NP-MRD: Showing NP-Card for (-)-Rhombifoline (NP0051284)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-04-27 22:39:56 UTC

Updated at

2022-04-27 22:39:56 UTC

NP-MRD ID

NP0051284

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Rhombifoline

Description

(1S,9R)-11-(but-3-en-1-yl)-7,11-diazatricyclo[7.3.1.0²,⁷]Trideca-2,4-dien-6-one belongs to the class of organic compounds known as cytisine and derivatives. These are lupin alkaloids with a structure based on the cytisine skeleton, which is a tetracyclic ketone containing fused pyridine and piperidine rings that form pyrido[1,2a][1,5]diazocin-8-one. (-)-Rhombifoline is found in Ammodendron longiracemosum, Clathrotropis brachypetala , Clathrotropis glaucophylla, Echinosophora koreensis, Genista lydia var. antiochia, Genista lydia var. lydia, Genista tinctoria , Maackia amurensis , Maackia amurensis subsp. buergeri , Maackia tashiroi, Petteria ramentacea, Sophora chrysophylla, Sophora flavescens , Sophora franchetiana, Sophora microphylla , Sophora mollis , Sophora secundiflora , Spartium junceum , Thermopsis chinensis, Thermopsis lanceolata, Thermopsis macrophylla, Thermopsis rhombifolia, Ulex airensis, Ulex australis, Ulex densus, Ulex europaeus , Ulex minor and Ulex jussiaei. Based on a literature review very few articles have been published on (1S,9R)-11-(but-3-en-1-yl)-7,11-diazatricyclo[7.3.1.0²,⁷]Trideca-2,4-dien-6-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 38 40  0  0  0  0  0  0  0  0999 V2000
    4.1239   -0.6582    1.5874 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8940   -0.4082    0.2841 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5356    0.9553   -0.0992 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1984    1.1848   -0.7261 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0454    0.8484    0.0226 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8189   -0.5161    0.3448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3334   -1.1870   -0.3450 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3089   -0.7464   -1.8088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6648    0.7262   -1.7800 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1007    1.4574   -0.6285 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1877    0.7610   -1.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5079    0.0265   -0.4231 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6698   -0.8480    0.1598 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1214   -1.4740    1.3086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3681   -1.2396    1.8619 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2108   -0.3359    1.2428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7440    0.2753    0.1041 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5322    1.1035   -0.4529 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3926   -1.6398    1.9437 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0440    0.1360    2.2986 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0085   -1.2545   -0.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7060    1.6764    0.7544 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2882    1.2576   -0.9066 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1981    2.2868   -0.9990 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2286    0.6828   -1.7367 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615   -0.6853    1.4646 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7102   -1.1089    0.0472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1382   -2.2833   -0.3362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1488   -1.3391   -2.2775 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6173   -0.9805   -2.3218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3481    1.1998   -2.7454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8621    1.6880    0.1683 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2396    2.4829   -0.9670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5861    0.1707   -2.4964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5629    1.7998   -1.6149 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4742   -2.1890    1.8066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7366   -1.7193    2.7571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2042   -0.1060    1.6211 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  7 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 17 12  1  0
 12 11  1  0
  6  5  1  0
 12 13  1  0
 11  9  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
 10 32  1  0
 10 33  1  0
  9 31  1  6
  8 29  1  0
  8 30  1  0
  7 28  1  6
  6 26  1  0
  6 27  1  0
 14 36  1  0
 15 37  1  0
 16 38  1  0
 11 34  1  0
 11 35  1  0
M  END


  Mrv1652304282200392D          

 18 20  0  0  1  0            999 V2000
    4.1130    1.0240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1722    0.2011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4891   -0.2616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5483   -1.0845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7469    0.0986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6877    0.9215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3708    1.3842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0641    1.4615    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9797    0.3536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3840   -0.5842    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2069   -0.5251    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7603   -0.0442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7011    0.7787    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2412    1.4024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0817    1.0389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6985    0.4910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4814    0.7513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0982    0.2034    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  1  0  0  0  0
  6  7  2  0  0  0  0
  1  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
  5 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  8 14  1  0  0  0  0
 13 15  1  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
M  END
> <DATABASE_ID>
NP0051284

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C=CCCN1C[C@H]2C[C@@H](C1)C1=CC=CC(=O)N1C2

> <INCHI_IDENTIFIER>
InChI=1S/C15H20N2O/c1-2-3-7-16-9-12-8-13(11-16)14-5-4-6-15(18)17(14)10-12/h2,4-6,12-13H,1,3,7-11H2/t12-,13+/m1/s1

> <INCHI_KEY>
ZVTFRRVBMAUIQW-OLZOCXBDSA-N

> <FORMULA>
C15H20N2O

> <MOLECULAR_WEIGHT>
244.338

> <EXACT_MASS>
244.157563272

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
27.799166940767737

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,9R)-11-(but-3-en-1-yl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one

