NP-MRD: Showing NP-Card for Lobatamide A (NP0021003)

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Record Information

Version

2.0

Created at

2021-01-06 06:19:04 UTC

Updated at

2021-07-15 17:35:12 UTC

NP-MRD ID

NP0021003

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lobatamide A

Provided By

NPAtlas

Description

Lobatamide A is found in Aplidium lobatum and Gynuella sunshinyii. Lobatamide A was first documented in 2020 (PMID: 32040255).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI

  Mrv1652306242120403D          

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M  END

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M  END

  Mrv1652306242120403D          

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    4.4091    0.6754   -0.7919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1301    1.2578   -0.4539 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.1263    0.8407   -0.6591 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -0.6556   -3.0697   -1.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
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  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
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 31 32  1  0  0  0  0
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 37 13  1  0  0  0  0
 34 28  1  0  0  0  0
  1 38  1  0  0  0  0
  1 39  1  0  0  0  0
  1 40  1  0  0  0  0
  4 41  1  0  0  0  0
  5 42  1  0  0  0  0
  6 43  1  0  0  0  0
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 30 67  1  0  0  0  0
 31 68  1  0  0  0  0
 33 69  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021003

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C2C(=C([H])C([H])=C1[H])C([H])([H])\C([H])=C(C([H])([H])[H])/[C@]([H])(O[H])\C([H])=C([H])/[C@]([H])(OC(=O)C([H])([H])[C@]([H])(OC2=O)C([H])([H])C(\[H])=C(/[H])N([H])C(=O)C(\[H])=C(\[H])/C(/[H])=N/OC([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C27H32N2O8/c1-18-11-13-20-7-4-9-23(31)26(20)27(34)37-21(17-25(33)36-19(2)12-14-22(18)30)8-5-15-28-24(32)10-6-16-29-35-3/h4-7,9-12,14-16,19,21-22,30-31H,8,13,17H2,1-3H3,(H,28,32)/b10-6-,14-12-,15-5+,18-11-,29-16+/t19-,21-,22-/m1/s1

> <INCHI_KEY>
JYHIHHYYXXKTTJ-ZZGNQKHNSA-N

> <FORMULA>
C27H32N2O8

> <MOLECULAR_WEIGHT>
512.559

> <EXACT_MASS>
512.215865998

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
53.96192925268034

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2Z,4E)-N-[(1E)-3-[(3R,7R,10R)-10,17-dihydroxy-7,11-dimethyl-1,5-dioxo-3,4,5,7,10,13-hexahydro-1H-2,6-benzodioxacyclopentadecin-3-yl]prop-1-en-1-yl]-4-(methoxyimino)but-2-enamide

> <ALOGPS_LOGP>
3.08

> <JCHEM_LOGP>
3.346063185

> <ALOGPS_LOGS>
-4.92

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.956094179571398

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.647552284153948

> <JCHEM_PKA_STRONGEST_BASIC>
3.7833978961500647

> <JCHEM_POLAR_SURFACE_AREA>
143.75

> <JCHEM_REFRACTIVITY>
140.08220000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.13e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2Z,4E)-N-[(1E)-3-[(3R,7R,10R)-10,17-dihydroxy-7,11-dimethyl-1,5-dioxo-4,7,10,13-tetrahydro-3H-2,6-benzodioxacyclopentadecin-3-yl]prop-1-en-1-yl]-4-(methoxyimino)but-2-enamide

