NP-MRD: Showing NP-Card for (1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one (NP0251614)

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Record Information

Version

2.0

Created at

2022-09-07 14:51:48 UTC

Updated at

2022-09-07 14:51:48 UTC

NP-MRD ID

NP0251614

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one

Description

Sophorasine B 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. Based on a literature review very few articles have been published on Sophorasine B.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 42  0  0  0  0  0  0  0  0999 V2000
    4.8617   -0.2627   -0.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    0.5450    0.6454 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0980    1.2818   -0.2940 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9277   -0.3162    1.4440 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5252   -0.9768    2.3330 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5086   -0.5006    1.3516 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7597   -0.0450    0.2703 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8269   -0.6307   -0.9932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6260   -0.7527   -1.5192 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0530    0.6741   -1.7645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2000    1.3091   -0.3868 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0264    1.1425    0.4713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3870    0.6594    0.1973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3874    1.3768    0.7922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5047    0.7427    1.3370 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5669   -0.6295    1.2554 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5669   -1.3203    0.6629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5877   -2.5561    0.5707 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4871   -0.6666    0.1401 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4238   -1.4388   -0.4777 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6915   -0.2428   -1.1962 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7895   -1.3378    0.2072 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8820    0.0675    0.1187 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3927    1.2505    1.2900 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7702    1.7010   -0.8992 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9824   -0.1637    2.3173 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3113   -1.6394    1.4171 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2159   -1.6698   -0.8947 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3496   -0.0550   -1.7672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6115   -1.3296   -2.4771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0808    0.6354   -2.1958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3548    1.2172   -2.3965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3406    2.4016   -0.5577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3742    1.0899    1.5377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6130    2.0918    0.4744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3364    2.4551    0.8545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3176    1.2570    1.8151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4317   -1.1445    1.6740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8136   -1.8063    0.3998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8743   -2.4136   -0.8634 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
 19 20  1  0
 12  7  1  0
 19 13  1  0
 20  9  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  1
  3 25  1  0
  6 26  1  0
  6 27  1  0
  8 28  1  0
  8 29  1  0
  9 30  1  6
 10 31  1  0
 10 32  1  0
 11 33  1  6
 12 34  1  0
 12 35  1  0
 14 36  1  0
 15 37  1  0
 16 38  1  0
 20 39  1  0
 20 40  1  0
M  END


  Mrv1652309072216512D          

 20 22  0  0  1  0            999 V2000
    7.7283    2.0522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1187    1.4963    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.2954    0.6905    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3325    1.7463    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1558    2.5521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7229    1.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9367    1.4403    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8667    2.2624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2360    2.7942    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1662    1.6853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5828    0.7397    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4049    0.8096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9521    1.2715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2752    0.7999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5283    1.1503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4584    1.9723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1353    2.4439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0654    3.2659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8822    2.0935    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4140    2.7242    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  1  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
 11 10  1  1  0  0  0
 11 12  1  0  0  0  0
  7 12  1  0  0  0  0
 11 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
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 13 19  1  0  0  0  0
 19 20  1  0  0  0  0
  9 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0251614

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](O)C(=O)CN1C[C@@H]2C[C@H](C1)C1=CC=CC(=O)N1C2

> <INCHI_IDENTIFIER>
InChI=1S/C15H20N2O3/c1-10(18)14(19)9-16-6-11-5-12(8-16)13-3-2-4-15(20)17(13)7-11/h2-4,10-12,18H,5-9H2,1H3/t10-,11+,12-/m1/s1

> <INCHI_KEY>
TYNIDTXHMHOCQE-GRYCIOLGSA-N

> <FORMULA>
C15H20N2O3

> <MOLECULAR_WEIGHT>
276.336

> <EXACT_MASS>
276.147392512

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
28.453923246413964

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
-0.33768064233333356

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
17.2200122438829

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.675210355829638

> <JCHEM_PKA_STRONGEST_BASIC>
6.827366357071714

> <JCHEM_POLAR_SURFACE_AREA>
60.85

> <JCHEM_REFRACTIVITY>
78.05479999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      14.426   3.831   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.288   2.793   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      13.618   1.289   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      11.821   3.260   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      11.491   4.764   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      10.683   2.222   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       9.215   2.689   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       9.085   4.223   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.907   5.216   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.777   3.146   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.688   1.381   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.222   1.511   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.511   2.373   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.247   1.493   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.853   2.147   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.722   3.682   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.986   4.562   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.855   6.096   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0       5.380   3.908   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       6.373   5.085   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   20                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11    7                                                       
CONECT   13   11   14   19                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   13   20                                                  
CONECT   20   19    9                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₀N₂O₃

Average Mass

276.3360 Da

Monoisotopic Mass

276.14739 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@@H](O)C(=O)CN1C[C@@H]2C[C@H](C1)C1=CC=CC(=O)N1C2

InChI Identifier

InChI=1S/C15H20N2O3/c1-10(18)14(19)9-16-6-11-5-12(8-16)13-3-2-4-15(20)17(13)7-11/h2-4,10-12,18H,5-9H2,1H3/t10-,11+,12-/m1/s1

InChI Key

TYNIDTXHMHOCQE-GRYCIOLGSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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
Acyloin
Monosaccharide
Piperidine
Pyridine
Heteroaromatic compound
Alpha-hydroxy ketone
1,3-aminoalcohol
Alpha-aminoketone
Tertiary aliphatic amine
Ketone
Lactam
Tertiary amine
Secondary alcohol
Azacycle
Organoheterocyclic compound
Organic oxide
Organic nitrogen compound
Carbonyl group
Amine
Organonitrogen compound
Organooxygen compound
Alcohol
Hydrocarbon derivative
Organic oxygen compound
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00007726

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101599488

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one (NP0251614)

MOL for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)

3D MOL for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)

3D SDF for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)

3D-SDF for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)

PDB for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)

3D PDB for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)

SMILES for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)

INCHI for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)

Structure for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)

3D Structure for NP0251614 ((1r,9s)-11-[(3r)-3-hydroxy-2-oxobutyl]-7,11-diazatricyclo[7.3.1.0²,⁷]trideca-2,4-dien-6-one)