1  0  0  0  0
 28  2  1  0  0  0  0
 26 18  2  0  0  0  0
 25 20  1  0  0  0  0
  1 29  1  0  0  0  0
  1 30  1  0  0  0  0
  1 31  1  0  0  0  0
  3 32  1  0  0  0  0
  3 33  1  0  0  0  0
  4 34  1  0  0  0  0
  4 35  1  0  0  0  0
  5 36  1  6  0  0  0
  6 37  1  0  0  0  0
  8 38  1  0  0  0  0
  8 39  1  0  0  0  0
  9 40  1  0  0  0  0
 12 41  1  0  0  0  0
 13 42  1  6  0  0  0
 14 43  1  0  0  0  0
 14 44  1  0  0  0  0
 15 45  1  0  0  0  0
 15 46  1  0  0  0  0
 17 47  1  0  0  0  0
 19 48  1  0  0  0  0
 21 49  1  0  0  0  0
 22 50  1  0  0  0  0
 23 51  1  0  0  0  0
 24 52  1  0  0  0  0
 27 53  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0009106

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@@]1(C([H])([H])O[H])[C@@]([H])(O[H])C([H])([H])C([H])([H])[C@@]2(C3=C([H])C4=C(N([H])C5=C([H])C([H])=C([H])C([H])=C45)C([H])=C3C([H])([H])C([H])([H])[C@@]12[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C23H25NO4/c1-22-9-8-20(26)23(12-25,21(27)28)19(22)7-6-13-10-18-15(11-16(13)22)14-4-2-3-5-17(14)24-18/h2-5,10-11,19-20,24-26H,6-9,12H2,1H3,(H,27,28)/t19-,20+,22-,23-/m1/s1

> <INCHI_KEY>
OLMKVWKEEMDZBW-IRMYBRCSSA-N

> <FORMULA>
C23H25NO4

> <MOLECULAR_WEIGHT>
379.456

> <EXACT_MASS>
379.178358289

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
41.71391801847568

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,4S,4aR,13bS)-3-hydroxy-4-(hydroxymethyl)-13b-methyl-1H,2H,3H,4H,4aH,5H,6H,8H,13bH-naphtho[2,1-b]carbazole-4-carboxylic acid

> <ALOGPS_LOGP>
3.16

> <JCHEM_LOGP>
3.1098132269999996

> <ALOGPS_LOGS>
-4.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.39370996177923

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.422394927591087

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8922117017192113

> <JCHEM_POLAR_SURFACE_AREA>
93.55000000000001

> <JCHEM_REFRACTIVITY>
105.95760000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.46e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
oridamycin B

