NP-MRD: Showing NP-Card for Chrysopentamine (NP0068661)

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Record Information

Version

2.0

Created at

2022-04-28 13:55:26 UTC

Updated at

2022-04-28 13:55:26 UTC

NP-MRD ID

NP0068661

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Chrysopentamine

Description

Chrysopentamine is found in Strychnos usambarensis.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282215552D          

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M  CHG  1  18   1
M  END

     RDKit          3D

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M  CHG  1   5   1
M  END


  Mrv1652304282215552D          

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    3.2683    5.4447    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8203    6.0578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6273    5.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8822    5.1016    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6359    5.4372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4433    5.4447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1884    4.6601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8558    4.1751    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3814    4.4885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8294    5.1016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0843    5.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8913    6.0578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0950    2.1347    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3435   -1.6618    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  2  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  4 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 14 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 18 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  2  0  0  0  0
 21 26  1  0  0  0  0
 27 26  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 27 32  1  0  0  0  0
 32 33  1  0  0  0  0
 29 34  1  6  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 28 36  1  6  0  0  0
 35 37  1  0  0  0  0
 37 38  2  0  0  0  0
 38 39  1  0  0  0  0
 39 40  2  0  0  0  0
 34 40  1  0  0  0  0
 20 41  1  0  0  0  0
  1 42  1  0  0  0  0
M  CHG  1  18   1
M  END
> <DATABASE_ID>
NP0068661

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CCC[C@@H]1C1=C(O)C=CC2=C1NC1=C2C=C[N+]2=CC(C=C)=C(C[C@H]3[C@@H]4NC5=C(C=CC=C5)[C@@H]4CCN3C)C(O)=C12

> <INCHI_IDENTIFIER>
InChI=1S/C35H37N5O2/c1-4-20-19-40-17-14-24-22-11-12-29(41)30(27-10-7-15-38(27)2)32(22)37-33(24)34(40)35(42)25(20)18-28-31-23(13-16-39(28)3)21-8-5-6-9-26(21)36-31/h4-6,8-9,11-12,14,17,19,23,27-28,31,36H,1,7,10,13,15-16,18H2,2-3H3,(H2,37,41,42)/p+1/t23-,27+,28-,31+/m0/s1

> <INCHI_KEY>
GPIUTZXRHBDBLI-GOGGMHKJSA-O

> <FORMULA>
C35H38N5O2

> <MOLECULAR_WEIGHT>
560.721

> <EXACT_MASS>
560.302001904

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
64.24293287015598

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-{[(1S,4aS,9aR)-2-methyl-1H,2H,3H,4H,4aH,9H,9aH-pyrido[3,4-b]indol-1-yl]methyl}-5-ethenyl-3,14-dihydroxy-15-[(2R)-1-methylpyrrolidin-2-yl]-7lambda5,17-diazatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,6,8,11(16),12,14-octaen-7-ylium

> <ALOGPS_LOGP>
1.84

> <JCHEM_LOGP>
2.7880300345805233

> <ALOGPS_LOGS>
-5.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
7.5474503699803

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.254067166927633

> <JCHEM_PKA_STRONGEST_BASIC>
11.890603561220837

> <JCHEM_POLAR_SURFACE_AREA>
78.86000000000001

> <JCHEM_REFRACTIVITY>
172.27039999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.65e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-{[(1S,4aS,9aR)-2-methyl-1H,3H,4H,4aH,9H,9aH-pyrido[3,4-b]indol-1-yl]methyl}-5-ethenyl-3,14-dihydroxy-15-[(2R)-1-methylpyrrolidin-2-yl]-7lambda5,17-diazatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,6,8,11(16),12,14-octaen-7-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

