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Showing NP-Card for Corymbotin D (NP0333184)

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Record Information
Version2.0
Created at2024-05-12 05:36:39 UTC
Updated at2024-09-03 04:21:30 UTC
NP-MRD IDNP0333184
Natural Product DOIhttps://doi.org/10.57994/2509
Secondary Accession NumbersNone
Natural Product Identification
Common NameCorymbotin D
DescriptionNot Available
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0333184 (Corymbotin D )


  Mrv2104 01242308132D          

 34 36  0  0  1  0            999 V2000
   -0.3626    3.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3444    3.5623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0662    3.9619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3292    2.7149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8860    2.0445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7065    2.1307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8166    1.4374    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8254    1.4955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4666    2.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2800    2.8986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2559    1.8548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7915   -0.4182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5615   -0.0849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2239   -0.5767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6563    0.7346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9039   -1.2406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5809   -1.2282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4838   -2.1002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7280   -2.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0636   -1.9420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6366   -3.2510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3010   -3.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6595   -0.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4859    2.1228    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  7  6  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
 12  7  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 15 14  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 15 20  1  0  0  0  0
 20 21  2  0  0  0  0
  5 21  1  0  0  0  0
 12 21  1  6  0  0  0
 13 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  2  0  0  0  0
 22 30  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
 33 32  1  0  0  0  0
 12 33  1  0  0  0  0
 33 34  1  1  0  0  0
M  END
Download

3D MOL for NP0333184 (Corymbotin D )

Download
3D SDF for NP0333184 (Corymbotin D )

  Mrv2104 01242308132D          

 34 36  0  0  1  0            999 V2000
   -0.3626    3.9875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3444    3.5623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0662    3.9619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3292    2.7149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8860    2.0445    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7065    2.1307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8166    1.4374    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8254    1.4955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4666    2.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2800    2.8986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2559    1.8548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7915   -0.4182    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5615   -0.0849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2239   -0.5767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6563    0.7346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9039   -1.2406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5809   -1.2282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4838   -2.1002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7280   -2.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0636   -1.9420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6366   -3.2510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3010   -3.7401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6595   -0.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4859    2.1228    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  7  6  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
 12  7  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 15 14  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 15 20  1  0  0  0  0
 20 21  2  0  0  0  0
  5 21  1  0  0  0  0
 12 21  1  6  0  0  0
 13 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  2  0  0  0  0
 22 30  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
 33 32  1  0  0  0  0
 12 33  1  0  0  0  0
 33 34  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0333184

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C[C@H](O)[C@@]23[C@H](OC(C)=O)O[C@H](OC(C)=O)C2=C[C@H](C[C@H]3[C@]1(C)C\C=C(/C)C=C)OC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H36O8/c1-8-14(2)9-10-25(7)15(3)11-22(30)26-20(12-19(13-21(25)26)31-16(4)27)23(32-17(5)28)34-24(26)33-18(6)29/h8-9,12,15,19,21-24,30H,1,10-11,13H2,2-7H3/b14-9+/t15-,19-,21+,22+,23+,24-,25-,26-/m1/s1

> <INCHI_KEY>
WJNZZTDLRUZPHL-SKBJODTMSA-N

> <FORMULA>
C26H36O8

> <MOLECULAR_WEIGHT>
476.566

> <EXACT_MASS>
476.241018119

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
50.95037339856649

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,3R,5S,6aS,7R,8R,10S,10aS)-3,5-bis(acetyloxy)-10-hydroxy-7,8-dimethyl-7-[(2E)-3-methylpenta-2,4-dien-1-yl]-1H,3H,5H,6H,6aH,7H,8H,9H,10H-naphtho[1,8a-c]furan-1-yl acetate

