NP-MRD: Showing NP-Card for Jadomycin DNV (NP0010463)

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Record Information

Version

2.0

Created at

2021-01-05 19:58:28 UTC

Updated at

2021-07-15 17:06:10 UTC

NP-MRD ID

NP0010463

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Jadomycin DNV

Provided By

NPAtlas

Description

Jadomycin DNV belongs to the class of organic compounds known as phenanthridines and derivatives. These are polycyclic compounds containing a phenanthridine moiety, which is a tricyclic system with two benzene rings joined by a pyridine forming a non-linear skeleton. Hydrogenated derivatives are also included. Jadomycin DNV is found in Streptomyces and Streptomyces venezuelae. Jadomycin DNV was first documented in 2011 (PMID: 22050382). Based on a literature review very few articles have been published on Jadomycin DNV.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242107383D          

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M  END

     RDKit          3D

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M  END


  Mrv1652306242107383D          

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M  END
> <DATABASE_ID>
NP0010463

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C2C(=C([H])C(=C1[H])C([H])([H])[H])[C@@]1([H])OC(=O)[C@]([H])(N1C1=C2C(=O)C2=C([H])C([H])=C([H])C(O[C@]3([H])O[C@@]([H])(C([H])([H])[H])[C@]([H])(O[H])[C@]([H])(O[H])C3([H])[H])=C2C1=O)C([H])([H])C([H])([H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C29H29NO9/c1-4-6-16-29(36)39-28-15-9-12(2)10-17(31)21(15)23-24(30(16)28)27(35)22-14(26(23)34)7-5-8-19(22)38-20-11-18(32)25(33)13(3)37-20/h5,7-10,13,16,18,20,25,28,31-33H,4,6,11H2,1-3H3/t13-,16+,18+,20-,25-,28+/m0/s1

> <INCHI_KEY>
UISVOFCCNUPNLI-QEFXOZJESA-N

> <FORMULA>
C29H29NO9

> <MOLECULAR_WEIGHT>
535.549

> <EXACT_MASS>
535.184231518

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
57.21416812774814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,6R)-19-{[(2S,4R,5R,6S)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-11-hydroxy-9-methyl-3-propyl-5-oxa-2-azapentacyclo[11.8.0.0^{2,6}.0^{7,12}.0^{15,20}]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione

> <ALOGPS_LOGP>
2.42

> <JCHEM_LOGP>
3.473279261999999

> <ALOGPS_LOGS>
-3.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.87188393089021

