NP-MRD: Showing NP-Card for Rubescin R (NP0332511)

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Record Information

Version

1.0

Created at

2024-02-15 20:04:48 UTC

Updated at

2024-04-19 10:10:05 UTC

NP-MRD ID

NP0332511

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rubescin R

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02152420042D          

 33 39  0  0  1  0            999 V2000
    4.3065    0.0340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6949    0.5877    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9307    0.8987    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0242    0.0790    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8180    1.7159    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7480    2.5380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0446    2.1292    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5226    1.5166    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7549    1.3025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1440    0.7152    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2778   -0.0989    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6084    1.0694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5039    1.8928    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1034    2.4596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9143    2.3077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3093    3.0320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7426    3.6315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9973    3.2777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3182    2.0446    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1782    2.7035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6955    2.8021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5433    2.8204    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3631    2.9121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0784    2.2118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4534    0.7417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2420    0.4137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3323   -0.4064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2559   -0.1109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6413   -0.8403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3463    1.0939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2336    1.9112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4694    2.2222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3567    3.0394    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  5  3  1  0  0  0  0
  5  6  1  6  0  0  0
  7  5  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 13 12  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 14 18  1  0  0  0  0
 19  9  1  0  0  0  0
 13 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 22 21  1  0  0  0  0
  7 22  1  0  0  0  0
 22 23  1  6  0  0  0
  7 23  1  6  0  0  0
  8 24  1  6  0  0  0
  8 25  1  0  0  0  0
  9 25  1  0  0  0  0
 25 26  1  0  0  0  0
  3 26  1  0  0  0  0
 26 27  2  0  0  0  0
  2 28  1  1  0  0  0
 28 29  1  0  0  0  0
  2 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
  5 32  1  0  0  0  0
 32 33  2  0  0  0  0
M  END


  Mrv2104 02152420042D          

 33 39  0  0  1  0            999 V2000
    4.3065    0.0340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6949    0.5877    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9307    0.8987    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0242    0.0790    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8180    1.7159    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7480    2.5380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0446    2.1292    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5226    1.5166    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7549    1.3025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1440    0.7152    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2778   -0.0989    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6084    1.0694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5039    1.8928    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1034    2.4596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9143    2.3077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3093    3.0320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7426    3.6315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9973    3.2777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3182    2.0446    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1782    2.7035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6955    2.8021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5433    2.8204    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3631    2.9121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0784    2.2118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4534    0.7417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2420    0.4137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3323   -0.4064    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2559   -0.1109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6413   -0.8403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3463    1.0939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2336    1.9112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4694    2.2222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3567    3.0394    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  5  3  1  0  0  0  0
  5  6  1  6  0  0  0
  7  5  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
 13 12  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 14 18  1  0  0  0  0
 19  9  1  0  0  0  0
 13 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 22 21  1  0  0  0  0
  7 22  1  0  0  0  0
 22 23  1  6  0  0  0
  7 23  1  6  0  0  0
  8 24  1  6  0  0  0
  8 25  1  0  0  0  0
  9 25  1  0  0  0  0
 25 26  1  0  0  0  0
  3 26  1  0  0  0  0
 26 27  2  0  0  0  0
  2 28  1  1  0  0  0
 28 29  1  0  0  0  0
  2 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
  5 32  1  0  0  0  0
 32 33  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332511

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12C(=O)C3[C@]4(C)[C@]5(O[C@H]5C[C@@]5(C)[C@@H](C[C@@H](O)C345)C3=COC=C3)[C@@]1(C)C(=O)C=C[C@@]2(C)CO

> <INCHI_IDENTIFIER>
InChI=1S/C26H30O6/c1-21(12-27)7-5-15(28)23(3)19(21)18(30)20-24(4)25(20)16(29)9-14(13-6-8-31-11-13)22(25,2)10-17-26(23,24)32-17/h5-8,11,14,16-17,19-20,27,29H,9-10,12H2,1-4H3/t14-,16+,17-,19-,20?,21-,22-,23-,24-,25?,26+/m0/s1

> <INCHI_KEY>
MSPFOKFOKOUMSG-BGLCYZRFSA-N

> <FORMULA>
C26H30O6

> <MOLECULAR_WEIGHT>
438.52

> <EXACT_MASS>
438.204238686

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
46.003256947038224

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,6R,7S,10S,12R,14R,15S,17S)-14-(furan-3-yl)-12-hydroxy-6-(hydroxymethyl)-2,6,10,15-tetramethyl-18-oxahexacyclo[8.8.0.0^{1,17}.0^{2,7}.0^{9,11}.0^{11,15}]octadec-4-ene-3,8-dione

> <JCHEM_LOGP>
1.7387535380000005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.187418110331956

