NP-MRD: Showing NP-Card for Abyssomicin 5 (NP0013639)

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Record Information

Version

1.0

Created at

2021-01-05 22:56:57 UTC

Updated at

2021-07-15 17:15:03 UTC

NP-MRD ID

NP0013639

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Abyssomicin 5

Provided By

NPAtlas

Description

Abyssomicin 5 is found in Streptomyces sp. It was first documented in 2005 (PMID: 16235927). Based on a literature review very few articles have been published on (1S,4S,5R,7S,14S)-2,4,10-trihydroxy-1,7,16-trimethyl-13,17-dioxapentacyclo[9.5.2.0³,¹⁴.0⁵,¹⁸.0¹⁴,¹⁸]Octadec-10-ene-6,12-dione (PMID: 25560385) (PMID: 30070834) (PMID: 31788711) (PMID: 26975378) (PMID: 21989685) (PMID: 19028103).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242119383D          

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M  END

     RDKit          3D

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  Mrv1652306242119383D          

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   -2.6019    2.2233   -1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0004    2.9439    0.0350 H   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  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 26 25  1  6  0  0  0
 23  2  1  0  0  0  0
 20  4  1  0  0  0  0
 26  4  1  0  0  0  0
 26  8  1  0  0  0  0
 26 17  1  0  0  0  0
  1 27  1  0  0  0  0
  1 28  1  0  0  0  0
  1 29  1  0  0  0  0
  2 30  1  1  0  0  0
  3 31  1  0  0  0  0
  3 32  1  0  0  0  0
 10 33  1  0  0  0  0
 11 34  1  0  0  0  0
 11 35  1  0  0  0  0
 12 36  1  0  0  0  0
 12 37  1  0  0  0  0
 13 38  1  6  0  0  0
 14 39  1  0  0  0  0
 14 40  1  0  0  0  0
 14 41  1  0  0  0  0
 17 42  1  1  0  0  0
 18 43  1  1  0  0  0
 19 44  1  0  0  0  0
 20 45  1  1  0  0  0
 21 46  1  6  0  0  0
 22 47  1  0  0  0  0
 24 48  1  0  0  0  0
 24 49  1  0  0  0  0
 24 50  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0013639

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O\C1=C2/C(=O)O[C@]34C([H])([H])[C@]([H])(C([H])([H])[H])[C@@]5(O[C@]23[C@]([H])(C(=O)[C@@]([H])(C([H])([H])[H])C([H])([H])C1([H])[H])[C@@]([H])(O[H])[C@@]4([H])[C@]5([H])O[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C19H24O7/c1-7-4-5-9(20)10-16(24)25-18-6-8(2)17(3)15(23)12(18)14(22)11(13(7)21)19(10,18)26-17/h7-8,11-12,14-15,20,22-23H,4-6H2,1-3H3/b10-9+/t7-,8-,11+,12-,14+,15-,17-,18-,19-/m0/s1

> <INCHI_KEY>
WXMZHRVVOZXDJP-YQQCXHNNSA-N

> <FORMULA>
C19H24O7

> <MOLECULAR_WEIGHT>
364.394

> <EXACT_MASS>
364.152203113

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
35.24669762851313

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,4S,5R,7S,14R)-2,4,10-trihydroxy-1,7,16-trimethyl-13,17-dioxapentacyclo[9.5.2.0^{3,14}.0^{5,18}.0^{14,18}]octadec-10-ene-6,12-dione

> <ALOGPS_LOGP>
0.40

> <JCHEM_LOGP>
0.3634228069999993

> <ALOGPS_LOGS>
-1.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.134058862133948

