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Showing NP-Card for 3'-Prenylrubranine (NP0054847)

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Record Information
Version2.0
Created at2022-04-28 01:04:15 UTC
Updated at2022-04-28 01:04:15 UTC
NP-MRD IDNP0054847
Secondary Accession NumbersNone
Natural Product Identification
Common Name3'-Prenylrubranine
Description3'-Prenylrubranine belongs to the class of organic compounds known as 3-prenylated chalcones. These are chalcones featuring a C5-isoprenoid unit at the 3-position. Thus, 3'-prenylrubranine is considered to be a flavonoid. 3'-Prenylrubranine is found in Mallotus philippensis . 3'-Prenylrubranine was first documented in 2009 (PMID: 19336896). Based on a literature review very few articles have been published on 3'-prenylrubranine.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0054847 (3'-Prenylrubranine)


  Mrv1652304282203042D          

 34 38  0  0  1  0            999 V2000
    5.5158    4.5146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9670    3.8986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1591    4.0659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9001    4.8491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4489    5.4651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2567    5.2979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2260    3.1153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6772    2.4993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9363    1.7161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7442    1.5488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3875    1.1001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5591    1.3001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0827    0.6042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2816   -0.2204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1275   -0.3194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6763    0.3140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4879    0.1656    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4259   -1.0885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2412   -1.2146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5397   -1.9837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3550   -2.1098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0228   -2.6267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5481   -0.7641    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6710   -0.4870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9523    0.0579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3120    0.7616    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8019    1.3703    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0225    0.9847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9626    0.0912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2896    2.0889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1413    2.0601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6164    2.5658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3010    2.9138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2789   -1.2129    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
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 26 25  1  1  0  0  0
 13 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  6  0  0  0
 28 29  1  0  0  0  0
 24 29  1  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  0  0  0  0
 12 31  1  0  0  0  0
 30 32  1  0  0  0  0
 30 33  1  0  0  0  0
 24 34  1  1  0  0  0
M  END
Download

3D MOL for NP0054847 (3'-Prenylrubranine)

Download
3D SDF for NP0054847 (3'-Prenylrubranine)

  Mrv1652304282203042D          

 34 38  0  0  1  0            999 V2000
    5.5158    4.5146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9670    3.8986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1591    4.0659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9001    4.8491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4489    5.4651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2567    5.2979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2260    3.1153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6772    2.4993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9363    1.7161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7442    1.5488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3875    1.1001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5591    1.3001    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0827    0.6042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2816   -0.2204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1275   -0.3194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6763    0.3140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4879    0.1656    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4259   -1.0885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2412   -1.2146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5397   -1.9837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3550   -2.1098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0228   -2.6267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5481   -0.7641    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6710   -0.4870    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9523    0.0579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3120    0.7616    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8019    1.3703    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0225    0.9847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9626    0.0912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2896    2.0889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1413    2.0601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6164    2.5658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3010    2.9138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2789   -1.2129    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
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 26 25  1  1  0  0  0
 13 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  6  0  0  0
 28 29  1  0  0  0  0
 24 29  1  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  0  0  0  0
 12 31  1  0  0  0  0
 30 32  1  0  0  0  0
 30 33  1  0  0  0  0
 24 34  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0054847

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC1=C(O)C(C(=O)\C=C\C2=CC=CC=C2)=C2OC(C)(C)[C@H]3CC[C@]4(C)C[C@@H]3C2=C1O4

> <INCHI_IDENTIFIER>
InChI=1S/C30H34O4/c1-18(2)11-13-20-26(32)25(23(31)14-12-19-9-7-6-8-10-19)28-24-21-17-30(5,34-27(20)24)16-15-22(21)29(3,4)33-28/h6-12,14,21-22,32H,13,15-17H2,1-5H3/b14-12+/t21-,22-,30+/m0/s1

> <INCHI_KEY>
FYCUILMSDSLIGD-NLBJBFNFSA-N

> <FORMULA>
C30H34O4

> <MOLECULAR_WEIGHT>
458.598

> <EXACT_MASS>
458.245709575

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
52.04207420629166

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E)-1-[(1R,4S,13S)-9-hydroxy-1,5,5-trimethyl-10-(3-methylbut-2-en-1-yl)-6,15-dioxatetracyclo[9.3.1.0^{4,13}.0^{7,12}]pentadeca-7,9,11-trien-8-yl]-3-phenylprop-2-en-1-one

> <ALOGPS_LOGP>
7.01

> <JCHEM_LOGP>
7.321431879666665

> <ALOGPS_LOGS>
-6.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.93791218518964