> <JCHEM_LOGP>
2.8116274189999997

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.456737486544874

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0364230233852716

> <JCHEM_POLAR_SURFACE_AREA>
108.36

> <JCHEM_REFRACTIVITY>
123.98029999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3R,5S,6aS,7R,8R,10S,10aS)-3,5-bis(acetyloxy)-10-hydroxy-7,8-dimethyl-7-[(2E)-3-methylpenta-2,4-dien-1-yl]-1H,3H,5H,6H,6aH,8H,9H,10H-naphtho[1,8a-c]furan-1-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0333184 (Corymbotin D )
Download
PDB for NP0333184 (Corymbotin D )
HEADER    PROTEIN                                 24-JAN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JAN-23         0                                  
HETATM    1  C   UNK     0      -0.677   7.443   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.643   6.650   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.990   7.396   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       0.615   5.068   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.654   3.816   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.185   3.977   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.391   2.683   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.274   2.792   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.471   3.911   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.123   5.411   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       7.944   3.462   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.478  -0.781   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -2.915  -0.158   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.151  -1.077   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -3.092   1.371   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.554  -2.316   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.818  -2.293   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.636  -3.920   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.226  -4.538   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.985  -3.625   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.055  -6.069   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.295  -6.981   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.831  -0.665   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       4.640   3.963   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   21                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    7   13   21   33                                             
CONECT   13   12   14   22                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   15   21                                                       
CONECT   21   20    5   12                                                  
CONECT   22   13   23   24   30                                             
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28                                                            
CONECT   30   22   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   12   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

Download
3D PDB for NP0333184 (Corymbotin D )
Download
SMILES for NP0333184 (Corymbotin D )
C[C@@H]1C[C@H](O)[C@@]23[C@H](OC(C)=O)O[C@H](OC(C)=O)C2=C[C@H](C[C@H]3[C@]1(C)C\C=C(/C)C=C)OC(C)=O
Download
INCHI for NP0333184 (Corymbotin D )
InChI=1S/C26H36O8/c1-8-14(2)9-10-25(7)15(3)11-22(30)26-20(12-19(13-21(25)26)31-16(4)27)23(32-17(5)28)34-24(26)33-18(6)29/h8-9,12,15,19,21-24,30H,1,10-11,13H2,2-7H3/b14-9+/t15-,19-,21+,22+,23+,24-,25-,26-/m1/s1
Download
View in JSmol
SynonymsNot Available
Chemical FormulaC26H36O8
Average Mass476.5660 Da
Monoisotopic Mass476.24102 Da
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry NumberNot Available
SMILES
C[C@@H]1C[C@H](O)[C@@]23[C@H](OC(C)=O)O[C@H](OC(C)=O)C2=C[C@H](C[C@H]3[C@]1(C)C\C=C(/C)C=C)OC(C)=O
InChI Identifier
InChI=1S/C26H36O8/c1-8-14(2)9-10-25(7)15(3)11-22(30)26-20(12-19(13-21(25)26)31-16(4)27)23(32-17(5)28)34-24(26)33-18(6)29/h8-9,12,15,19,21-24,30H,1,10-11,13H2,2-7H3/b14-9+/t15-,19-,21+,22+,23+,24-,25-,26-/m1/s1
InChI KeyWJNZZTDLRUZPHL-SKBJODTMSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
HSQC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)eliane.garo@unibas.chNot AvailableNot Available2024-05-12View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)eliane.garo@unibas.chNot AvailableNot Available2024-05-12View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)eliane.garo@unibas.chNot AvailableNot Available2024-05-12View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, CDCl3, experimental)eliane.garo@unibas.chNot AvailableNot Available2024-05-12View Spectrum
NOESY NMR[1H, 1H] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)eliane.garo@unibas.chNot AvailableNot Available2024-05-12View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
corymbosa
      Not Available
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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References
General References
  1. Syafni N, Faleschini MT, Garifulina A, Danton O, Gupta MP, Hering S, Hamburger M: Clerodane Diterpenes from Casearia corymbosa as Allosteric GABA(A) Receptor Modulators. J Nat Prod. 2022 May 27;85(5):1201-1210. doi: 10.1021/acs.jnatprod.1c00840. Epub  2022 Apr 27. [PubMed:35475609  ]