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.183451633222713

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2528866875223716

> <JCHEM_POLAR_SURFACE_AREA>
142.83

> <JCHEM_REFRACTIVITY>
138.2183

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.07e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,6R)-19-{[(2S,4R,5R,6S)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-11-hydroxy-9-methyl-3-propyl-5-oxa-2-azapentacyclo[11.8.0.0^{2,6}.0^{7,12}.0^{15,20}]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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 22 33  1  0
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 37 38  2  0
 18 39  1  0
 39  4  1  0
 39  8  1  0
 16  9  1  0
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 32 24  1  0
  1 40  1  0
  1 41  1  0
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  4 47  1  6
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 33 66  1  0
 34 67  1  0
 35 68  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      -2.948   2.452  -3.487  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.471   3.104  -2.205  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.621   2.089  -1.380  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.451   0.990  -1.101  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.637   1.427  -0.292  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.898   2.496   0.250  0.00  0.00           O+0
HETATM    7  O   UNK     0      -4.425   0.283  -0.289  0.00  0.00           O+0
HETATM    8  C   UNK     0      -3.626  -0.813  -0.781  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.889  -2.078  -0.186  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.181  -2.568  -0.354  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.591  -3.781   0.146  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.990  -4.285  -0.050  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.667  -4.515   0.835  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.349  -4.067   1.034  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.507  -4.877   1.737  0.00  0.00           O+0
HETATM   16  C   UNK     0      -2.990  -2.865   0.523  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.645  -2.304   0.696  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.401  -1.098   0.167  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.041  -0.561   0.333  0.00  0.00           C+0
HETATM   20  O   UNK     0       0.201   0.558  -0.152  0.00  0.00           O+0
HETATM   21  C   UNK     0       1.022  -1.269   1.032  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.291  -0.673   1.139  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.433   0.552   0.567  0.00  0.00           O+0
HETATM   24  C   UNK     0       3.578   1.305   0.559  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.078   1.627  -0.842  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.571   1.857  -0.731  0.00  0.00           C+0
HETATM   27  O   UNK     0       6.037   2.525  -1.839  0.00  0.00           O+0
HETATM   28  C   UNK     0       5.767   2.664   0.560  0.00  0.00           C+0
HETATM   29  O   UNK     0       6.699   3.669   0.218  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.477   3.378   0.875  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.768   4.376   1.999  0.00  0.00           C+0
HETATM   32  O   UNK     0       3.426   2.555   1.185  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.285  -1.365   1.807  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.984  -2.601   2.332  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.729  -3.156   2.209  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.720  -2.486   1.548  0.00  0.00           C+0
HETATM   37  C   UNK     0      -0.640  -3.056   1.398  0.00  0.00           C+0
HETATM   38  O   UNK     0      -0.802  -4.152   1.897  0.00  0.00           O+0
HETATM   39  N   UNK     0      -2.289  -0.264  -0.519  0.00  0.00           N+0
HETATM   40  H   UNK     0      -3.959   2.008  -3.371  0.00  0.00           H+0
HETATM   41  H   UNK     0      -2.254   1.707  -3.886  0.00  0.00           H+0
HETATM   42  H   UNK     0      -3.074   3.264  -4.238  0.00  0.00           H+0
HETATM   43  H   UNK     0      -3.324   3.480  -1.673  0.00  0.00           H+0
HETATM   44  H   UNK     0      -1.801   3.938  -2.524  0.00  0.00           H+0
HETATM   45  H   UNK     0      -1.282   2.777  -0.552  0.00  0.00           H+0
HETATM   46  H   UNK     0      -0.801   1.955  -2.157  0.00  0.00           H+0
HETATM   47  H   UNK     0      -2.971   0.748  -2.116  0.00  0.00           H+0
HETATM   48  H   UNK     0      -3.773  -0.768  -1.886  0.00  0.00           H+0
HETATM   49  H   UNK     0      -5.933  -1.998  -0.900  0.00  0.00           H+0
HETATM   50  H   UNK     0      -7.278  -5.011   0.719  0.00  0.00           H+0
HETATM   51  H   UNK     0      -7.683  -3.426  -0.128  0.00  0.00           H+0
HETATM   52  H   UNK     0      -6.991  -4.812  -1.029  0.00  0.00           H+0
HETATM   53  H   UNK     0      -4.913  -5.465   1.251  0.00  0.00           H+0
HETATM   54  H   UNK     0      -2.797  -5.787   2.112  0.00  0.00           H+0
HETATM   55  H   UNK     0       4.405   0.817   1.099  0.00  0.00           H+0
HETATM   56  H   UNK     0       3.629   2.542  -1.260  0.00  0.00           H+0
HETATM   57  H   UNK     0       3.861   0.803  -1.551  0.00  0.00           H+0
HETATM   58  H   UNK     0       6.114   0.892  -0.563  0.00  0.00           H+0
HETATM   59  H   UNK     0       6.960   2.239  -2.104  0.00  0.00           H+0
HETATM   60  H   UNK     0       6.128   2.031   1.387  0.00  0.00           H+0
HETATM   61  H   UNK     0       7.432   3.282  -0.339  0.00  0.00           H+0
HETATM   62  H   UNK     0       4.263   4.030  -0.022  0.00  0.00           H+0
HETATM   63  H   UNK     0       3.814   4.628   2.472  0.00  0.00           H+0
HETATM   64  H   UNK     0       5.492   3.964   2.721  0.00  0.00           H+0
HETATM   65  H   UNK     0       5.213   5.311   1.590  0.00  0.00           H+0
HETATM   66  H   UNK     0       4.282  -0.933   1.909  0.00  0.00           H+0
HETATM   67  H   UNK     0       3.746  -3.151   2.854  0.00  0.00           H+0
HETATM   68  H   UNK     0       1.487  -4.135   2.624  0.00  0.00           H+0
CONECT    1    2   40   41   42                                             
CONECT    2    1    3   43   44                                             
CONECT    3    2    4   45   46                                             
CONECT    4    3    5   39   47                                             
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   39   48                                             
CONECT    9    8   10   16                                                  
CONECT   10    9   11   49                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11   50   51   52                                             
CONECT   13   11   14   53                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14   54                                                       
CONECT   16   14   17    9                                                  
CONECT   17   16   18   37                                                  
CONECT   18   17   19   39                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   36                                                  
CONECT   22   21   23   33                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   32   55                                             
CONECT   25   24   26   56   57                                             
CONECT   26   25   27   28   58                                             
CONECT   27   26   59                                                       
CONECT   28   26   29   30   60                                             
CONECT   29   28   61                                                       
CONECT   30   28   31   32   62                                             
CONECT   31   30   63   64   65                                             
CONECT   32   30   24                                                       
CONECT   33   22   34   66                                                  
CONECT   34   33   35   67                                                  
CONECT   35   34   36   68                                                  
CONECT   36   35   37   21                                                  
CONECT   37   36   38   17                                                  
CONECT   38   37                                                            
CONECT   39   18    4    8                                                  
CONECT   40    1                                                            
CONECT   41    1                                                            
CONECT   42    1                                                            
CONECT   43    2                                                            
CONECT   44    2                                                            
CONECT   45    3                                                            
CONECT   46    3                                                            
CONECT   47    4                                                            
CONECT   48    8                                                            
CONECT   49   10                                                            
CONECT   50   12                                                            
CONECT   51   12                                                            
CONECT   52   12                                                            
CONECT   53   13                                                            
CONECT   54   15                                                            
CONECT   55   24                                                            
CONECT   56   25                                                            
CONECT   57   25                                                            
CONECT   58   26                                                            
CONECT   59   27                                                            
CONECT   60   28                                                            
CONECT   61   29                                                            
CONECT   62   30                                                            
CONECT   63   31                                                            
CONECT   64   31                                                            
CONECT   65   31                                                            
CONECT   66   33                                                            
CONECT   67   34                                                            
CONECT   68   35                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  146    0
END

