NP-MRD: Showing NP-Card for Protorifamycin I (NP0062071)

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Record Information

Version

2.0

Created at

2022-04-28 06:44:51 UTC

Updated at

2022-04-28 06:44:51 UTC

NP-MRD ID

NP0062071

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Protorifamycin I

Description

Protorifamycin I is found in Amycolatopsis mediterranei mutant strain N813.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208442D          

 46 48  0  0  1  0            999 V2000
   -0.4589   -0.1980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1560   -0.7736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9378   -0.4787    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5661   -1.0133    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1056    0.3493    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5353    0.9655    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304282208442D          

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    3.0395    1.4300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9749    2.6683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3290    2.5754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7552    3.1682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0953    3.0146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9553    3.2126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8359    3.1142    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6321    2.7692    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2685    2.2386    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7382    1.5546    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0048    0.7706    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0499   -0.0563    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8702   -0.8646    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4792   -1.5946    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9057   -2.1919    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1924   -2.6124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3927   -2.8248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5666   -2.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7740   -2.5870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0674   -2.1578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5555   -2.8048    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4788   -1.5604    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4431   -3.3427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4175   -2.8390    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1466   -2.0796    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6437   -1.1516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8721   -0.1239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8147    0.9273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4757    1.9244    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8784    2.7942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0647    3.4717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0481    3.9114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4638    4.4938    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7944    3.7828    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  2  0  0  0  0
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  5 12  1  0  0  0  0
 11 13  1  0  0  0  0
 10 14  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
  2 34  1  0  0  0  0
 31 35  1  0  0  0  0
 27 36  1  1  0  0  0
 26 37  1  6  0  0  0
 25 38  1  1  0  0  0
 24 39  1  6  0  0  0
 23 40  1  1  0  0  0
 22 41  1  1  0  0  0
 21 42  1  6  0  0  0
 20 43  1  1  0  0  0
 19 44  1  6  0  0  0
 44 45  1  0  0  0  0
 17 46  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0062071

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1\C=C/C=C(C)\C(=O)NC2=CC(=O)C3=C(C=C(C)C(O)=C3C(=O)\C(C)=C/[C@H](CO)[C@@H](O)[C@H](C)[C@@H](O)[C@@H](C)[C@H](O)[C@@H](C)[C@@H]1O)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C35H45NO10/c1-15-9-8-10-16(2)35(46)36-24-13-25(38)26-23(34(24)45)12-18(4)30(41)27(26)29(40)17(3)11-22(14-37)33(44)21(7)32(43)20(6)31(42)19(5)28(15)39/h8-13,15,19-22,28,31-33,37,39,41-44H,14H2,1-7H3,(H,36,46)/b9-8-,16-10-,17-11-/t15-,19-,20-,21+,22+,28+,31+,32-,33-/m0/s1

> <INCHI_KEY>
DWSNNJANRGBGNU-VJAKMTIGSA-N

> <FORMULA>
C35H45NO10

> <MOLECULAR_WEIGHT>
639.742

> <EXACT_MASS>
639.304346653

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
91

> <JCHEM_AVERAGE_POLARIZABILITY>
67.20504039160369

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(7Z,9R,10R,11S,12R,13S,14R,15S,16R,17S,18E,20Z)-4,10,12,14,16-pentahydroxy-9-(hydroxymethyl)-3,7,11,13,15,17,21-heptamethyl-23-azatricyclo[22.3.1.0^{5,27}]octacosa-1(27),2,4,7,18,20,24-heptaene-6,22,26,28-tetrone

> <ALOGPS_LOGP>
2.20

> <JCHEM_LOGP>
1.8347952703333341

> <ALOGPS_LOGS>
-3.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.542445860588092

