NP-MRD: Showing NP-Card for Picrasidine S (NP0138471)

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Record Information

Version

1.0

Created at

2022-06-29 17:31:02 UTC

Updated at

2022-06-29 17:31:03 UTC

NP-MRD ID

NP0138471

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Picrasidine S

Description

Picrasidine S belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole. Picrasidine S is found in Picrasma quassioides. Picrasidine S is a moderately basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004181502512D          

 38 44  0  0  0  0            999 V2000
    0.1102   -1.1844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8826   -2.3866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1886   -2.8326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2278   -3.6566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9611   -4.0347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6551   -3.5887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6159   -2.7647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3875   -2.4727    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9036   -3.1164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7273   -3.1635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1799   -2.4738    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  7 38  1  0  0  0  0
 10 38  2  0  0  0  0
M  CHG  1  33   1
M  END

     RDKit          3D

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  1 39  1  0
  1 40  1  0
  1 41  1  0
M  CHG  1  32   1
M  END


  Mrv1533004181502512D          

 38 44  0  0  0  0            999 V2000
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 28 29  1  0  0  0  0
 27 30  1  0  0  0  0
 23 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 16 32  1  0  0  0  0
 22 32  2  0  0  0  0
 15 33  1  0  0  0  0
 11 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 35 38  1  0  0  0  0
  7 38  1  0  0  0  0
 10 38  2  0  0  0  0
M  CHG  1  33   1
M  END
> <DATABASE_ID>
NP0138471

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=CC2=C1NC1=C2C(OC)=C[N+]2=C1CCCC2C1=NC=C(OC)C2=C1NC1=C2C=CC=C1OC

> <INCHI_IDENTIFIER>
InChI=1S/C30H28N4O4/c1-35-20-12-6-9-17-25-23(38-4)15-34-18(28(25)32-26(17)20)10-7-11-19(34)29-30-24(22(37-3)14-31-29)16-8-5-13-21(36-2)27(16)33-30/h5-6,8-9,12-15,19H,7,10-11H2,1-4H3,(H,31,33)/p+1

> <INCHI_KEY>
ZHIAAGUQJJWYBK-UHFFFAOYSA-O

> <FORMULA>
C30H29N4O4

> <MOLECULAR_WEIGHT>
509.585

> <EXACT_MASS>
509.21833185

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
56.66486944599404

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-{4,8-dimethoxy-9H-pyrido[3,4-b]indol-1-yl}-9,15-dimethoxy-7λ⁵,17-diazatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-1(10),2(7),8,11(16),12,14-hexaen-7-ylium

> <ALOGPS_LOGP>
1.86

> <JCHEM_LOGP>
-0.44587882247174626

> <ALOGPS_LOGS>
-5.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
9.98150384988695

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.202278972783763

> <JCHEM_PKA_STRONGEST_BASIC>
2.546034769399498

> <JCHEM_POLAR_SURFACE_AREA>
85.27

> <JCHEM_REFRACTIVITY>
144.75379999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.76e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-{4,8-dimethoxy-9H-pyrido[3,4-b]indol-1-yl}-9,15-dimethoxy-7λ⁵,17-diazatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-1(10),2(7),8,11(16),12,14-hexaen-7-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 18-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-APR-15         0                                  
HETATM    1  C   UNK     0       0.206  -2.211   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.574  -2.917   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.648  -4.455   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.352  -5.287   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.425  -6.826   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.794  -7.531   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.090  -6.699   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.016  -5.161   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       4.457  -4.616   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       5.420  -5.817   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.958  -5.905   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.803  -4.618   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.340  -4.706   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.033  -6.081   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.188  -7.369   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.880  -8.744   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      11.418  -8.832   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      12.110 -10.208   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.265 -11.495   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      11.958 -12.871   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      11.113 -14.158   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.728 -11.407   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.634 -12.491   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.707 -14.029   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       7.411 -14.862   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.042 -14.156   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.969 -12.618   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       4.600 -11.912   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       3.305 -12.744   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.265 -11.785   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0       7.513 -10.265   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       9.035 -10.032   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0       7.650  -7.281   0.000  0.00  0.00           N+1
HETATM   34  C   UNK     0       6.805  -8.568   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       5.268  -8.480   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       4.423  -9.768   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       2.885  -9.680   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.575  -7.105   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   38                                                  
CONECT    8    7    3    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   38                                                  
CONECT   11   10   12   33                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   33                                                  
CONECT   16   15   17   32                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   19   23   32                                                  
CONECT   23   22   24   30                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   27   23   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31   16   22                                                  
CONECT   33   15   11   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   38                                                  
CONECT   36   35   37                                                       
CONECT   37   36                                                            
CONECT   38   35    7   10                                                  
MASTER        0    0    0    0    0    0    0    0   38    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₂₉N₄O₄

Average Mass

509.5850 Da

Monoisotopic Mass

509.21833 Da

IUPAC Name

6-{4,8-dimethoxy-9H-pyrido[3,4-b]indol-1-yl}-9,15-dimethoxy-7λ⁵,17-diazatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-1(10),2(7),8,11(16),12,14-hexaen-7-ylium

Traditional Name

6-{4,8-dimethoxy-9H-pyrido[3,4-b]indol-1-yl}-9,15-dimethoxy-7λ⁵,17-diazatetracyclo[8.7.0.0²,⁷.0¹¹,¹⁶]heptadeca-1(10),2(7),8,11(16),12,14-hexaen-7-ylium

CAS Registry Number

112503-87-4

SMILES

COC1=CC=CC2=C1NC1=C2C(OC)=C[N+]2=C1CCCC2C1=NC=C(OC)C2=C1NC1=C2C=CC=C1OC

InChI Identifier

InChI=1S/C30H28N4O4/c1-35-20-12-6-9-17-25-23(38-4)15-34-18(28(25)32-26(17)20)10-7-11-19(34)29-30-24(22(37-3)14-31-29)16-8-5-13-21(36-2)27(16)33-30/h5-6,8-9,12-15,19H,7,10-11H2,1-4H3,(H,31,33)/p+1

InChI Key

ZHIAAGUQJJWYBK-UHFFFAOYSA-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, 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

Species Name	Source	Reference
Picrasma quassioides	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Harmala alkaloids

Sub Class

Not Available

Direct Parent

Harmala alkaloids

Alternative Parents

Substituents

Harman
Beta-carboline
Pyridoindole
Bipyridine
Indole
Indole or derivatives
Anisole
Phenol ether
Alkyl aryl ether
Benzenoid
Pyridine
Pyridinium
Heteroaromatic compound
Pyrrole
Organoheterocyclic compound
Azacycle
Ether
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxygen compound
Organic cation
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	1.86	ALOGPS
logP	-0.45	ChemAxon
logS	-6	ALOGPS
pKa (Strongest Acidic)	9.2	ChemAxon
pKa (Strongest Basic)	2.55	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	85.27 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	144.75 m³·mol⁻¹	ChemAxon
Polarizability	56.66 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	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

5318873

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Picrasidine S (NP0138471)

MOL for NP0138471 (Picrasidine S)

3D MOL for NP0138471 (Picrasidine S)

3D SDF for NP0138471 (Picrasidine S)

3D-SDF for NP0138471 (Picrasidine S)

PDB for NP0138471 (Picrasidine S)

3D PDB for NP0138471 (Picrasidine S)

SMILES for NP0138471 (Picrasidine S)

INCHI for NP0138471 (Picrasidine S)

Structure for NP0138471 (Picrasidine S)

3D Structure for NP0138471 (Picrasidine S)