> <ALOGPS_LOGP>
2.77

> <JCHEM_LOGP>
1.1231053586666657

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.29744942362708

> <JCHEM_POLAR_SURFACE_AREA>
23.550000000000004

> <JCHEM_REFRACTIVITY>
76.14070000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.17e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,9R)-11-(but-3-en-1-yl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one

> <JCHEM_VEBER_RULE>
1

$$$$

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       7.678   1.911   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.788   0.375   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.513  -0.488   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.623  -2.024   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       5.128   0.184   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       5.017   1.720   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.292   2.584   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.853   2.728   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.696   0.660   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.583  -1.091   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.120  -0.980   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.419  -0.083   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       1.309   1.454   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       2.317   2.618   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.153   1.939   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.304   0.917   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.765   1.402   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.917   0.380   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   11                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    1                                                       
CONECT    8    6    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10    5                                                       
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13    8                                                       
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₀N₂O

Average Mass

244.3380 Da

Monoisotopic Mass

244.15756 Da

IUPAC Name

(1S,9R)-11-(but-3-en-1-yl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one

Traditional Name

(1S,9R)-11-(but-3-en-1-yl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one

CAS Registry Number

Not Available

SMILES

C=CCCN1C[C@H]2C[C@@H](C1)C1=CC=CC(=O)N1C2

InChI Identifier

InChI=1S/C15H20N2O/c1-2-3-7-16-9-12-8-13(11-16)14-5-4-6-15(18)17(14)10-12/h2,4-6,12-13H,1,3,7-11H2/t12-,13+/m1/s1

InChI Key

ZVTFRRVBMAUIQW-OLZOCXBDSA-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
Ammodendron longiracemosum	Plant	KNApSAcK
Clathrotropis brachypetala	Plant	KNApSAcK
Clathrotropis glaucophylla	Plant	KNApSAcK
Echinosophora koreensis	Plant	KNApSAcK
Genista lydia var. antiochia	Plant	KNApSAcK
Genista lydia var. lydia	Plant	KNApSAcK
Genista tinctoria	Plant	KNApSAcK
Maackia amurensis	Plant	KNApSAcK
Maackia amurensis subsp. buergeri	Plant	KNApSAcK
Maackia tashiroi	Plant	KNApSAcK
Petteria ramentacea	Plant	KNApSAcK
Sophora chrysophylla	Plant	KNApSAcK
Sophora flavescens	Plant	KNApSAcK
Sophora franchetiana	Plant	KNApSAcK
Sophora microphylla	Plant	KNApSAcK
Sophora mollis	Plant	KNApSAcK
Sophora secundiflora	Plant	KNApSAcK
Spartium junceum	Plant	KNApSAcK
Thermopsis chinensis	Plant	KNApSAcK
Thermopsis lanceolata	Plant	KNApSAcK
Thermopsis macrophylla	Plant	KNApSAcK
Thermopsis rhombifolia	Plant	KNApSAcK
Ulex airensis	Plant	KNApSAcK
Ulex australis	Plant	KNApSAcK
Ulex densus	Plant	KNApSAcK
Ulex europaeus	Plant	KNApSAcK
Ulex minor	Plant	KNApSAcK
Ulex parviflorus subsp. jussiaei	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cytisine and derivatives. These are lupin alkaloids with a structure based on the cytisine skeleton, which is a tetracyclic ketone containing fused pyridine and piperidine rings that form pyrido[1,2a][1,5]diazocin-8-one.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Lupin alkaloids

Sub Class

Cytisine and derivatives

Direct Parent

Cytisine and derivatives

Alternative Parents

Substituents

Cytisine
Pyridinone
Aralkylamine
Piperidine
Pyridine
Heteroaromatic compound
Lactam
Tertiary amine
Tertiary aliphatic amine
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	2.77	ALOGPS
logP	1.12	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Basic)	9.3	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	23.55 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	76.14 m³·mol⁻¹	ChemAxon
Polarizability	27.8 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

5422580

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

7067420

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Rhombifoline (NP0051284)

MOL for NP0051284 ((-)-Rhombifoline)

3D MOL for NP0051284 ((-)-Rhombifoline)

3D SDF for NP0051284 ((-)-Rhombifoline)

3D-SDF for NP0051284 ((-)-Rhombifoline)

PDB for NP0051284 ((-)-Rhombifoline)

3D PDB for NP0051284 ((-)-Rhombifoline)

SMILES for NP0051284 ((-)-Rhombifoline)

INCHI for NP0051284 ((-)-Rhombifoline)

Structure for NP0051284 ((-)-Rhombifoline)

3D Structure for NP0051284 ((-)-Rhombifoline)