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 53 57  0  0  0  0  0  0  0  0999 V2000
   -1.0171    1.5493    1.8085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8700    0.7106    0.5623 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0396    1.5236   -0.6715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4344    2.0214   -0.7962 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5090    1.1600   -0.2565 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1990    1.7465    0.8165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1338   -0.2798   -0.0052 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2075   -0.9408   -1.4081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4909   -0.8238   -1.9203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2346   -0.8932    0.7393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2550   -0.2148    0.9870 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2628   -2.1951    1.2136 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7767   -0.5081    0.5453 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7349   -1.2123    1.8695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3523   -1.2258    2.4638 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7315   -0.8073    1.5687 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0082   -1.3661    1.6602 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0474   -0.9915    0.8452 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3364   -1.3866    0.7564 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9673   -0.7041   -0.2264 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2654   -0.7352   -0.7092 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6429    0.0908   -1.7452 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6839    0.9335   -2.2676 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3907    0.9670   -1.7894 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0149    0.1442   -0.7575 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8146   -0.0177   -0.1066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5486    0.5342   -0.1952 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5190    0.1568    0.6188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6703    1.1272    2.5680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0452    1.7973    2.2827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4474    2.5476    1.5023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6812    0.9745   -1.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3814    2.4359   -0.5951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5293    3.0240   -0.2807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5822    2.2879   -1.8849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3123    1.1260   -1.0618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8669    1.4864    1.6825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4517   -0.5307   -2.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0008   -2.0224   -1.2761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4307   -0.1900   -2.6978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6034   -2.9869    0.7073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2406   -1.2270   -0.1539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9805   -2.2993    1.6686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4804   -0.8016    2.5913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3267   -0.6516    3.4433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0663   -2.2659    2.8170 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2023   -2.1344    2.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7949   -2.1089    1.3487 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9919   -1.4042   -0.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6681    0.0806   -2.1418 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9790    1.5833   -3.0818 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6367    1.6279   -2.1984 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3711    1.2887   -0.9339 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  7 10  1  1
 10 11  2  0
 10 12  1  0
  7 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  1  0
 27 28  2  0
 13  2  1  0
 28 16  1  0
 28  2  1  0
 26 18  2  0
 25 20  1  0
  1 29  1  0
  1 30  1  0
  1 31  1  0
  3 32  1  0
  3 33  1  0
  4 34  1  0
  4 35  1  0
  5 36  1  6
  6 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
 12 41  1  0
 13 42  1  6
 14 43  1  0
 14 44  1  0
 15 45  1  0
 15 46  1  0
 17 47  1  0
 19 48  1  0
 21 49  1  0
 22 50  1  0
 23 51  1  0
 24 52  1  0
 27 53  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0      -1.017   1.549   1.809  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.870   0.711   0.562  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.040   1.524  -0.672  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.434   2.021  -0.796  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.509   1.160  -0.257  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.199   1.746   0.817  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.134  -0.280  -0.005  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.208  -0.941  -1.408  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.491  -0.824  -1.920  0.00  0.00           O+0
HETATM   10  C   UNK     0      -4.235  -0.893   0.739  0.00  0.00           C+0
HETATM   11  O   UNK     0      -5.255  -0.215   0.987  0.00  0.00           O+0
HETATM   12  O   UNK     0      -4.263  -2.195   1.214  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.777  -0.508   0.545  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.735  -1.212   1.869  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.352  -1.226   2.464  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.732  -0.807   1.569  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.008  -1.366   1.660  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.047  -0.992   0.845  0.00  0.00           C+0
HETATM   19  N   UNK     0       4.336  -1.387   0.756  0.00  0.00           N+0
HETATM   20  C   UNK     0       4.967  -0.704  -0.226  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.265  -0.735  -0.709  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.643   0.091  -1.745  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.684   0.934  -2.268  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.391   0.967  -1.789  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.015   0.144  -0.758  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.815  -0.018  -0.107  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.549   0.534  -0.195  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.519   0.157   0.619  0.00  0.00           C+0
HETATM   29  H   UNK     0      -1.670   1.127   2.568  0.00  0.00           H+0
HETATM   30  H   UNK     0      -0.045   1.797   2.283  0.00  0.00           H+0
HETATM   31  H   UNK     0      -1.447   2.548   1.502  0.00  0.00           H+0
HETATM   32  H   UNK     0      -0.681   0.975  -1.566  0.00  0.00           H+0
HETATM   33  H   UNK     0      -0.381   2.436  -0.595  0.00  0.00           H+0
HETATM   34  H   UNK     0      -2.529   3.024  -0.281  0.00  0.00           H+0
HETATM   35  H   UNK     0      -2.582   2.288  -1.885  0.00  0.00           H+0
HETATM   36  H   UNK     0      -4.312   1.126  -1.062  0.00  0.00           H+0
HETATM   37  H   UNK     0      -3.867   1.486   1.683  0.00  0.00           H+0
HETATM   38  H   UNK     0      -2.452  -0.531  -2.089  0.00  0.00           H+0
HETATM   39  H   UNK     0      -3.001  -2.022  -1.276  0.00  0.00           H+0
HETATM   40  H   UNK     0      -4.431  -0.190  -2.698  0.00  0.00           H+0
HETATM   41  H   UNK     0      -4.603  -2.987   0.707  0.00  0.00           H+0
HETATM   42  H   UNK     0      -1.241  -1.227  -0.154  0.00  0.00           H+0
HETATM   43  H   UNK     0      -1.980  -2.299   1.669  0.00  0.00           H+0
HETATM   44  H   UNK     0      -2.480  -0.802   2.591  0.00  0.00           H+0
HETATM   45  H   UNK     0      -0.327  -0.652   3.443  0.00  0.00           H+0
HETATM   46  H   UNK     0      -0.066  -2.266   2.817  0.00  0.00           H+0
HETATM   47  H   UNK     0       2.202  -2.134   2.407  0.00  0.00           H+0
HETATM   48  H   UNK     0       4.795  -2.109   1.349  0.00  0.00           H+0
HETATM   49  H   UNK     0       6.992  -1.404  -0.281  0.00  0.00           H+0
HETATM   50  H   UNK     0       7.668   0.081  -2.142  0.00  0.00           H+0
HETATM   51  H   UNK     0       5.979   1.583  -3.082  0.00  0.00           H+0
HETATM   52  H   UNK     0       3.637   1.628  -2.198  0.00  0.00           H+0
HETATM   53  H   UNK     0       1.371   1.289  -0.934  0.00  0.00           H+0
CONECT    1    2   29   30   31                                             
CONECT    2    1    3   13   28                                             
CONECT    3    2    4   32   33                                             
CONECT    4    3    5   34   35                                             
CONECT    5    4    6    7   36                                             
CONECT    6    5   37                                                       
CONECT    7    5    8   10   13                                             
CONECT    8    7    9   38   39                                             
CONECT    9    8   40                                                       
CONECT   10    7   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   41                                                       
CONECT   13    7   14    2   42                                             
CONECT   14   13   15   43   44                                             
CONECT   15   14   16   45   46                                             
CONECT   16   15   17   28                                                  
CONECT   17   16   18   47                                                  
CONECT   18   17   19   26                                                  
CONECT   19   18   20   48                                                  
CONECT   20   19   21   25                                                  
CONECT   21   20   22   49                                                  
CONECT   22   21   23   50                                                  
CONECT   23   22   24   51                                                  
CONECT   24   23   25   52                                                  
CONECT   25   24   26   20                                                  
CONECT   26   25   27   18                                                  
CONECT   27   26   28   53                                                  
CONECT   28   27   16    2                                                  
CONECT   29    1                                                            
CONECT   30    1                                                            
CONECT   31    1                                                            
CONECT   32    3                                                            
CONECT   33    3                                                            
CONECT   34    4                                                            
CONECT   35    4                                                            
CONECT   36    5                                                            
CONECT   37    6                                                            
CONECT   38    8                                                            
CONECT   39    8                                                            
CONECT   40    9                                                            
CONECT   41   12                                                            
CONECT   42   13                                                            
CONECT   43   14                                                            
CONECT   44   14                                                            
CONECT   45   15                                                            
CONECT   46   15                                                            
CONECT   47   17                                                            
CONECT   48   19                                                            
CONECT   49   21                                                            
CONECT   50   22                                                            
CONECT   51   23                                                            
CONECT   52   24                                                            
CONECT   53   27                                                            
MASTER        0    0    0    0    0    0    0    0   53    0  114    0
END