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.277540157476016

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1379909759138815

> <JCHEM_POLAR_SURFACE_AREA>
113.29

> <JCHEM_REFRACTIVITY>
88.47050000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.63e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4S,5R,7S,14R)-2,4,10-trihydroxy-1,7,16-trimethyl-13,17-dioxapentacyclo[9.5.2.0^{3,14}.0^{5,18}.0^{14,18}]octadec-10-ene-6,12-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 50 54  0  0  0  0  0  0  0  0999 V2000
   -4.0440   -0.1031   -1.2708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2088   -0.2706   -0.0311 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4085   -1.5441   -0.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0878   -1.3108    0.6482 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3760   -2.5256    0.6878 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1610   -2.6145   -0.6264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2363   -3.6139   -1.3657 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6279   -1.2550   -0.9554 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6368   -1.1405   -1.7822 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0799   -2.3758   -2.2060 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4323    0.0041   -2.3766 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6090    0.2945   -1.4414 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1718    0.9943   -0.1876 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3178    1.1516    0.7944 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1018    0.1765    0.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5163   -0.9082    0.8118 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6667    0.3776    0.8073 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3449   -0.2363    2.1393 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5093    0.6399    3.1953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1568   -0.5262    1.9003 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7465    0.8351    1.5113 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9847    0.9864    2.2024 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1319    0.8316    0.0518 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6574    2.1562   -0.3813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0817    0.4706   -0.8187 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2179   -0.3702   -0.1888 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0400   -0.5463   -1.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1948    0.9416   -1.5628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5931   -0.7144   -2.1041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8144   -0.2633    0.8992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9331   -2.4144    0.3366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1719   -1.7560   -1.1231 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8446   -2.4433   -2.8876 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8038   -0.2869   -3.3575 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8325    0.9203   -2.4418 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3369    0.8550   -2.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0918   -0.6577   -1.1349 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7859    2.0203   -0.3857 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9508    1.7712    1.6411 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1911    1.6197    0.3203 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6033    0.1698    1.2332 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4745    1.4715    0.7464 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8793   -1.1782    2.2567 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5974    1.5707    2.8724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6341   -0.9782    2.7563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1538    1.6843    1.8217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8694    0.6633    3.1240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6945    2.2598   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6019    2.2233   -1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0004    2.9439    0.0350 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  1
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  6
 23 25  1  0
 26 25  1  6
 23  2  1  0
 20  4  1  0
 26  4  1  0
 26  8  1  0
 26 17  1  0
  1 27  1  0
  1 28  1  0
  1 29  1  0
  2 30  1  1
  3 31  1  0
  3 32  1  0
 10 33  1  0
 11 34  1  0
 11 35  1  0
 12 36  1  0
 12 37  1  0
 13 38  1  6
 14 39  1  0
 14 40  1  0
 14 41  1  0
 17 42  1  1
 18 43  1  1
 19 44  1  0
 20 45  1  1
 21 46  1  6
 22 47  1  0
 24 48  1  0
 24 49  1  0
 24 50  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      -4.044  -0.103  -1.271  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.209  -0.271  -0.031  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.409  -1.544  -0.043  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.088  -1.311   0.648  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.376  -2.526   0.688  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.161  -2.615  -0.626  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.236  -3.614  -1.366  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.628  -1.255  -0.955  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.637  -1.141  -1.782  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.080  -2.376  -2.206  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.432   0.004  -2.377  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.609   0.295  -1.441  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.172   0.994  -0.188  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.318   1.152   0.794  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.102   0.177   0.473  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.516  -0.908   0.812  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.667   0.378   0.807  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.345  -0.236   2.139  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.509   0.640   3.195  0.00  0.00           O+0