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      13.869  -1.571   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      15.276  -0.944   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.437   0.587   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.191   1.493   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.784   0.866   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.623  -0.665   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.216  -1.292   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.896  -2.798   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.364  -2.959   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.738  -1.552   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       9.882  -0.522   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       9.721   1.010   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      11.753   2.011   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      12.523   3.344   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      14.030   3.024   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      15.060   4.169   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      14.584   5.633   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      13.078   5.953   0.000  0.00  0.00           N+1
HETATM   19  C   UNK     0      12.048   4.809   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.541   5.129   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.065   6.594   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.096   7.738   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.602   7.418   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.620   9.203   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      11.650  10.347   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.559   6.914   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.083   8.379   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.577   8.699   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.101  10.163   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.131  11.308   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.638  10.988   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       9.114   9.523   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      10.520  10.149   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.561  10.163   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.085   8.699   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0       5.331   7.794   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0       2.579   8.379   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       1.548   9.523   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       2.024  10.988   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       3.530  11.308   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       9.511   3.985   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      13.708  -3.102   0.000  0.00  0.00           O+0
CONECT    1    2    6   42                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   15                                                  
CONECT    5    4    6   13                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    7   12                                                  
CONECT   12   11                                                            
CONECT   13    5   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14    4   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18   14   20                                                  
CONECT   20   19   21   41                                                  
CONECT   21   20   22   26                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22   18                                                       
CONECT   24   22   25                                                       
CONECT   25   24                                                            
CONECT   26   21   27                                                       
CONECT   27   26   28   32                                                  
CONECT   28   27   29   36                                                  
CONECT   29   28   30   34                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   27   33                                                  
CONECT   33   32                                                            
CONECT   34   29   35   40                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35   28                                                       
CONECT   37   35   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   34                                                       
CONECT   41   20                                                            
CONECT   42    1                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   98    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₅H₃₈N₅O₂

Average Mass

560.7210 Da

Monoisotopic Mass

560.30200 Da

IUPAC Name

4-{[(1S,4aS,9aR)-2-methyl-1H,2H,3H,4H,4aH,9H,9aH-pyrido[3,4-b]indol-1-yl]methyl}-5-ethenyl-3,14-dihydroxy-15-[(2R)-1-methylpyrrolidin-2-yl]-7lambda5,17-diazatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,6,8,11(16),12,14-octaen-7-ylium

Traditional Name

4-{[(1S,4aS,9aR)-2-methyl-1H,3H,4H,4aH,9H,9aH-pyrido[3,4-b]indol-1-yl]methyl}-5-ethenyl-3,14-dihydroxy-15-[(2R)-1-methylpyrrolidin-2-yl]-7lambda5,17-diazatetracyclo[8.7.0.0^{2,7}.0^{11,16}]heptadeca-1(10),2,4,6,8,11(16),12,14-octaen-7-ylium

CAS Registry Number

Not Available

SMILES

CN1CCC[C@@H]1C1=C(O)C=CC2=C1NC1=C2C=C[N+]2=CC(C=C)=C(C[C@H]3[C@@H]4NC5=C(C=CC=C5)[C@@H]4CCN3C)C(O)=C12

InChI Identifier

InChI=1S/C35H37N5O2/c1-4-20-19-40-17-14-24-22-11-12-29(41)30(27-10-7-15-38(27)2)32(22)37-33(24)34(40)35(42)25(20)18-28-31-23(13-16-39(28)3)21-8-5-6-9-26(21)36-31/h4-6,8-9,11-12,14,17,19,23,27-28,31,36H,1,7,10,13,15-16,18H2,2-3H3,(H2,37,41,42)/p+1/t23-,27+,28-,31+/m0/s1

InChI Key

GPIUTZXRHBDBLI-GOGGMHKJSA-O

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
Strychnos usambarensis	Plant	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	1.84	ALOGPS
logP	2.79	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	5.25	ChemAxon
pKa (Strongest Basic)	11.89	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	78.86 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	172.27 m³·mol⁻¹	ChemAxon
Polarizability	64.24 Å³	ChemAxon
Number of Rings	8	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for Chrysopentamine (NP0068661)

MOL for NP0068661 (Chrysopentamine)

3D MOL for NP0068661 (Chrysopentamine)

3D SDF for NP0068661 (Chrysopentamine)

3D-SDF for NP0068661 (Chrysopentamine)

PDB for NP0068661 (Chrysopentamine)

3D PDB for NP0068661 (Chrysopentamine)

SMILES for NP0068661 (Chrysopentamine)

INCHI for NP0068661 (Chrysopentamine)

Structure for NP0068661 (Chrysopentamine)

3D Structure for NP0068661 (Chrysopentamine)