NP-MRD: Showing NP-Card for Picrasidine L (NP0068872)

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Record Information

Version

2.0

Created at

2022-04-28 14:08:38 UTC

Updated at

2022-04-28 14:08:38 UTC

NP-MRD ID

NP0068872

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Picrasidine L

Description

CHEMBL3400663 belongs to the class of organic compounds known as indolonaphthyridine alkaloids. These are a numerous and relatively straightforward subgroup of the b-carbolines, e.G. Canthin-6-one, in which an additional C3 unit is attached between C-1 and the indole nitrogen to form an additional ring. The group includes a few dimeric examples, such as Haplophytine. Picrasidine L is found in Eurycoma longifolia Jack , Eurycoma longifolida, Picrasma quassinoides Bennet, Picrasma quassioides and Picrasma quassioides D.Don.Benn. . CHEMBL3400663 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 32  0  0  0  0  0  0  0  0999 V2000
    3.9547   -0.5011   -0.2462 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5289   -0.6882   -0.2046 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9478   -1.9064   -0.2988 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5791   -2.1191   -0.2621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2887   -1.0543   -0.1222 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2920    0.1907   -0.0255 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6287    1.1546    0.1068 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1424    2.4165    0.2092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9936    3.3314    0.3338 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2249    2.6731    0.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6201    3.8772    0.2774 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    1.6916    0.0410 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7269    0.3964   -0.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8220    0.5426    0.0973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0798    1.0420    0.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1738    0.1795    0.1604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9663   -1.1807    0.0195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6858   -1.7281   -0.0874 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6534   -0.8489   -0.0451 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3431    0.1917    0.5048 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4173   -1.5045   -0.0309 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3169   -0.2197   -1.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6362   -2.7458   -0.4092 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1435   -3.1018   -0.3394 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2475    1.8667    0.0137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2294    2.1037    0.3080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1811    0.5726    0.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8235   -1.8498   -0.0097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5009   -2.7818   -0.1976 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  2  0
 13  2  1  0
 19  5  1  0
 13  6  1  0
 19 14  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  4 24  1  0
 15 26  1  0
 16 27  1  0
 17 28  1  0
 18 29  1  0
 12 25  1  0
M  END


  Mrv1533004241518202D          

 19 22  0  0  0  0            999 V2000
   -1.4424   -0.4639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6354   -0.6354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3805   -1.4201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4265   -1.5916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9785   -0.9785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7236   -0.1939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0834   -0.0224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1164    0.9622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5511    1.4471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4649    2.2676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3048    1.1115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9722    1.5964    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3910    0.2910    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0584   -0.1939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8654   -0.0224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4174   -0.6354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1625   -1.4201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3555   -1.5916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8035   -0.9785    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  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  6 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  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  2  0  0  0  0
  5 19  1  0  0  0  0
 14 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0068872

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=CC2=C3N(C4=CC=CC=C24)C(=O)C(=O)C=C13

> <INCHI_IDENTIFIER>
InChI=1S/C15H10N2O2/c1-16-7-6-10-9-4-2-3-5-11(9)17-14(10)12(16)8-13(18)15(17)19/h2-8H,1H3

> <INCHI_KEY>
YIFMSNBQADOPBX-UHFFFAOYSA-N

> <FORMULA>
C15H10N2O2

> <MOLECULAR_WEIGHT>
250.257

> <EXACT_MASS>
250.07422757

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
25.921953296136103

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-methyl-1,6-diazatetracyclo[7.6.1.0⁵,¹⁶.0¹⁰,¹⁵]hexadeca-4,7,9(16),10,12,14-hexaene-2,3-dione

> <ALOGPS_LOGP>
2.59

> <JCHEM_LOGP>
1.456625273666666

> <ALOGPS_LOGS>
-2.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.481411640475748

> <JCHEM_POLAR_SURFACE_AREA>
42.31

> <JCHEM_REFRACTIVITY>
73.01830000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.25e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-methyl-1,6-diazatetracyclo[7.6.1.0⁵,¹⁶.0¹⁰,¹⁵]hexadeca-4,7,9(16),10,12,14-hexaene-2,3-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0      -2.693  -0.866   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -1.186  -1.186   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -0.710  -2.651   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.796  -2.971   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.827  -1.827   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.351  -0.362   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.156  -0.042   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.217   1.796   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.029   2.701   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.868   4.233   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.436   2.075   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.681   2.980   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       2.597   0.543   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       3.842  -0.362   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.349  -0.042   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.379  -1.186   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.903  -2.651   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.397  -2.971   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.367  -1.827   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   19                                                  
CONECT    6    5    7   13                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    6   14                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18    5   14                                                  
MASTER        0    0    0    0    0    0    0    0   19    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₀N₂O₂

Average Mass

250.2570 Da

Monoisotopic Mass

250.07423 Da

IUPAC Name

6-methyl-1,6-diazatetracyclo[7.6.1.0⁵,¹⁶.0¹⁰,¹⁵]hexadeca-4,7,9(16),10,12,14-hexaene-2,3-dione

Traditional Name

6-methyl-1,6-diazatetracyclo[7.6.1.0⁵,¹⁶.0¹⁰,¹⁵]hexadeca-4,7,9(16),10,12,14-hexaene-2,3-dione

CAS Registry Number

Not Available

SMILES

CN1C=CC2=C3N(C4=CC=CC=C24)C(=O)C(=O)C=C13

InChI Identifier

InChI=1S/C15H10N2O2/c1-16-7-6-10-9-4-2-3-5-11(9)17-14(10)12(16)8-13(18)15(17)19/h2-8H,1H3

InChI Key

YIFMSNBQADOPBX-UHFFFAOYSA-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, 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
Eurycoma longifolia	Plant	KNApSAcK
Eurycoma longifolida	Plant	KNApSAcK
Picrasma quassinoides Bennet	Plant	KNApSAcK
Picrasma quassioides	LOTUS Database	35616633
Picrasma quassioides D.Don.Benn.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolonaphthyridine alkaloids. These are a numerous and relatively straightforward subgroup of the b-carbolines, e.G. Canthin-6-one, in which an additional C3 unit is attached between C-1 and the indole nitrogen to form an additional ring. The group includes a few dimeric examples, such as Haplophytine.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Indolonaphthyridine alkaloids

Sub Class

Not Available

Direct Parent

Indolonaphthyridine alkaloids

Alternative Parents

Substituents

Indolo[3,2-1de][1,5]naphthyridine
Beta-carboline
Pyridoindole
Naphthyridine
Indole
Indole or derivatives
Indolizine
Pyrrolopyridine
Pyridinone
Pyridine
Benzenoid
Heteroaromatic compound
Vinylogous amide
Pyrrole
Lactam
Cyclic ketone
Organoheterocyclic compound
Azacycle
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
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
logP	2.59	ALOGPS
logP	1.46	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	42.31 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	73.02 m³·mol⁻¹	ChemAxon
Polarizability	25.92 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

5324104

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Picrasidine L (NP0068872)

MOL for NP0068872 (Picrasidine L)

3D MOL for NP0068872 (Picrasidine L)

3D SDF for NP0068872 (Picrasidine L)

3D-SDF for NP0068872 (Picrasidine L)

PDB for NP0068872 (Picrasidine L)

3D PDB for NP0068872 (Picrasidine L)

SMILES for NP0068872 (Picrasidine L)

INCHI for NP0068872 (Picrasidine L)

Structure for NP0068872 (Picrasidine L)

3D Structure for NP0068872 (Picrasidine L)