HETATM   20  C   UNK     0      -1.157  -0.526   1.900  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.746   0.835   1.511  0.00  0.00           C+0
HETATM   22  O   UNK     0      -2.985   0.986   2.202  0.00  0.00           O+0
HETATM   23  C   UNK     0      -2.132   0.832   0.052  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.657   2.156  -0.381  0.00  0.00           C+0
HETATM   25  O   UNK     0      -1.082   0.471  -0.819  0.00  0.00           O+0
HETATM   26  C   UNK     0      -0.218  -0.370  -0.189  0.00  0.00           C+0
HETATM   27  H   UNK     0      -5.040  -0.546  -1.059  0.00  0.00           H+0
HETATM   28  H   UNK     0      -4.195   0.942  -1.563  0.00  0.00           H+0
HETATM   29  H   UNK     0      -3.593  -0.714  -2.104  0.00  0.00           H+0
HETATM   30  H   UNK     0      -3.814  -0.263   0.899  0.00  0.00           H+0
HETATM   31  H   UNK     0      -2.933  -2.414   0.337  0.00  0.00           H+0
HETATM   32  H   UNK     0      -2.172  -1.756  -1.123  0.00  0.00           H+0
HETATM   33  H   UNK     0       2.845  -2.443  -2.888  0.00  0.00           H+0
HETATM   34  H   UNK     0       2.804  -0.287  -3.357  0.00  0.00           H+0
HETATM   35  H   UNK     0       1.833   0.920  -2.442  0.00  0.00           H+0
HETATM   36  H   UNK     0       4.337   0.855  -2.029  0.00  0.00           H+0
HETATM   37  H   UNK     0       4.092  -0.658  -1.135  0.00  0.00           H+0
HETATM   38  H   UNK     0       2.786   2.020  -0.386  0.00  0.00           H+0
HETATM   39  H   UNK     0       3.951   1.771   1.641  0.00  0.00           H+0
HETATM   40  H   UNK     0       5.191   1.620   0.320  0.00  0.00           H+0
HETATM   41  H   UNK     0       4.603   0.170   1.233  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.475   1.472   0.746  0.00  0.00           H+0
HETATM   43  H   UNK     0       0.879  -1.178   2.257  0.00  0.00           H+0
HETATM   44  H   UNK     0       0.597   1.571   2.872  0.00  0.00           H+0
HETATM   45  H   UNK     0      -1.634  -0.978   2.756  0.00  0.00           H+0
HETATM   46  H   UNK     0      -1.154   1.684   1.822  0.00  0.00           H+0
HETATM   47  H   UNK     0      -2.869   0.663   3.124  0.00  0.00           H+0
HETATM   48  H   UNK     0      -3.695   2.260  -0.012  0.00  0.00           H+0
HETATM   49  H   UNK     0      -2.602   2.223  -1.492  0.00  0.00           H+0
HETATM   50  H   UNK     0      -2.000   2.944   0.035  0.00  0.00           H+0
CONECT    1    2   27   28   29                                             
CONECT    2    1    3   23   30                                             
CONECT    3    2    4   31   32                                             
CONECT    4    3    5   20   26                                             
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   26                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9   33                                                       
CONECT   11    9   12   34   35                                             
CONECT   12   11   13   36   37                                             
CONECT   13   12   14   15   38                                             
CONECT   14   13   39   40   41                                             
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   26   42                                             
CONECT   18   17   19   20   43                                             
CONECT   19   18   44                                                       
CONECT   20   18   21    4   45                                             
CONECT   21   20   22   23   46                                             
CONECT   22   21   47                                                       
CONECT   23   21   24   25    2                                             
CONECT   24   23   48   49   50                                             
CONECT   25   23   26                                                       
CONECT   26   25    4    8   17                                             
CONECT   27    1                                                            
CONECT   28    1                                                            
CONECT   29    1                                                            
CONECT   30    2                                                            
CONECT   31    3                                                            
CONECT   32    3                                                            
CONECT   33   10                                                            
CONECT   34   11                                                            
CONECT   35   11                                                            
CONECT   36   12                                                            
CONECT   37   12                                                            
CONECT   38   13                                                            
CONECT   39   14                                                            
CONECT   40   14                                                            
CONECT   41   14                                                            
CONECT   42   17                                                            
CONECT   43   18                                                            
CONECT   44   19                                                            
CONECT   45   20                                                            
CONECT   46   21                                                            
CONECT   47   22                                                            
CONECT   48   24                                                            
CONECT   49   24                                                            
CONECT   50   24                                                            
MASTER        0    0    0    0    0    0    0    0   50    0  108    0
END