RDKit          3D

53 57  0  0  0  0  0  0  0  0999 V2000
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   -0.3523   -1.2258    2.4638 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.3364   -1.3866    0.7564 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9673   -0.7041   -0.2264 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2654   -0.7352   -0.7092 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6429    0.0908   -1.7452 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6839    0.9335   -2.2676 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3907    0.9670   -1.7894 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0149    0.1442   -0.7575 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8146   -0.0177   -0.1066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5486    0.5342   -0.1952 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5190    0.1568    0.6188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6703    1.1272    2.5680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0452    1.7973    2.2827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4474    2.5476    1.5023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6812    0.9745   -1.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3814    2.4359   -0.5951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5293    3.0240   -0.2807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5822    2.2879   -1.8849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3123    1.1260   -1.0618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8669    1.4864    1.6825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4517   -0.5307   -2.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0008   -2.0224   -1.2761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4307   -0.1900   -2.6978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6034   -2.9869    0.7073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2406   -1.2270   -0.1539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9805   -2.2993    1.6686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4804   -0.8016    2.5913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3267   -0.6516    3.4433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0663   -2.2659    2.8170 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2023   -2.1344    2.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7949   -2.1089    1.3487 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9919   -1.4042   -0.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6681    0.0806   -2.1418 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9790    1.5833   -3.0818 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6367    1.6279   -2.1984 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3711    1.2887   -0.9339 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  7 10  1  1
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  7 13  1  0
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 15 16  1  0
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 22 23  2  0
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 26 27  1  0
 27 28  2  0
 13  2  1  0
 28 16  1  0
 28  2  1  0
 26 18  2  0
 25 20  1  0
  1 29  1  0
  1 30  1  0
  1 31  1  0
  3 32  1  0
  3 33  1  0
  4 34  1  0
  4 35  1  0
  5 36  1  6
  6 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
 12 41  1  0
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 14 43  1  0
 14 44  1  0
 15 45  1  0
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 17 47  1  0
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 22 50  1  0
 23 51  1  0
 24 52  1  0
 27 53  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(16R,17S,18S,21S)-18-Hydroxy-17-(hydroxymethyl)-21-methyl-10-azapentacyclo[11.8.0.0,.0,.0,]henicosa-1,3(11),4,6,8,12-hexaene-17-carboxylate	Generator

