NP-MRD: Showing NP-Card for Pachypodanthine (NP0069244)

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Record Information

Version

2.0

Created at

2022-04-28 14:35:15 UTC

Updated at

2022-04-28 14:35:15 UTC

NP-MRD ID

NP0069244

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pachypodanthine

Description

Pachypodantine belongs to the class of organic compounds known as aporphines. These are quinoline alkaloids containing the dibenzo[de,g]quinoline ring system or a dehydrogenated derivative thereof. Pachypodanthine is found in Duguetia flagellaris, Duguetia staudtii, Greenwayodendron oliveri, Greenwayodendron suaveolens, Pachypodanthium staudtii Engl.et Diels. and Polyalthia suaveolens. Based on a literature review very few articles have been published on pachypodantine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 43  0  0  0  0  0  0  0  0999 V2000
   -4.0829   -0.5997   -0.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8708   -0.6065   -0.6911 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7664   -0.4648    0.1527 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8810   -1.6192    0.1650 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4518   -2.8647    0.3736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6725   -4.0148    0.4042 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6871   -3.8928    0.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2955   -2.6494    0.0088 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4943   -1.5494   -0.0136 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0798   -0.2346   -0.2386 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4734   -0.1020   -0.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0197    1.1611   -0.6309 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2061    2.2733   -0.6601 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8534    2.1847   -0.4875 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3120    0.9035   -0.2761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1462    0.8462   -0.0959 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4507    1.8317    0.9354 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0646    3.1638    0.6160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0882    3.3182   -0.5076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3989    0.9880   -0.7759 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6912   -0.2503   -0.0986 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5349   -0.9787   -0.4501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8594   -0.7243   -0.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3200    0.4010    0.3894 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2422   -1.3737    0.7075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2300   -0.4068    1.1903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5277   -3.0048    0.5223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1480   -4.9644    0.5683 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2640   -4.8065    0.2515 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3541   -2.7008   -0.1171 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6352    3.2439   -0.8224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5757    1.2825   -1.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4644    1.7929    1.1190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9978    3.7261    0.3119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7273    3.7353    1.5316 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5321    4.2329   -0.2661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5813    3.4427   -1.4945 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6192   -0.6992   -0.4558 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6980   -0.0204    0.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 14  1  0
 14 13  1  0
 13 12  2  0
 12 11  1  0
 11 22  1  0
 22 21  1  0
 21 20  1  0
 11 10  2  0
 10  9  1  0
  9  8  2  0
  8  7  1  0
  7  6  2  0
  6  5  1  0
  5  4  2  0
 10 15  1  0
  4  3  1  0
 15 16  1  0
 15 14  2  0
 20 12  1  0
  4  9  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  3 26  1  1
 16 32  1  6
 17 33  1  0
 18 34  1  0
 18 35  1  0
 19 36  1  0
 19 37  1  0
 13 31  1  0
 21 38  1  0
 21 39  1  0
  8 30  1  0
  7 29  1  0
  6 28  1  0
  5 27  1  0
M  END


  Mrv1652304282216352D          

 22 26  0  0  1  0            999 V2000
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7565    2.6145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4209    3.3682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6005    3.2820    0.0000 O   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
  9 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  8 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
  7 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 18 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0069244

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H]1[C@H]2NCCC3=CC4=C(OCO4)C(C4=CC=CC=C14)=C23

> <INCHI_IDENTIFIER>
InChI=1S/C18H17NO3/c1-20-17-12-5-3-2-4-11(12)15-14-10(6-7-19-16(14)17)8-13-18(15)22-9-21-13/h2-5,8,16-17,19H,6-7,9H2,1H3/t16-,17-/m0/s1

> <INCHI_KEY>
OBJBIHSGZLMMBX-IRXDYDNUSA-N

> <FORMULA>
C18H17NO3

> <MOLECULAR_WEIGHT>
295.338

> <EXACT_MASS>
295.120843411

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
32.130104203625955

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(12S,13S)-13-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0^{2,6}.0^{8,20}.0^{14,19}]icosa-1(20),2(6),7,14,16,18-hexaene

> <ALOGPS_LOGP>
1.83

> <JCHEM_LOGP>
2.6657279146666664

> <ALOGPS_LOGS>
-3.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.496054141497858

> <JCHEM_POLAR_SURFACE_AREA>
39.72

> <JCHEM_REFRACTIVITY>
82.45720000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.04e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(12S,13S)-13-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0^{2,6}.0^{8,20}.0^{14,19}]icosa-1(20),2(6),7,14,16,18-hexaene

> <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       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       5.145   4.880   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.519   6.287   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.988   6.126   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   19                                                  
CONECT    8    7    9   16                                                  
CONECT    9    8   10   13                                                  
CONECT   10    9    4   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13    9   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15    8   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   22                                                  
CONECT   19   18    7   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   18                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₁₇NO₃

Average Mass

295.3380 Da

Monoisotopic Mass

295.12084 Da

IUPAC Name

(12S,13S)-13-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0^{2,6}.0^{8,20}.0^{14,19}]icosa-1(20),2(6),7,14,16,18-hexaene

Traditional Name

(12S,13S)-13-methoxy-3,5-dioxa-11-azapentacyclo[10.7.1.0^{2,6}.0^{8,20}.0^{14,19}]icosa-1(20),2(6),7,14,16,18-hexaene

CAS Registry Number

Not Available

SMILES

CO[C@@H]1[C@H]2NCCC3=CC4=C(OCO4)C(C4=CC=CC=C14)=C23

InChI Identifier

InChI=1S/C18H17NO3/c1-20-17-12-5-3-2-4-11(12)15-14-10(6-7-19-16(14)17)8-13-18(15)22-9-21-13/h2-5,8,16-17,19H,6-7,9H2,1H3/t16-,17-/m0/s1

InChI Key

OBJBIHSGZLMMBX-IRXDYDNUSA-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
Duguetia flagellaris	Plant	KNApSAcK
Duguetia staudtii	LOTUS Database	35616633
Greenwayodendron oliveri	LOTUS Database	35616633
Greenwayodendron suaveolens	LOTUS Database	35616633
Pachypodanthium staudtii Engl.et Diels.	Plant	KNApSAcK
Polyalthia suaveolens	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aporphines. These are quinoline alkaloids containing the dibenzo[de,g]quinoline ring system or a dehydrogenated derivative thereof.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Aporphines

Sub Class

Not Available

Direct Parent

Aporphines

Alternative Parents

Substituents

Aporphine
Benzoquinoline
Phenanthrene
Naphthalene
Quinoline
Tetrahydroisoquinoline
Benzodioxole
Aralkylamine
Benzenoid
Organoheterocyclic compound
Dialkyl ether
Secondary aliphatic amine
Ether
Oxacycle
Azacycle
Secondary amine
Acetal
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organopnictogen compound
Amine
Organic nitrogen 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	1.83	ALOGPS
logP	2.67	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Basic)	8.5	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	39.72 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	82.46 m³·mol⁻¹	ChemAxon
Polarizability	32.13 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

23339090

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44566390

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pachypodanthine (NP0069244)

MOL for NP0069244 (Pachypodanthine)

3D MOL for NP0069244 (Pachypodanthine)

3D SDF for NP0069244 (Pachypodanthine)

3D-SDF for NP0069244 (Pachypodanthine)

PDB for NP0069244 (Pachypodanthine)

3D PDB for NP0069244 (Pachypodanthine)

SMILES for NP0069244 (Pachypodanthine)

INCHI for NP0069244 (Pachypodanthine)

Structure for NP0069244 (Pachypodanthine)

3D Structure for NP0069244 (Pachypodanthine)