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 69 70  0  0  0  0  0  0  0  0999 V2000
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  2  3  1  0
  3  4  2  0
  4  5  1  0
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 13 14  1  0
 14 15  1  0
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 17 18  1  0
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 29 30  1  0
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 31 32  1  0
 32 33  1  0
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 34 35  1  0
 35 36  2  0
 35 37  1  0
 37 13  1  0
 34 28  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  4 41  1  0
  5 42  1  0
  6 43  1  0
  9 44  1  0
 10 45  1  0
 11 46  1  0
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 27 65  1  0
 29 66  1  0
 30 67  1  0
 31 68  1  0
 33 69  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       7.327  -3.559   0.552  0.00  0.00           C+0
HETATM    2  O   UNK     0       6.076  -2.993   0.158  0.00  0.00           O+0
HETATM    3  N   UNK     0       6.114  -1.771  -0.444  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.086  -1.353  -1.111  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.404  -0.181  -1.823  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.674   0.860  -1.969  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.390   1.264  -1.544  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.141   2.486  -2.007  0.00  0.00           O+0
HETATM    9  N   UNK     0       4.409   0.675  -0.792  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.130   1.258  -0.454  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.654   2.417  -0.777  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.302   2.937  -0.378  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.398   1.936   0.277  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.126   0.841  -0.659  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.296  -0.493  -0.154  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.300  -0.750   0.967  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.115  -1.418  -0.596  0.00  0.00           O+0
HETATM   18  C   UNK     0      -1.500  -2.298  -1.622  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.353  -1.560  -2.912  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.722  -3.009  -1.380  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.896  -2.442  -1.199  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.959  -0.957  -1.251  0.00  0.00           C+0
HETATM   23  O   UNK     0      -4.471  -0.772  -2.596  0.00  0.00           O+0
HETATM   24  C   UNK     0      -5.042  -0.381  -0.472  0.00  0.00           C+0
HETATM   25  C   UNK     0      -6.414  -0.948  -0.726  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.870   0.572   0.401  0.00  0.00           C+0
HETATM   27  C   UNK     0      -3.587   1.143   0.672  0.00  0.00           C+0
HETATM   28  C   UNK     0      -3.114   1.050   2.132  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.803   0.110   2.853  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.493  -0.074   4.203  0.00  0.00           C+0
HETATM   31  C   UNK     0      -2.487   0.706   4.788  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.818   1.654   3.989  0.00  0.00           C+0
HETATM   33  O   UNK     0      -0.801   2.434   4.608  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.136   1.825   2.649  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.331   2.856   1.909  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.258   3.900   2.628  0.00  0.00           O+0
HETATM   37  O   UNK     0      -0.761   2.709   0.654  0.00  0.00           O+0
HETATM   38  H   UNK     0       7.176  -4.282   1.363  0.00  0.00           H+0
HETATM   39  H   UNK     0       8.009  -2.738   0.863  0.00  0.00           H+0
HETATM   40  H   UNK     0       7.780  -4.007  -0.366  0.00  0.00           H+0
HETATM   41  H   UNK     0       7.920  -2.128  -1.142  0.00  0.00           H+0
HETATM   42  H   UNK     0       8.437  -0.196  -2.313  0.00  0.00           H+0
HETATM   43  H   UNK     0       7.254   1.640  -2.621  0.00  0.00           H+0
HETATM   44  H   UNK     0       4.514  -0.273  -0.392  0.00  0.00           H+0
HETATM   45  H   UNK     0       2.471   0.647   0.184  0.00  0.00           H+0
HETATM   46  H   UNK     0       3.281   3.081  -1.394  0.00  0.00           H+0
HETATM   47  H   UNK     0       1.520   3.818   0.260  0.00  0.00           H+0
HETATM   48  H   UNK     0       0.828   3.385  -1.302  0.00  0.00           H+0
HETATM   49  H   UNK     0       0.946   1.520   1.138  0.00  0.00           H+0
HETATM   50  H   UNK     0      -0.788   1.188  -1.255  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.871   0.701  -1.453  0.00  0.00           H+0
HETATM   52  H   UNK     0      -0.656  -3.070  -1.636  0.00  0.00           H+0
HETATM   53  H   UNK     0      -2.173  -1.836  -3.648  0.00  0.00           H+0
HETATM   54  H   UNK     0      -0.447  -1.948  -3.430  0.00  0.00           H+0
HETATM   55  H   UNK     0      -1.190  -0.489  -2.853  0.00  0.00           H+0
HETATM   56  H   UNK     0      -2.632  -4.115  -1.350  0.00  0.00           H+0
HETATM   57  H   UNK     0      -4.752  -3.081  -1.022  0.00  0.00           H+0
HETATM   58  H   UNK     0      -3.047  -0.435  -1.368  0.00  0.00           H+0
HETATM   59  H   UNK     0      -4.606   0.204  -2.619  0.00  0.00           H+0
HETATM   60  H   UNK     0      -6.965  -1.130   0.207  0.00  0.00           H+0
HETATM   61  H   UNK     0      -7.022  -0.255  -1.340  0.00  0.00           H+0
HETATM   62  H   UNK     0      -6.376  -1.898  -1.292  0.00  0.00           H+0
HETATM   63  H   UNK     0      -5.781   0.927   0.933  0.00  0.00           H+0
HETATM   64  H   UNK     0      -3.714   2.274   0.591  0.00  0.00           H+0
HETATM   65  H   UNK     0      -2.771   0.933   0.014  0.00  0.00           H+0
HETATM   66  H   UNK     0      -4.583  -0.511   2.448  0.00  0.00           H+0
HETATM   67  H   UNK     0      -3.996  -0.792   4.820  0.00  0.00           H+0
HETATM   68  H   UNK     0      -2.217   0.592   5.836  0.00  0.00           H+0
HETATM   69  H   UNK     0      -0.595   2.292   5.564  0.00  0.00           H+0
CONECT    1    2   38   39   40                                             
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   41                                                  
CONECT    5    4    6   42                                                  
CONECT    6    5    7   43                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   44                                                  
CONECT   10    9   11   45                                                  
CONECT   11   10   12   46                                                  
CONECT   12   11   13   47   48                                             
CONECT   13   12   14   37   49                                             
CONECT   14   13   15   50   51                                             
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   20   52                                             
CONECT   19   18   53   54   55                                             
CONECT   20   18   21   56                                                  
CONECT   21   20   22   57                                                  
CONECT   22   21   23   24   58                                             
CONECT   23   22   59                                                       
CONECT   24   22   25   26                                                  
CONECT   25   24   60   61   62                                             
CONECT   26   24   27   63                                                  
CONECT   27   26   28   64   65                                             
CONECT   28   27   29   34                                                  
CONECT   29   28   30   66                                                  
CONECT   30   29   31   67                                                  
CONECT   31   30   32   68                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32   69                                                       
CONECT   34   32   35   28                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   13                                                       
CONECT   38    1                                                            
CONECT   39    1                                                            
CONECT   40    1                                                            
CONECT   41    4                                                            
CONECT   42    5                                                            
CONECT   43    6                                                            
CONECT   44    9                                                            
CONECT   45   10                                                            
CONECT   46   11                                                            
CONECT   47   12                                                            
CONECT   48   12                                                            
CONECT   49   13                                                            
CONECT   50   14                                                            
CONECT   51   14                                                            
CONECT   52   18                                                            
CONECT   53   19                                                            
CONECT   54   19                                                            
CONECT   55   19                                                            
CONECT   56   20                                                            
CONECT   57   21                                                            
CONECT   58   22                                                            
CONECT   59   23                                                            
CONECT   60   25                                                            
CONECT   61   25                                                            
CONECT   62   25                                                            
CONECT   63   26                                                            
CONECT   64   27                                                            
CONECT   65   27                                                            
CONECT   66   29                                                            
CONECT   67   30                                                            
CONECT   68   31                                                            
CONECT   69   33                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  140    0
END