Chemical Formula

C₂₃H₂₅NO₄

Average Mass

379.4560 Da

Monoisotopic Mass

379.17836 Da

IUPAC Name

(3S,4S,4aR,13bS)-3-hydroxy-4-(hydroxymethyl)-13b-methyl-1H,2H,3H,4H,4aH,5H,6H,8H,13bH-naphtho[2,1-b]carbazole-4-carboxylic acid

Traditional Name

oridamycin B

CAS Registry Number

Not Available

SMILES

C[C@]12CC[C@H](O)[C@@](CO)([C@@H]1CCC1=C2C=C2C(NC3=CC=CC=C23)=C1)C(O)=O

InChI Identifier

InChI=1S/C23H25NO4/c1-22-9-8-20(26)23(12-25,21(27)28)19(22)7-6-13-10-18-15(11-16(13)22)14-4-2-3-5-17(14)24-18/h2-5,10-11,19-20,24-26H,6-9,12H2,1H3,(H,27,28)/t19-,20+,22-,23-/m1/s1

InChI Key

OLMKVWKEEMDZBW-IRMYBRCSSA-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
Streptomyces sp. KS84	NPAtlas	20369841

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroid acids. Steroid acids are compounds containing a carboxyl group attached to a steroid backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid acids

Direct Parent

Steroid acids

Alternative Parents

Substituents

Diterpenoid
Steroid acid
15-hydroxysteroid
Hydroxysteroid
Phenanthrene
Carbazole
Tetralin
Indole
Indole or derivatives
Beta-hydroxy acid
Hydroxy acid
Benzenoid
Cyclic alcohol
Heteroaromatic compound
Pyrrole
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Alcohol
Organic oxygen compound
Primary alcohol
Organooxygen compound
Carbonyl group
Organonitrogen compound
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	3.16	ALOGPS
logP	3.11	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	4.42	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	93.55 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	105.96 m³·mol⁻¹	ChemAxon
Polarizability	41.71 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA009191

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

35000172

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46211629

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Trotta AH: Toward a Unified Total Synthesis of the Xiamycin and Oridamycin Families of Indolosesquiterpenes. J Org Chem. 2017 Dec 15;82(24):13500-13516. doi: 10.1021/acs.joc.7b02623. Epub 2017 Dec 5. [PubMed:29171266 ]
Trotta AH: Total Synthesis of Oridamycins A and B. Org Lett. 2015 Jul 2;17(13):3358-61. doi: 10.1021/acs.orglett.5b01629. Epub 2015 Jun 12. [PubMed:26069989 ]
Meng Z, Yu H, Li L, Tao W, Chen H, Wan M, Yang P, Edmonds DJ, Zhong J, Li A: Total synthesis and antiviral activity of indolosesquiterpenoids from the xiamycin and oridamycin families. Nat Commun. 2015 Feb 4;6:6096. doi: 10.1038/ncomms7096. [PubMed:25648883 ]

Showing NP-Card for Oridamycin B (NP0009106)

MOL for NP0009106 (Oridamycin B)

3D MOL for NP0009106 (Oridamycin B)

3D SDF for NP0009106 (Oridamycin B)

3D-SDF for NP0009106 (Oridamycin B)

PDB for NP0009106 (Oridamycin B)

3D PDB for NP0009106 (Oridamycin B)

SMILES for NP0009106 (Oridamycin B)

INCHI for NP0009106 (Oridamycin B)

Structure for NP0009106 (Oridamycin B)

3D Structure for NP0009106 (Oridamycin B)