RDKit          3D

50 54  0  0  0  0  0  0  0  0999 V2000
   -4.0440   -0.1031   -1.2708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2088   -0.2706   -0.0311 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4085   -1.5441   -0.0431 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0878   -1.3108    0.6482 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3760   -2.5256    0.6878 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1610   -2.6145   -0.6264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2363   -3.6139   -1.3657 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6279   -1.2550   -0.9554 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6368   -1.1405   -1.7822 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0799   -2.3758   -2.2060 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4323    0.0041   -2.3766 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6090    0.2945   -1.4414 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1718    0.9943   -0.1876 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3178    1.1516    0.7944 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1018    0.1765    0.4725 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5163   -0.9082    0.8118 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6667    0.3776    0.8073 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3449   -0.2363    2.1393 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5093    0.6399    3.1953 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1568   -0.5262    1.9003 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7465    0.8351    1.5113 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9847    0.9864    2.2024 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1319    0.8316    0.0518 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6574    2.1562   -0.3813 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0817    0.4706   -0.8187 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2179   -0.3702   -0.1888 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0400   -0.5463   -1.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1948    0.9416   -1.5628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5931   -0.7144   -2.1041 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8144   -0.2633    0.8992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9331   -2.4144    0.3366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1719   -1.7560   -1.1231 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8446   -2.4433   -2.8876 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8038   -0.2869   -3.3575 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8325    0.9203   -2.4418 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3369    0.8550   -2.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0918   -0.6577   -1.1349 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7859    2.0203   -0.3857 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9508    1.7712    1.6411 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1911    1.6197    0.3203 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6033    0.1698    1.2332 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4745    1.4715    0.7464 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8793   -1.1782    2.2567 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5974    1.5707    2.8724 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6341   -0.9782    2.7563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1538    1.6843    1.8217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8694    0.6633    3.1240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6945    2.2598   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6019    2.2233   -1.4924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0004    2.9439    0.0350 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  1
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  6
 23 25  1  0
 26 25  1  6
 23  2  1  0
 20  4  1  0
 26  4  1  0
 26  8  1  0
 26 17  1  0
  1 27  1  0
  1 28  1  0
  1 29  1  0
  2 30  1  1
  3 31  1  0
  3 32  1  0
 10 33  1  0
 11 34  1  0
 11 35  1  0
 12 36  1  0
 12 37  1  0
 13 38  1  6
 14 39  1  0
 14 40  1  0
 14 41  1  0
 17 42  1  1
 18 43  1  1
 19 44  1  0
 20 45  1  1
 21 46  1  6
 22 47  1  0
 24 48  1  0
 24 49  1  0
 24 50  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₁₉H₂₄O₇

Average Mass

364.3940 Da

Monoisotopic Mass

364.15220 Da

IUPAC Name

(1S,4S,5R,7S,14R)-2,4,10-trihydroxy-1,7,16-trimethyl-13,17-dioxapentacyclo[9.5.2.0^{3,14}.0^{5,18}.0^{14,18}]octadec-10-ene-6,12-dione

Traditional Name

(1S,4S,5R,7S,14R)-2,4,10-trihydroxy-1,7,16-trimethyl-13,17-dioxapentacyclo[9.5.2.0^{3,14}.0^{5,18}.0^{14,18}]octadec-10-ene-6,12-dione

CAS Registry Number

Not Available

SMILES

CC1C[C@@]23OC(=O)\C4=C(O)\CC[C@H](C)C(=O)[C@@H]5[C@@H](O)C2C(O)[C@@]1(C)OC345

InChI Identifier

InChI=1S/C19H24O7/c1-7-4-5-9(20)10-16(24)25-18-6-8(2)17(3)15(23)12(18)14(22)11(13(7)21)19(10,18)26-17/h7-8,11-12,14-15,20,22-23H,4-6H2,1-3H3/b10-9+/t7-,8?,11+,12?,14+,15?,17-,18-,19?/m0/s1