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.48025153343897

> <JCHEM_PKA_STRONGEST_BASIC>
-2.77612007248356

> <JCHEM_POLAR_SURFACE_AREA>
100.27000000000001

> <JCHEM_REFRACTIVITY>
115.11689999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,6R,7S,10S,12R,14R,15S,17S)-14-(furan-3-yl)-12-hydroxy-6-(hydroxymethyl)-2,6,10,15-tetramethyl-18-oxahexacyclo[8.8.0.0^{1,17}.0^{2,7}.0^{9,11}.0^{11,15}]octadec-4-ene-3,8-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-FEB-24   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-FEB-24         0                                  
HETATM    1  C   UNK     0       8.039   0.064   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.897   1.097   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.471   1.678   0.000  0.00  0.00           C+0
HETATM    4  H   UNK     0       5.645   0.147   0.000  0.00  0.00           H+0
HETATM    5  C   UNK     0       5.260   3.203   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.130   4.738   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.817   3.975   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.842   2.831   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.409   2.431   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.269   1.335   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.519  -0.185   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.136   1.996   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.941   3.533   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.060   4.591   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.573   4.308   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -4.311   5.660   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -3.253   6.779   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.862   6.118   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.594   3.817   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.333   5.047   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.298   5.231   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.881   5.265   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       4.411   5.436   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       2.013   4.129   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.713   1.385   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.185   0.772   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       4.354  -0.759   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       6.078  -0.207   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       6.797  -1.569   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       8.113   2.042   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       7.903   3.568   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.476   4.148   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       6.266   5.674   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   28   30                                             
CONECT    3    2    4    5   26                                             
CONECT    4    3                                                            
CONECT    5    3    6    7   32                                             
CONECT    6    5                                                            
CONECT    7    5    8   22   23                                             
CONECT    8    7    9   24   25                                             
CONECT    9    8   10   19   25                                             
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   19                                                  
CONECT   14   13   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   14                                                       
CONECT   19    9   13   20   21                                             
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21    7   23                                                  
CONECT   23   22    7                                                       
CONECT   24    8                                                            
CONECT   25    8    9   26                                                  
CONECT   26   25    3   27                                                  
CONECT   27   26                                                            
CONECT   28    2   29                                                       
CONECT   29   28                                                            
CONECT   30    2   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31    5   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₀O₆

Average Mass

438.5200 Da

Monoisotopic Mass

438.20424 Da

IUPAC Name

(1S,2S,6R,7S,10S,12R,14R,15S,17S)-14-(furan-3-yl)-12-hydroxy-6-(hydroxymethyl)-2,6,10,15-tetramethyl-18-oxahexacyclo[8.8.0.0^{1,17}.0^{2,7}.0^{9,11}.0^{11,15}]octadec-4-ene-3,8-dione

Traditional Name

(1S,2S,6R,7S,10S,12R,14R,15S,17S)-14-(furan-3-yl)-12-hydroxy-6-(hydroxymethyl)-2,6,10,15-tetramethyl-18-oxahexacyclo[8.8.0.0^{1,17}.0^{2,7}.0^{9,11}.0^{11,15}]octadec-4-ene-3,8-dione

CAS Registry Number

Not Available

SMILES

[H][C@@]12C(=O)C3[C@]4(C)[C@]5(O[C@H]5C[C@@]5(C)[C@@H](C[C@@H](O)C345)C3=COC=C3)[C@@]1(C)C(=O)C=C[C@@]2(C)CO

InChI Identifier

InChI=1S/C26H30O6/c1-21(12-27)7-5-15(28)23(3)19(21)18(30)20-24(4)25(20)16(29)9-14(13-6-8-31-11-13)22(25,2)10-17-26(23,24)32-17/h5-8,11,14,16-17,19-20,27,29H,9-10,12H2,1-4H3/t14-,16+,17-,19-,20?,21-,22-,23-,24-,25?,26+/m0/s1

InChI Key

MSPFOKFOKOUMSG-BGLCYZRFSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMQC NMR	[Proton, Carbon¹³] NMR Spectrum (2D, 600 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Not Available	Not Available	2024-02-15	View Spectrum
HMBC NMR	[Proton, Carbon¹³] NMR Spectrum (2D, 600 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Not Available	Not Available	2024-02-15	View Spectrum
1D NMR	[Carbon¹³, ] NMR Spectrum (2D, 151 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Not Available	Not Available	2024-02-15	View Spectrum
1D NMR	[Proton, ] NMR Spectrum (2D, 600 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Not Available	Not Available	2024-02-15	View Spectrum
NOESY NMR	[Proton, Proton] NMR Spectrum (2D, 600 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Not Available	Not Available	2024-02-15	View Spectrum
COSY NMR	[Proton, Proton] NMR Spectrum (2D, 600 MHz, CDCL3, experimental)	kngoto@p.kanazawa-u.ac.jp	Not Available	Not Available	2024-02-15	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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	1.74	ChemAxon
pKa (Strongest Acidic)	14.48	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	100.27 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	115.12 m³·mol⁻¹	ChemAxon
Polarizability	46 Å³	ChemAxon
Number of Rings	7	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

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References

General References

Not Available

Showing NP-Card for Rubescin R (NP0332511)

MOL for NP0332511 (Rubescin R)

3D MOL for NP0332511 (Rubescin R)

3D SDF for NP0332511 (Rubescin R)

3D-SDF for NP0332511 (Rubescin R)

PDB for NP0332511 (Rubescin R)

3D PDB for NP0332511 (Rubescin R)

SMILES for NP0332511 (Rubescin R)

INCHI for NP0332511 (Rubescin R)

Structure for NP0332511 (Rubescin R)

3D Structure for NP0332511 (Rubescin R)