NP-MRD: Showing NP-Card for Prodigiosin R1 (NP0007822)

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Record Information

Version

2.0

Created at

2020-12-09 05:20:35 UTC

Updated at

2021-07-15 16:58:38 UTC

NP-MRD ID

NP0007822

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Prodigiosin R1

Provided By

NPAtlas

Description

Prodigiosin R1 is found in Streptomyces griseoviridis. Prodigiosin R1 was first documented in 2008 (PMID: 18553921). Based on a literature review very few articles have been published on 2-Isobutyl-13-[(3-methoxy-5,5'-bi[1H-pyrrole]-2-yl)methylene]-12-azabicyclo[9.2.1]Tetradeca-1(14),11-diene.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242106043D          

 68 71  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306242106043D          

 68 71  0  0  0  0            999 V2000
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 31 68  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0007822

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]N1C([H])=C([H])C([H])=C1C1=N\C(=C(/[H])C2=C3C([H])=C(N2[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[C@]3([H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])C(OC([H])([H])[H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C27H37N3O/c1-19(2)15-20-11-8-6-4-5-7-9-12-21-16-22(20)24(29-21)17-26-27(31-3)18-25(30-26)23-13-10-14-28-23/h10,13-14,16-20,28-29H,4-9,11-12,15H2,1-3H3/b26-17+/t20-/m1/s1

> <INCHI_KEY>
FMYDORNOPXGCEO-UHFFFAOYSA-N

> <FORMULA>
C27H37N3O

> <MOLECULAR_WEIGHT>
419.613

> <EXACT_MASS>
419.293662823

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
51.131251329488066

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-13-{[(5E)-4-methoxy-1'H,5H-[2,2'-bipyrrole]-5-ylidene]methyl}-2-(2-methylpropyl)-12-azabicyclo[9.2.1]tetradeca-1(13),11(14)-diene

> <ALOGPS_LOGP>
6.82

> <JCHEM_LOGP>
6.315427297000001

> <ALOGPS_LOGS>
-6.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.129016968570916

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.44605481149394

> <JCHEM_PKA_STRONGEST_BASIC>
4.8619671761859085

> <JCHEM_POLAR_SURFACE_AREA>
53.169999999999995

> <JCHEM_REFRACTIVITY>
132.5144

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.24e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-13-{[(5E)-4-methoxy-1'H-[2,2'-bipyrrole]-5-ylidene]methyl}-2-(2-methylpropyl)-12-azabicyclo[9.2.1]tetradeca-1(13),11(14)-diene