InChI Key

WXMZHRVVOZXDJP-YQQCXHNNSA-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.	NPAtlas	25560385

Chemical Taxonomy

Classification

Not classified

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	0.4	ALOGPS
logP	0.36	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	9.28	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.29 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	88.47 m³·mol⁻¹	ChemAxon
Polarizability	35.25 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

NPA028397

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

146684553

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Leon B, Navarro G, Dickey BJ, Stepan G, Tsai A, Jones GS, Morales ME, Barnes T, Ahmadyar S, Tsiang M, Geleziunas R, Cihlar T, Pagratis N, Tian Y, Yu H, Linington RG: Abyssomicin 2 reactivates latent HIV-1 by a PKC- and HDAC-independent mechanism. Org Lett. 2015 Jan 16;17(2):262-5. doi: 10.1021/ol503349y. Epub 2015 Jan 5. [PubMed:25560385 ]
Huang H, Song Y, Li X, Wang X, Ling C, Qin X, Zhou Z, Li Q, Wei X, Ju J: Abyssomicin Monomers and Dimers from the Marine-Derived Streptomyces koyangensis SCSIO 5802. J Nat Prod. 2018 Aug 24;81(8):1892-1898. doi: 10.1021/acs.jnatprod.8b00448. Epub 2018 Aug 2. [PubMed:30070834 ]
Wang Q, Xie F, Tong Y, Habisch R, Yang B, Zhang L, Muller R, Fu C: Dual-function chromogenic screening-based CRISPR/Cas9 genome editing system for actinomycetes. Appl Microbiol Biotechnol. 2020 Jan;104(1):225-239. doi: 10.1007/s00253-019-10223-4. Epub 2019 Dec 2. [PubMed:31788711 ]
Huang P, Xie F, Ren B, Wang Q, Wang J, Wang Q, Abdel-Mageed WM, Liu M, Han J, Oyeleye A, Shen J, Song F, Dai H, Liu X, Zhang L: Anti-MRSA and anti-TB metabolites from marine-derived Verrucosispora sp. MS100047. Appl Microbiol Biotechnol. 2016 Sep;100(17):7437-47. doi: 10.1007/s00253-016-7406-y. Epub 2016 Mar 15. [PubMed:26975378 ]
Goodfellow M, Stach JE, Brown R, Bonda AN, Jones AL, Mexson J, Fiedler HP, Zucchi TD, Bull AT: Verrucosispora maris sp. nov., a novel deep-sea actinomycete isolated from a marine sediment which produces abyssomicins. Antonie Van Leeuwenhoek. 2012 Jan;101(1):185-93. doi: 10.1007/s10482-011-9651-5. Epub 2011 Oct 12. [PubMed:21989685 ]
Nicolaou KC, Chen JS, Dalby SM: From nature to the laboratory and into the clinic. Bioorg Med Chem. 2009 Mar 15;17(6):2290-303. doi: 10.1016/j.bmc.2008.10.089. Epub 2008 Nov 6. [PubMed:19028103 ]
Snider BB, Zou Y: Synthesis of the carbocyclic skeleton of abyssomicins C and D. Org Lett. 2005 Oct 27;7(22):4939-41. doi: 10.1021/ol0518941. [PubMed:16235927 ]

Showing NP-Card for Abyssomicin 5 (NP0013639)

MOL for NP0013639 (Abyssomicin 5)

3D MOL for NP0013639 (Abyssomicin 5)

3D SDF for NP0013639 (Abyssomicin 5)

3D-SDF for NP0013639 (Abyssomicin 5)

PDB for NP0013639 (Abyssomicin 5)

3D PDB for NP0013639 (Abyssomicin 5)

SMILES for NP0013639 (Abyssomicin 5)

INCHI for NP0013639 (Abyssomicin 5)

Structure for NP0013639 (Abyssomicin 5)

3D Structure for NP0013639 (Abyssomicin 5)