RDKit          3D

69 70  0  0  0  0  0  0  0  0999 V2000
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    2.6538    2.4165   -0.7768 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3979    1.9359    0.2772 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1263    0.8407   -0.6591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2962   -0.4927   -0.1539 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.2166    0.5924    5.8364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5952    2.2917    5.5641 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
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 32 33  1  0
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 34 35  1  0
 35 36  2  0
 35 37  1  0
 37 13  1  0
 34 28  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  4 41  1  0
  5 42  1  0
  6 43  1  0
  9 44  1  0
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 29 66  1  0
 30 67  1  0
 31 68  1  0
 33 69  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₂₇H₃₂N₂O₈

Average Mass

512.5590 Da

Monoisotopic Mass

512.21587 Da

IUPAC Name

(2Z,4E)-N-[(1E)-3-[(3R,7R,10R)-10,17-dihydroxy-7,11-dimethyl-1,5-dioxo-3,4,5,7,10,13-hexahydro-1H-2,6-benzodioxacyclopentadecin-3-yl]prop-1-en-1-yl]-4-(methoxyimino)but-2-enamide

Traditional Name

(2Z,4E)-N-[(1E)-3-[(3R,7R,10R)-10,17-dihydroxy-7,11-dimethyl-1,5-dioxo-4,7,10,13-tetrahydro-3H-2,6-benzodioxacyclopentadecin-3-yl]prop-1-en-1-yl]-4-(methoxyimino)but-2-enamide

CAS Registry Number

Not Available

SMILES

CO\N=C\C=C/C(=O)N\C=C\CC1CC(=O)OC(C)\C=C/C(O)\C(C)=C/CC2=C(C(O)=CC=C2)C(=O)O1

InChI Identifier

InChI=1S/C27H32N2O8/c1-18-11-13-20-7-4-9-23(31)26(20)27(34)37-21(17-25(33)36-19(2)12-14-22(18)30)8-5-15-28-24(32)10-6-16-29-35-3/h4-7,9-12,14-16,19,21-22,30-31H,8,13,17H2,1-3H3,(H,28,32)/b10-6-,14-12-,15-5+,18-11-,29-16+

InChI Key

JYHIHHYYXXKTTJ-ZZGNQKHNSA-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
Aplidium lobatum	Animalia	KNApSAcK
Gynuella sunshinyii	NPAtlas	32040255

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	3.08	ALOGPS
logP	3.35	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	9.65	ChemAxon
pKa (Strongest Basic)	3.78	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	143.75 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	140.08 m³·mol⁻¹	ChemAxon
Polarizability	53.96 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Ueoka R, Meoded RA, Gran-Scheuch A, Bhushan A, Fraaije MW, Piel J: Genome Mining of Oxidation Modules in trans-Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl. 2020 May 11;59(20):7761-7765. doi: 10.1002/anie.201916005. Epub 2020 Mar 19. [PubMed:32040255 ]

Showing NP-Card for Lobatamide A (NP0021003)

MOL for NP0021003 (Lobatamide A)

3D MOL for NP0021003 (Lobatamide A)

3D SDF for NP0021003 (Lobatamide A)

3D-SDF for NP0021003 (Lobatamide A)

PDB for NP0021003 (Lobatamide A)

3D PDB for NP0021003 (Lobatamide A)

SMILES for NP0021003 (Lobatamide A)

INCHI for NP0021003 (Lobatamide A)

Structure for NP0021003 (Lobatamide A)

3D Structure for NP0021003 (Lobatamide A)