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 68 71  0  0  0  0  0  0  0  0999 V2000
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  4 35  1  0
  7 36  1  0
  8 37  1  0
  9 38  1  0
 10 39  1  0
 13 40  1  0
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 29 64  1  0
 30 65  1  0
 30 66  1  0
 31 67  1  0
 31 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       2.667   1.745  -3.070  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.066   0.695  -2.333  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.679   0.254  -1.161  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.980   0.010  -0.977  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.236  -0.437   0.384  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.522  -0.802   0.977  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.742  -0.784   0.333  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.717  -1.196   1.226  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.087  -1.465   2.419  0.00  0.00           C+0
HETATM   10  N   UNK     0       5.781  -1.217   2.226  0.00  0.00           N+0
HETATM   11  N   UNK     0       3.118  -0.453   0.979  0.00  0.00           N+0
HETATM   12  C   UNK     0       2.050  -0.038   0.116  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.788   0.053   0.479  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.296   0.508  -0.417  0.00  0.00           C+0
HETATM   15  N   UNK     0      -0.257   1.688  -1.060  0.00  0.00           N+0
HETATM   16  C   UNK     0      -1.394   1.823  -1.801  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.185   0.711  -1.643  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.498  -0.106  -0.776  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.916  -1.435  -0.175  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.840  -2.455  -0.213  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.198  -3.819   0.331  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.060  -4.734   0.118  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.402  -3.883   1.819  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.454  -1.191   1.217  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.544  -0.086   1.121  0.00  0.00           C+0
HETATM   26  C   UNK     0      -3.108   1.216   1.697  0.00  0.00           C+0
HETATM   27  C   UNK     0      -4.005   2.372   1.420  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.066   2.881   0.028  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.796   3.561  -0.379  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.712   3.935  -1.833  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.673   3.095  -2.567  0.00  0.00           C+0
HETATM   32  H   UNK     0       2.736   2.655  -2.437  0.00  0.00           H+0
HETATM   33  H   UNK     0       2.101   1.945  -4.005  0.00  0.00           H+0
HETATM   34  H   UNK     0       3.722   1.452  -3.290  0.00  0.00           H+0
HETATM   35  H   UNK     0       4.724   0.134  -1.750  0.00  0.00           H+0
HETATM   36  H   UNK     0       6.909  -0.497  -0.695  0.00  0.00           H+0
HETATM   37  H   UNK     0       8.772  -1.300   1.064  0.00  0.00           H+0
HETATM   38  H   UNK     0       7.575  -1.814   3.340  0.00  0.00           H+0
HETATM   39  H   UNK     0       5.027  -1.326   2.946  0.00  0.00           H+0
HETATM   40  H   UNK     0       0.489  -0.188   1.487  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.551   2.381  -0.960  0.00  0.00           H+0
HETATM   42  H   UNK     0      -3.204   0.520  -2.148  0.00  0.00           H+0
HETATM   43  H   UNK     0      -2.784  -1.935  -0.663  0.00  0.00           H+0
HETATM   44  H   UNK     0       0.092  -2.102   0.306  0.00  0.00           H+0
HETATM   45  H   UNK     0      -0.527  -2.669  -1.297  0.00  0.00           H+0
HETATM   46  H   UNK     0      -2.031  -4.227  -0.261  0.00  0.00           H+0
HETATM   47  H   UNK     0      -0.258  -5.719   0.500  0.00  0.00           H+0
HETATM   48  H   UNK     0       0.348  -4.742  -0.932  0.00  0.00           H+0
HETATM   49  H   UNK     0       0.821  -4.329   0.807  0.00  0.00           H+0
HETATM   50  H   UNK     0      -0.793  -4.753   2.265  0.00  0.00           H+0
HETATM   51  H   UNK     0      -1.032  -3.020   2.385  0.00  0.00           H+0
HETATM   52  H   UNK     0      -2.447  -4.208   2.105  0.00  0.00           H+0
HETATM   53  H   UNK     0      -3.004  -2.063   1.608  0.00  0.00           H+0
HETATM   54  H   UNK     0      -1.760  -0.827   1.950  0.00  0.00           H+0
HETATM   55  H   UNK     0      -3.837  -0.030   0.058  0.00  0.00           H+0
HETATM   56  H   UNK     0      -4.486  -0.435   1.642  0.00  0.00           H+0
HETATM   57  H   UNK     0      -3.176   1.066   2.833  0.00  0.00           H+0
HETATM   58  H   UNK     0      -2.044   1.436   1.548  0.00  0.00           H+0
HETATM   59  H   UNK     0      -5.022   2.085   1.799  0.00  0.00           H+0
HETATM   60  H   UNK     0      -3.697   3.203   2.108  0.00  0.00           H+0
HETATM   61  H   UNK     0      -4.867   3.691   0.036  0.00  0.00           H+0
HETATM   62  H   UNK     0      -4.426   2.089  -0.626  0.00  0.00           H+0
HETATM   63  H   UNK     0      -2.775   4.529   0.208  0.00  0.00           H+0
HETATM   64  H   UNK     0      -1.908   3.013  -0.048  0.00  0.00           H+0
HETATM   65  H   UNK     0      -3.684   3.710  -2.301  0.00  0.00           H+0
HETATM   66  H   UNK     0      -2.545   5.009  -1.926  0.00  0.00           H+0
HETATM   67  H   UNK     0      -1.944   3.033  -3.593  0.00  0.00           H+0
HETATM   68  H   UNK     0      -0.765   3.785  -2.547  0.00  0.00           H+0
CONECT    1    2   32   33   34                                             
CONECT    2    1    3                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    5   35                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8   36                                                  
CONECT    8    7    9   37                                                  
CONECT    9    8   10   38                                                  
CONECT   10    9    6   39                                                  
CONECT   11    5   12                                                       
CONECT   12   11   13    3                                                  
CONECT   13   12   14   40                                                  
CONECT   14   13   15   18                                                  
CONECT   15   14   16   41                                                  
CONECT   16   15   17   31                                                  
CONECT   17   16   18   42                                                  
CONECT   18   17   19   14                                                  
CONECT   19   18   20   24   43                                             
CONECT   20   19   21   44   45                                             
CONECT   21   20   22   23   46                                             
CONECT   22   21   47   48   49                                             
CONECT   23   21   50   51   52                                             
CONECT   24   19   25   53   54                                             
CONECT   25   24   26   55   56                                             
CONECT   26   25   27   57   58                                             
CONECT   27   26   28   59   60                                             
CONECT   28   27   29   61   62                                             
CONECT   29   28   30   63   64                                             
CONECT   30   29   31   65   66                                             
CONECT   31   30   16   67   68                                             
CONECT   32    1                                                            
CONECT   33    1                                                            
CONECT   34    1                                                            
CONECT   35    4                                                            
CONECT   36    7                                                            
CONECT   37    8                                                            
CONECT   38    9                                                            
CONECT   39   10                                                            
CONECT   40   13                                                            
CONECT   41   15                                                            
CONECT   42   17                                                            
CONECT   43   19                                                            
CONECT   44   20                                                            
CONECT   45   20                                                            
CONECT   46   21                                                            
CONECT   47   22                                                            
CONECT   48   22                                                            
CONECT   49   22                                                            
CONECT   50   23                                                            
CONECT   51   23                                                            
CONECT   52   23                                                            
CONECT   53   24                                                            
CONECT   54   24                                                            
CONECT   55   25                                                            
CONECT   56   25                                                            
CONECT   57   26                                                            
CONECT   58   26                                                            
CONECT   59   27                                                            
CONECT   60   27                                                            
CONECT   61   28                                                            
CONECT   62   28                                                            
CONECT   63   29                                                            
CONECT   64   29                                                            
CONECT   65   30                                                            
CONECT   66   30                                                            
CONECT   67   31                                                            
CONECT   68   31                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  142    0
END