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.504856803650592

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6455319568062476

> <JCHEM_POLAR_SURFACE_AREA>
201.68999999999997

> <JCHEM_REFRACTIVITY>
177.32630000000017

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.85e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(7Z,9R,10R,11S,12R,13S,14R,15S,16R,17S,18E,20Z)-4,10,12,14,16-pentahydroxy-9-(hydroxymethyl)-3,7,11,13,15,17,21-heptamethyl-23-azatricyclo[22.3.1.0^{5,27}]octacosa-1(27),2,4,7,18,20,24-heptaene-6,22,26,28-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -0.857  -0.370   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.291  -1.444   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.751  -0.893   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.923  -1.892   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.064   0.652   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.999   1.802   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.469   1.154   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.644   2.148   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.590   3.364   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.137   3.542   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.159   2.393   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.610   0.961   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.674   2.669   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.686   4.981   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.481   4.807   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.410   5.914   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       3.911   5.627   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.516   5.997   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.160   5.813   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.647   5.169   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.834   4.179   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.711   2.902   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.209   1.438   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.293  -0.105   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.958  -1.614   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.228  -2.977   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.157  -4.092   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.826  -4.876   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.333  -5.273   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.791  -5.253   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       3.311  -4.829   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.993  -4.028   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.037  -5.236   0.000  0.00  0.00           O+0
HETATM   34  N   UNK     0       0.894  -2.913   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0       2.694  -6.240   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      10.113  -5.299   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      11.474  -3.882   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      12.402  -2.150   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      12.828  -0.231   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      12.721   1.731   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      12.088   3.592   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      10.973   5.216   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0       9.454   6.480   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0       7.556   7.301   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0       6.466   8.388   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0       3.350   7.061   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    3   34                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   12                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    1    8                                                  
CONECT    8    7                                                            
CONECT    9    6   10   15                                                  
CONECT   10    9   11   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11    5                                                       
CONECT   13   11                                                            
CONECT   14   10                                                            
CONECT   15    9   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   46                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   44                                                  
CONECT   20   19   21   43                                                  
CONECT   21   20   22   42                                                  
CONECT   22   21   23   41                                                  
CONECT   23   22   24   40                                                  
CONECT   24   23   25   39                                                  
CONECT   25   24   26   38                                                  
CONECT   26   25   27   37                                                  
CONECT   27   26   28   36                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   35                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32    2                                                       
CONECT   35   31                                                            
CONECT   36   27                                                            
CONECT   37   26                                                            
CONECT   38   25                                                            
CONECT   39   24                                                            
CONECT   40   23                                                            
CONECT   41   22                                                            
CONECT   42   21                                                            
CONECT   43   20                                                            
CONECT   44   19   45                                                       
CONECT   45   44                                                            
CONECT   46   17                                                            
MASTER        0    0    0    0    0    0    0    0   46    0   96    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₅H₄₅NO₁₀

Average Mass

639.7420 Da

Monoisotopic Mass

639.30435 Da

IUPAC Name

(7Z,9R,10R,11S,12R,13S,14R,15S,16R,17S,18E,20Z)-4,10,12,14,16-pentahydroxy-9-(hydroxymethyl)-3,7,11,13,15,17,21-heptamethyl-23-azatricyclo[22.3.1.0^{5,27}]octacosa-1(27),2,4,7,18,20,24-heptaene-6,22,26,28-tetrone

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@H]1\C=C/C=C(C)\C(=O)NC2=CC(=O)C3=C(C=C(C)C(O)=C3C(=O)\C(C)=C/[C@H](CO)[C@@H](O)[C@H](C)[C@@H](O)[C@@H](C)[C@H](O)[C@@H](C)[C@@H]1O)C2=O

InChI Identifier

InChI=1S/C35H45NO10/c1-15-9-8-10-16(2)35(46)36-24-13-25(38)26-23(34(24)45)12-18(4)30(41)27(26)29(40)17(3)11-22(14-37)33(44)21(7)32(43)20(6)31(42)19(5)28(15)39/h8-13,15,19-22,28,31-33,37,39,41-44H,14H2,1-7H3,(H,36,46)/b9-8-,16-10-,17-11-/t15-,19-,20-,21+,22+,28+,31+,32-,33-/m0/s1

InChI Key

DWSNNJANRGBGNU-VJAKMTIGSA-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
Amycolatopsis mediterranei mutant strain N813	Bacteria	KNApSAcK

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	2.2	ALOGPS
logP	1.83	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	5.5	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	201.69 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	177.33 m³·mol⁻¹	ChemAxon
Polarizability	67.21 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	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

Not Available

Showing NP-Card for Protorifamycin I (NP0062071)

MOL for NP0062071 (Protorifamycin I)

3D MOL for NP0062071 (Protorifamycin I)

3D SDF for NP0062071 (Protorifamycin I)

3D-SDF for NP0062071 (Protorifamycin I)

PDB for NP0062071 (Protorifamycin I)

3D PDB for NP0062071 (Protorifamycin I)

SMILES for NP0062071 (Protorifamycin I)

INCHI for NP0062071 (Protorifamycin I)

Structure for NP0062071 (Protorifamycin I)

3D Structure for NP0062071 (Protorifamycin I)