NP-MRD: Showing NP-Card for Hymenotamayonin B (NP0332436)

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Record Information

Version

1.0

Created at

2024-01-24 04:45:36 UTC

Updated at

2024-05-14 23:06:49 UTC

NP-MRD ID

NP0332436

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hymenotamayonin B

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01242404452D          

 36 38  0  0  1  0            999 V2000
   -0.0425   -4.5208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5408   -3.9375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3377   -4.1510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3273   -3.1406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4696   -2.9270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6831   -2.1302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997   -1.5468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3133   -0.7499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2701   -0.1665    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0323   -0.4822    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0323   -1.3072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7468   -1.7197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7468   -2.5447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4612   -2.9572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323   -2.9572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5391   -0.0056    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0456    0.5957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2701    1.3579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323    1.6736    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7945    1.3579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3779    1.9412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1102    0.5957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7945   -0.1665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3779   -0.7499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7628    0.5957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0954    1.0806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323    2.4986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3178    2.9111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3178    3.7361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3966    4.1486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323    4.1486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1102   -0.5364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6935   -1.1197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4904   -0.9062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4800   -1.9166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0634   -2.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  9  8  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
  9 16  1  6  0  0  0
  9 17  1  0  0  0  0
 17 18  1  0  0  0  0
 19 18  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 22 23  1  0  0  0  0
 10 23  1  0  0  0  0
 23 24  2  0  0  0  0
 19 25  1  0  0  0  0
 10 25  1  0  0  0  0
 25 26  2  0  0  0  0
 19 27  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
  8 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  2  0  0  0  0
  6 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END


  Mrv2104 01242404452D          

 36 38  0  0  1  0            999 V2000
   -0.0425   -4.5208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5408   -3.9375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3377   -4.1510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3273   -3.1406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4696   -2.9270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6831   -2.1302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997   -1.5468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3133   -0.7499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2701   -0.1665    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0323   -0.4822    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0323   -1.3072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7468   -1.7197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7468   -2.5447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4612   -2.9572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323   -2.9572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5391   -0.0056    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0456    0.5957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2701    1.3579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323    1.6736    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7945    1.3579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3779    1.9412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1102    0.5957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7945   -0.1665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3779   -0.7499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7628    0.5957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0954    1.0806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323    2.4986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3178    2.9111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3178    3.7361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3966    4.1486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323    4.1486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1102   -0.5364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6935   -1.1197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4904   -0.9062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4800   -1.9166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0634   -2.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  9  8  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
  9 16  1  6  0  0  0
  9 17  1  0  0  0  0
 17 18  1  0  0  0  0
 19 18  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 22 23  1  0  0  0  0
 10 23  1  0  0  0  0
 23 24  2  0  0  0  0
 19 25  1  0  0  0  0
 10 25  1  0  0  0  0
 25 26  2  0  0  0  0
 19 27  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
  8 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  2  0  0  0  0
  6 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332436

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(CC[C@@]2(CC=C(C)C)C(O)=CC(=O)[C@]1(CC=C(C)C)C2=O)C1=CC(O)=C(O)C(CC=C(C)C)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H38O5/c1-18(2)7-8-21-15-22(16-24(31)27(21)34)23-11-13-29(12-9-19(3)4)25(32)17-26(33)30(23,28(29)35)14-10-20(5)6/h7,9-10,15-17,23,31-32,34H,8,11-14H2,1-6H3/t23-,29+,30-/m1/s1

> <INCHI_KEY>
HYXZZTKUORWYRE-GOQOSDJISA-N

> <FORMULA>
C30H38O5

> <MOLECULAR_WEIGHT>
478.629

> <EXACT_MASS>
478.271924324

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
53.65182334635782

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,5R,8R)-8-[3,4-dihydroxy-5-(3-methylbut-2-en-1-yl)phenyl]-4-hydroxy-1,5-bis(3-methylbut-2-en-1-yl)bicyclo[3.3.1]non-3-ene-2,9-dione