RDKit          3D

68 71  0  0  0  0  0  0  0  0999 V2000
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  2  3  1  0
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  5 11  2  0
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 12  3  1  0
 18 14  2  0
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  1 32  1  0
  1 33  1  0
  1 34  1  0
  4 35  1  0
  7 36  1  0
  8 37  1  0
  9 38  1  0
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 13 40  1  0
 15 41  1  0
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 31 67  1  0
 31 68  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₂₇H₃₇N₃O

Average Mass

419.6130 Da

Monoisotopic Mass

419.29366 Da

IUPAC Name

(2R)-13-{[(5E)-4-methoxy-1'H,5H-[2,2'-bipyrrole]-5-ylidene]methyl}-2-(2-methylpropyl)-12-azabicyclo[9.2.1]tetradeca-1(13),11(14)-diene

Traditional Name

(2R)-13-{[(5E)-4-methoxy-1'H-[2,2'-bipyrrole]-5-ylidene]methyl}-2-(2-methylpropyl)-12-azabicyclo[9.2.1]tetradeca-1(13),11(14)-diene

CAS Registry Number

Not Available

SMILES

COC1=CC(=NC1=CC1=C2C=C(CCCCCCCCC2CC(C)C)N1)C1=CC=CN1

InChI Identifier

InChI=1S/C27H37N3O/c1-19(2)15-20-11-8-6-4-5-7-9-12-21-16-22(20)24(29-21)17-26-27(31-3)18-25(30-26)23-13-10-14-28-23/h10,13-14,16-20,28-29H,4-9,11-12,15H2,1-3H3

InChI Key

FMYDORNOPXGCEO-UHFFFAOYSA-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 griseoviridis	NPAtlas	18553921

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	6.82	ALOGPS
logP	6.32	ChemAxon
logS	-6.9	ALOGPS
pKa (Strongest Acidic)	15.45	ChemAxon
pKa (Strongest Basic)	4.86	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	53.17 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	132.51 m³·mol⁻¹	ChemAxon
Polarizability	51.13 Å³	ChemAxon
Number of Rings	4	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

NPA005906

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78434749

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

136738617

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kawasaki T, Sakurai F, Hayakawa Y: A prodigiosin from the roseophilin producer Streptomyces griseoviridis. J Nat Prod. 2008 Jul;71(7):1265-7. doi: 10.1021/np7007494. Epub 2008 Jun 14. [PubMed:18553921 ]

Showing NP-Card for Prodigiosin R1 (NP0007822)

MOL for NP0007822 (Prodigiosin R1)

3D MOL for NP0007822 (Prodigiosin R1)

3D SDF for NP0007822 (Prodigiosin R1)

3D-SDF for NP0007822 (Prodigiosin R1)

PDB for NP0007822 (Prodigiosin R1)

3D PDB for NP0007822 (Prodigiosin R1)

SMILES for NP0007822 (Prodigiosin R1)

INCHI for NP0007822 (Prodigiosin R1)

Structure for NP0007822 (Prodigiosin R1)

3D Structure for NP0007822 (Prodigiosin R1)