NP-MRD: Showing NP-Card for Tsukushinamine A (NP0051289)

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Record Information

Version

2.0

Created at

2022-04-27 22:40:10 UTC

Updated at

2022-04-27 22:40:10 UTC

NP-MRD ID

NP0051289

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Tsukushinamine A

Description

(2R,3S,10S,12R)-2-(prop-2-en-1-yl)-1,8-diazatetracyclo[8.3.1.0³,⁸.0³,¹²]Tetradec-4-en-7-one belongs to the class of organic compounds known as 1,4-diazepanes. These are diazepanes having the two nitrogen atoms at position 1 and 4 of the diazepane ring. Tsukushinamine A is found in Sophora franchetiana. Based on a literature review very few articles have been published on (2R,3S,10S,12R)-2-(prop-2-en-1-yl)-1,8-diazatetracyclo[8.3.1.0³,⁸.0³,¹²]Tetradec-4-en-7-one.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282200402D          

 18 21  0  0  1  0            999 V2000
    4.6551    1.0276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8766    1.3330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1265    0.8592    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3376   -0.0133    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1320   -0.3031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2656   -1.1173    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7775    0.2137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7197   -0.6777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8240   -0.4950    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9483    0.0416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4193    0.7507    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9275    1.5469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5535    1.0841    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5377    1.5899    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7088    2.3970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4933    2.6524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6643    3.4594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1736    0.1887    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  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  1  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
 11 10  1  6  0  0  0
  3 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  3 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 13 18  1  0  0  0  0
  9 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051289

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C=CC[C@H]1N2C[C@H]3C[C@@H](C2)CN2C(=O)CC=C[C@@]132

> <INCHI_IDENTIFIER>
InChI=1S/C15H20N2O/c1-2-4-13-15-6-3-5-14(18)17(15)9-11-7-12(15)10-16(13)8-11/h2-3,6,11-13H,1,4-5,7-10H2/t11-,12+,13+,15-/m0/s1

> <INCHI_KEY>
DEDKBUWNGGQJMQ-JLNYLFASSA-N

> <FORMULA>
C15H20N2O

> <MOLECULAR_WEIGHT>
244.338

> <EXACT_MASS>
244.157563272

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
45.914264806937084

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3S,10S,12R)-2-(prop-2-en-1-yl)-1,8-diazatetracyclo[8.3.1.0^{3,8}.0^{3,12}]tetradec-4-en-7-one

> <ALOGPS_LOGP>
1.68

> <JCHEM_LOGP>
0.7917017823333321

> <ALOGPS_LOGS>
-1.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.476796641929683

> <JCHEM_POLAR_SURFACE_AREA>
23.550000000000004

> <JCHEM_REFRACTIVITY>
72.1074

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.33e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,10S,12R)-2-(prop-2-en-1-yl)-1,8-diazatetracyclo[8.3.1.0^{3,8}.0^{3,12}]tetradec-4-en-7-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       8.690   1.918   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.236   2.488   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.836   1.604   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       6.230  -0.025   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       7.713  -0.566   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       7.963  -2.086   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       8.918   0.399   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.077  -1.265   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.405  -0.924   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.637   0.078   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.516   1.401   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.598   2.888   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       2.900   2.024   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       4.737   2.968   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.056   4.474   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.521   4.951   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.840   6.458   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.191   0.352   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   11   14                                             
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    1                                                       
CONECT    8    4    9                                                       
CONECT    9    8   10   18                                                  
CONECT   10    9   11                                                       
CONECT   11   10    3   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13    3   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   13    9                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₀N₂O

Average Mass

244.3380 Da

Monoisotopic Mass

244.15756 Da

IUPAC Name

(2R,3S,10S,12R)-2-(prop-2-en-1-yl)-1,8-diazatetracyclo[8.3.1.0^{3,8}.0^{3,12}]tetradec-4-en-7-one

Traditional Name

(2R,3S,10S,12R)-2-(prop-2-en-1-yl)-1,8-diazatetracyclo[8.3.1.0^{3,8}.0^{3,12}]tetradec-4-en-7-one

CAS Registry Number

Not Available

SMILES

C=CC[C@H]1N2C[C@H]3C[C@@H](C2)CN2C(=O)CC=C[C@@]132

InChI Identifier

InChI=1S/C15H20N2O/c1-2-4-13-15-6-3-5-14(18)17(15)9-11-7-12(15)10-16(13)8-11/h2-3,6,11-13H,1,4-5,7-10H2/t11-,12+,13+,15-/m0/s1

InChI Key

DEDKBUWNGGQJMQ-JLNYLFASSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Sophora franchetiana	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,4-diazepanes. These are diazepanes having the two nitrogen atoms at position 1 and 4 of the diazepane ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazepanes

Sub Class

1,4-diazepanes

Direct Parent

1,4-diazepanes

Alternative Parents

Substituents

Azepane
1,4-diazepane
N-alkylpyrrolidine
Piperidine
Tertiary carboxylic acid amide
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Lactam
Carboxamide group
Amino acid or derivatives
Azacycle
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	1.68	ALOGPS
logP	0.79	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Basic)	10.48	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	2	ChemAxon
Refractivity	72.11 m³·mol⁻¹	ChemAxon
Polarizability	45.91 Å³	ChemAxon
Number of Rings	4	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

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

162980983

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Tsukushinamine A (NP0051289)

MOL for NP0051289 (Tsukushinamine A)

3D MOL for NP0051289 (Tsukushinamine A)

3D SDF for NP0051289 (Tsukushinamine A)

3D-SDF for NP0051289 (Tsukushinamine A)

PDB for NP0051289 (Tsukushinamine A)

3D PDB for NP0051289 (Tsukushinamine A)

SMILES for NP0051289 (Tsukushinamine A)

INCHI for NP0051289 (Tsukushinamine A)

Structure for NP0051289 (Tsukushinamine A)

3D Structure for NP0051289 (Tsukushinamine A)