> <JCHEM_LOGP>
7.299282062000002

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.146918408983051

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.400704515531435

> <JCHEM_PKA_STRONGEST_BASIC>
-6.304532098826531

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
144.12739999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5R,8R)-8-[3,4-dihydroxy-5-(3-methylbut-2-en-1-yl)phenyl]-4-hydroxy-1,5-bis(3-methylbut-2-en-1-yl)bicyclo[3.3.1]non-3-ene-2,9-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JAN-24   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JAN-24         0                                  
HETATM    1  C   UNK     0      -0.079  -8.439   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.010  -7.350   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.497  -7.748   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.611  -5.862   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.877  -5.464   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.275  -3.976   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.186  -2.887   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.585  -1.400   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.504  -0.311   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.927  -0.900   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.927  -2.440   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.261  -3.210   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.261  -4.750   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.594  -5.520   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.927  -5.520   0.000  0.00  0.00           C+0
HETATM   16  H   UNK     0      -1.006  -0.010   0.000  0.00  0.00           H+0
HETATM   17  C   UNK     0      -0.085   1.112   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.504   2.535   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.927   3.124   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.350   2.535   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.439   3.624   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       3.939   1.112   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.350  -0.311   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       4.439  -1.400   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.424   1.112   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.178   2.017   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.927   4.664   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.593   5.434   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.593   6.974   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -0.740   7.744   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       1.927   7.744   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -2.072  -1.001   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -3.161  -2.090   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -4.649  -1.692   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -2.763  -3.578   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -3.852  -4.667   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                                                       
CONECT    6    5    7   35                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   32                                                  
CONECT    9    8   10   16   17                                             
CONECT   10    9   11   23   25                                             
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16    9                                                            
CONECT   17    9   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   25   27                                             
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   10   24                                                  
CONECT   24   23                                                            
CONECT   25   19   10   26                                                  
CONECT   26   25                                                            
CONECT   27   19   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32    8   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    6   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₃₈O₅

Average Mass

478.6290 Da

Monoisotopic Mass

478.27192 Da

IUPAC Name

(1R,5R,8R)-8-[3,4-dihydroxy-5-(3-methylbut-2-en-1-yl)phenyl]-4-hydroxy-1,5-bis(3-methylbut-2-en-1-yl)bicyclo[3.3.1]non-3-ene-2,9-dione

Traditional Name

(1R,5R,8R)-8-[3,4-dihydroxy-5-(3-methylbut-2-en-1-yl)phenyl]-4-hydroxy-1,5-bis(3-methylbut-2-en-1-yl)bicyclo[3.3.1]non-3-ene-2,9-dione

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC[C@@]2(CC=C(C)C)C(O)=CC(=O)[C@]1(CC=C(C)C)C2=O)C1=CC(O)=C(O)C(CC=C(C)C)=C1

InChI Identifier

InChI=1S/C30H38O5/c1-18(2)7-8-21-15-22(16-24(31)27(21)34)23-11-13-29(12-9-19(3)4)25(32)17-26(33)30(23,28(29)35)14-10-20(5)6/h7,9-10,15-17,23,31-32,34H,8,11-14H2,1-6H3/t23-,29+,30-/m1/s1

InChI Key

HYXZZTKUORWYRE-GOQOSDJISA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	luis.guerrero@unige.ch	Not Available	Not Available	2024-01-24	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	luis.guerrero@unige.ch	Not Available	Not Available	2024-01-24	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	luis.guerrero@unige.ch	Not Available	Not Available	2024-01-24	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	luis.guerrero@unige.ch	Not Available	Not Available	2024-01-24	View Spectrum
1D NMR	[¹³C, ] NMR Spectrum (2D, 151 MHz, CD3OD, experimental)	luis.guerrero@unige.ch	Not Available	Not Available	2024-01-24	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	luis.guerrero@unige.ch	Not Available	Not Available	2024-01-24	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	luis.guerrero@unige.ch	Not Available	Not Available	2024-01-24	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600, CD₃OD, simulated)	luis.guerrero@unige.ch	University of Geneva	Luis Quiros-Guerrero, PhD	2024-05-14	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
punctata		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	7.3	ChemAxon
pKa (Strongest Acidic)	4.4	ChemAxon
pKa (Strongest Basic)	-6.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	144.13 m³·mol⁻¹	ChemAxon
Polarizability	53.65 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

Not Available

References

General References

Quiros-Guerrero LM, Marcourt L, Chaiwangrach N, Koval A, Ferreira Queiroz E, David B, Grondin A, Katanaev VL, Wolfender JL: Integration of Wnt-inhibitory activity and structural novelty scoring results to uncover novel bioactive natural products: new Bicyclo[3.3.1]non-3-ene-2,9-diones from the leaves of Hymenocardia punctata. Front Chem. 2024 Apr 4;12:1371982. doi: 10.3389/fchem.2024.1371982. eCollection 2024. [PubMed:38638877 ]

Showing NP-Card for Hymenotamayonin B (NP0332436)

MOL for NP0332436 (Hymenotamayonin B)

3D MOL for NP0332436 (Hymenotamayonin B)

3D SDF for NP0332436 (Hymenotamayonin B)

3D-SDF for NP0332436 (Hymenotamayonin B)

PDB for NP0332436 (Hymenotamayonin B)

3D PDB for NP0332436 (Hymenotamayonin B)

SMILES for NP0332436 (Hymenotamayonin B)

INCHI for NP0332436 (Hymenotamayonin B)

Structure for NP0332436 (Hymenotamayonin B)

3D Structure for NP0332436 (Hymenotamayonin B)