RDKit          3D

68 73  0  0  0  0  0  0  0  0999 V2000
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   -4.6670   -4.5148    0.8348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3492   -4.0666    1.0344 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.7457   -3.1515    2.8545 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4871   -4.1347    2.6243 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
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  1 40  1  0
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  4 47  1  6
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 35 68  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₂₉H₂₉NO₉

Average Mass

535.5490 Da

Monoisotopic Mass

535.18423 Da

IUPAC Name

(3R,6R)-19-{[(2S,4R,5R,6S)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-11-hydroxy-9-methyl-3-propyl-5-oxa-2-azapentacyclo[11.8.0.0^{2,6}.0^{7,12}.0^{15,20}]henicosa-1(13),7,9,11,15,17,19-heptaene-4,14,21-trione

Traditional Name

CAS Registry Number

Not Available

SMILES

CCC[C@H]1N2C(OC1=O)C1=CC(C)=CC(O)=C1C1=C2C(=O)C2=C(C=CC=C2O[C@H]2CC(O)[C@@H](O)C(C)O2)C1=O

InChI Identifier

InChI=1S/C29H29NO9/c1-4-6-16-29(36)39-28-15-9-12(2)10-17(31)21(15)23-24(30(16)28)27(35)22-14(26(23)34)7-5-8-19(22)38-20-11-18(32)25(33)13(3)37-20/h5,7-10,13,16,18,20,25,28,31-33H,4,6,11H2,1-3H3/t13?,16-,18?,20+,25+,28?/m1/s1

InChI Key

UISVOFCCNUPNLI-QEFXOZJESA-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	NPAtlas	22050382
Streptomyces venezuelae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthridines and derivatives. These are polycyclic compounds containing a phenanthridine moiety, which is a tricyclic system with two benzene rings joined by a pyridine forming a non-linear skeleton. Hydrogenated derivatives are also included.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Quinolines and derivatives

Sub Class

Benzoquinolines

Direct Parent

Phenanthridines and derivatives

Alternative Parents

Substituents

Phenanthridine
Alpha-amino acid ester
Quinoline quinone
Naphthoquinone
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Naphthalene
Alpha-amino acid or derivatives
Aryl ketone
Quinone
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Oxazolidinone
Benzenoid
Oxane
Monosaccharide
Vinylogous amide
Oxazolidine
Secondary alcohol
1,2-diol
Lactone
Ketone
Carboxylic acid ester
Acetal
Azacycle
Oxacycle
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Enamine
Organooxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Alcohol
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	2.42	ALOGPS
logP	3.47	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	8.18	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	142.83 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	138.22 m³·mol⁻¹	ChemAxon
Polarizability	57.21 Å³	ChemAxon
Number of Rings	6	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

NPAtlas ID

NPA018759

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78445555

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139588329

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Dupuis SN, Veinot T, Monro SM, Douglas SE, Syvitski RT, Goralski KB, McFarland SA, Jakeman DL: Jadomycins derived from the assimilation and incorporation of norvaline and norleucine. J Nat Prod. 2011 Nov 28;74(11):2420-4. doi: 10.1021/np200689w. Epub 2011 Nov 3. [PubMed:22050382 ]

Showing NP-Card for Jadomycin DNV (NP0010463)

MOL for NP0010463 (Jadomycin DNV)

3D MOL for NP0010463 (Jadomycin DNV)

3D SDF for NP0010463 (Jadomycin DNV)

3D-SDF for NP0010463 (Jadomycin DNV)

PDB for NP0010463 (Jadomycin DNV)

3D PDB for NP0010463 (Jadomycin DNV)

SMILES for NP0010463 (Jadomycin DNV)

INCHI for NP0010463 (Jadomycin DNV)

Structure for NP0010463 (Jadomycin DNV)

3D Structure for NP0010463 (Jadomycin DNV)