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.344997500065008

> <JCHEM_PKA_STRONGEST_BASIC>
-4.628229083845681

> <JCHEM_POLAR_SURFACE_AREA>
55.760000000000005

> <JCHEM_REFRACTIVITY>
137.46110000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.41e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2E)-1-[(1R,4S,13S)-9-hydroxy-1,5,5-trimethyl-10-(3-methylbut-2-en-1-yl)-6,15-dioxatetracyclo[9.3.1.0^{4,13}.0^{7,12}]pentadeca-7,9,11-trien-8-yl]-3-phenylprop-2-en-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0054847 (3'-Prenylrubranine)
Download
PDB for NP0054847 (3'-Prenylrubranine)
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      10.296   8.427   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.272   7.277   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.764   7.590   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.280   9.052   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.305  10.202   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.813   9.889   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.755   5.815   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.731   4.665   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.214   3.203   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      10.722   2.891   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.190   2.053   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.644   2.427   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.754   1.128   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.126  -0.411   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.705  -0.596   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.729   0.586   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      10.244   0.309   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       8.262  -2.032   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.784  -2.267   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.341  -3.703   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      11.863  -3.938   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.376  -4.903   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       4.756  -1.426   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       3.119  -0.909   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.644   0.108   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.316   1.422   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.364   2.558   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.909   1.838   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.797   0.170   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.274   3.899   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       5.864   3.846   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       3.017   4.789   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.295   5.439   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.387  -2.264   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    2    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   16                                                  
CONECT   12   11   13   31                                                  
CONECT   13   12   14   26                                                  
CONECT   14   13   15   23                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15   11   17                                                  
CONECT   17   16                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   14   24                                                       
CONECT   24   23   25   29   34                                             
CONECT   25   24   26                                                       
CONECT   26   25   13   27                                                  
CONECT   27   26   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28   24                                                       
CONECT   30   27   31   32   33                                             
CONECT   31   30   12                                                       
CONECT   32   30                                                            
CONECT   33   30                                                            
CONECT   34   24                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

Download
3D PDB for NP0054847 (3'-Prenylrubranine)
Download
SMILES for NP0054847 (3'-Prenylrubranine)
CC(C)=CCC1=C(O)C(C(=O)\C=C\C2=CC=CC=C2)=C2OC(C)(C)[C@H]3CC[C@]4(C)C[C@@H]3C2=C1O4
Download
INCHI for NP0054847 (3'-Prenylrubranine)
InChI=1S/C30H34O4/c1-18(2)11-13-20-26(32)25(23(31)14-12-19-9-7-6-8-10-19)28-24-21-17-30(5,34-27(20)24)16-15-22(21)29(3,4)33-28/h6-12,14,21-22,32H,13,15-17H2,1-5H3/b14-12+/t21-,22-,30+/m0/s1
Download
View in JSmol
SynonymsNot Available
Chemical FormulaC30H34O4
Average Mass458.5980 Da
Monoisotopic Mass458.24571 Da
IUPAC Name(2E)-1-[(1R,4S,13S)-9-hydroxy-1,5,5-trimethyl-10-(3-methylbut-2-en-1-yl)-6,15-dioxatetracyclo[9.3.1.0^{4,13}.0^{7,12}]pentadeca-7,9,11-trien-8-yl]-3-phenylprop-2-en-1-one
Traditional Name(2E)-1-[(1R,4S,13S)-9-hydroxy-1,5,5-trimethyl-10-(3-methylbut-2-en-1-yl)-6,15-dioxatetracyclo[9.3.1.0^{4,13}.0^{7,12}]pentadeca-7,9,11-trien-8-yl]-3-phenylprop-2-en-1-one
CAS Registry NumberNot Available
SMILES
CC(C)=CCC1=C(O)C(C(=O)\C=C\C2=CC=CC=C2)=C2OC(C)(C)[C@H]3CC[C@]4(C)C[C@@H]3C2=C1O4
InChI Identifier
InChI=1S/C30H34O4/c1-18(2)11-13-20-26(32)25(23(31)14-12-19-9-7-6-8-10-19)28-24-21-17-30(5,34-27(20)24)16-15-22(21)29(3,4)33-28/h6-12,14,21-22,32H,13,15-17H2,1-5H3/b14-12+/t21-,22-,30+/m0/s1
InChI KeyFYCUILMSDSLIGD-NLBJBFNFSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Mallotus philippensisPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 3-prenylated chalcones. These are chalcones featuring a C5-isoprenoid unit at the 3-position.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassLinear 1,3-diarylpropanoids  
Sub ClassChalcones and dihydrochalcones  
Direct Parent3-prenylated chalcones  
Alternative Parents
Substituents
  • 3-prenylated chalcone
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  • 2'-hydroxychalcone
    • 

  • Cinnamic acid or derivatives
    • 

  • 2,2-dimethyl-1-benzopyran
    • 

  • Chromane
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  • Benzopyran
    • 

  • 1-benzopyran
    • 

  • Aryl ketone
    • 

  • Styrene
    • 

  • Phenol
    • 

  • Alkyl aryl ether
    • 

  • Benzenoid
    • 

  • Monocyclic benzene moiety
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  • Vinylogous acid
    • 

  • Alpha,beta-unsaturated ketone
    • 

  • Acryloyl-group
    • 

  • Enone
    • 

  • Ketone
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Ether
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
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
logP7.01ALOGPS
logP7.32ChemAxon
logS-6.1ALOGPS
pKa (Strongest Acidic)7.34ChemAxon
pKa (Strongest Basic)-4.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area55.76 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity137.46 m³·mol⁻¹ChemAxon
Polarizability52.04 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00007158  
Chemspider ID24846081  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound42607682  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Zaidi SF, Yoshida I, Butt F, Yusuf MA, Usmanghani K, Kadowaki M, Sugiyama T: Potent bactericidal constituents from Mallotus philippinensis against clarithromycin and metronidazole resistant strains of Japanese and Pakistani Helicobacter pylori. Biol Pharm Bull. 2009 Apr;32(4):631-6. doi: 10.1248/bpb.32.631. [PubMed:19336896  ]