NP-MRD: Showing NP-Card for Valparicine (NP0077343)

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Record Information

Version

2.0

Created at

2022-04-28 22:30:27 UTC

Updated at

2022-04-28 22:30:27 UTC

NP-MRD ID

NP0077343

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Valparicine

Description

(1R,11R,12E,17S)-12-ethylidene-10-methylidene-8,14-diazapentacyclo[9.5.2.0¹,⁹.0²,⁷.0¹⁴,¹⁷]Octadeca-2,4,6,8-tetraene belongs to the class of organic compounds known as strychnos alkaloids. These are alkaloids having a core structure based on the strychnan, stemmadenine (seco-curan), or the akuammicine (curan) skeleton. Valparicine is found in Kopsia arborea. Based on a literature review very few articles have been published on (1R,11R,12E,17S)-12-ethylidene-10-methylidene-8,14-diazapentacyclo[9.5.2.0¹,⁹.0²,⁷.0¹⁴,¹⁷]Octadeca-2,4,6,8-tetraene.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304292200302D          

 21 25  0  0  1  0            999 V2000
    2.7182    1.0454    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6418    0.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4017   -0.1957    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9881    0.3880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5948    1.1132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0262    1.8164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8509    1.7944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2442    1.0692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8128    0.3660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8380   -0.2557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8364   -1.0807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0336    0.1640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4286    0.6350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9361    1.2509    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5206    1.9288    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2296    2.4227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9129    1.9184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6763    1.7136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4426    0.8548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3624    0.6740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6082   -0.1135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  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
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  6  0  0  0
 14 13  1  6  0  0  0
  1 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  1 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 12 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0077343

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C1\CN2CC[C@@]34[C@@H]2C[C@H]1C(=C)C3=NC1=C4C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C19H20N2/c1-3-13-11-21-9-8-19-15-6-4-5-7-16(15)20-18(19)12(2)14(13)10-17(19)21/h3-7,14,17H,2,8-11H2,1H3/b13-3-/t14-,17-,19+/m0/s1

> <INCHI_KEY>
KFXIUXCXSKTCNK-KLGAAMDDSA-N

> <FORMULA>
C19H20N2

> <MOLECULAR_WEIGHT>
276.383

> <EXACT_MASS>
276.162648652

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
49.68194743012799

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,11R,12E,17S)-12-ethylidene-10-methylidene-8,14-diazapentacyclo[9.5.2.0^{1,9}.0^{2,7}.0^{14,17}]octadeca-2(7),3,5,8-tetraene

> <ALOGPS_LOGP>
3.65

> <JCHEM_LOGP>
3.660623756666666

> <ALOGPS_LOGS>
-3.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.784406033986237

> <JCHEM_POLAR_SURFACE_AREA>
15.6

> <JCHEM_REFRACTIVITY>
88.65669999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.52e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,11R,12E,17S)-12-ethylidene-10-methylidene-8,14-diazapentacyclo[9.5.2.0^{1,9}.0^{2,7}.0^{14,17}]octadeca-2(7),3,5,8-tetraene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       5.074   1.951   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.931   0.298   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       6.350  -0.365   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.444   0.724   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.710   2.078   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.516   3.391   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.055   3.350   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.789   1.996   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.984   0.683   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.431  -0.477   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.428  -2.017   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.929   0.306   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   1.185   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.614   2.335   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       2.838   3.600   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       4.162   4.522   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.437   3.581   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.262   3.199   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.826   1.596   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.676   1.258   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.135  -0.212   0.000  0.00  0.00           C+0
CONECT    1    2    5   14   17                                             
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
CONECT   10    2   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13    1   15                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16    1                                                       
CONECT   18   15   19                                                       
CONECT   19   18   12   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₂₀N₂

Average Mass

276.3830 Da

Monoisotopic Mass

276.16265 Da

IUPAC Name

(1R,11R,12E,17S)-12-ethylidene-10-methylidene-8,14-diazapentacyclo[9.5.2.0^{1,9}.0^{2,7}.0^{14,17}]octadeca-2(7),3,5,8-tetraene

Traditional Name

(1R,11R,12E,17S)-12-ethylidene-10-methylidene-8,14-diazapentacyclo[9.5.2.0^{1,9}.0^{2,7}.0^{14,17}]octadeca-2(7),3,5,8-tetraene

CAS Registry Number

Not Available

SMILES

C\C=C1\CN2CC[C@@]34[C@@H]2C[C@H]1C(=C)C3=NC1=C4C=CC=C1

InChI Identifier

InChI=1S/C19H20N2/c1-3-13-11-21-9-8-19-15-6-4-5-7-16(15)20-18(19)12(2)14(13)10-17(19)21/h3-7,14,17H,2,8-11H2,1H3/b13-3-/t14-,17-,19+/m0/s1

InChI Key

KFXIUXCXSKTCNK-KLGAAMDDSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Kopsia arborea	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as strychnos alkaloids. These are alkaloids having a core structure based on the strychnan, stemmadenine (seco-curan), or the akuammicine (curan) skeleton.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Strychnos alkaloids

Sub Class

Not Available

Direct Parent

Strychnos alkaloids

Alternative Parents

Substituents

Strychnan skeleton
Stemmadenine-skeleton
3-alkylindole
Indolizidine
Indole or derivatives
Aralkylamine
Benzenoid
N-alkylpyrrolidine
Piperidine
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Ketimine
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Imine
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	3.65	ALOGPS
logP	3.66	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Basic)	9.78	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	15.6 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	88.66 m³·mol⁻¹	ChemAxon
Polarizability	49.68 Å³	ChemAxon
Number of Rings	5	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

163185538

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Valparicine (NP0077343)

MOL for NP0077343 (Valparicine)

3D MOL for NP0077343 (Valparicine)

3D SDF for NP0077343 (Valparicine)

3D-SDF for NP0077343 (Valparicine)

PDB for NP0077343 (Valparicine)

3D PDB for NP0077343 (Valparicine)

SMILES for NP0077343 (Valparicine)

INCHI for NP0077343 (Valparicine)

Structure for NP0077343 (Valparicine)

3D Structure for NP0077343 (Valparicine)