NP-MRD: Showing NP-Card for 3-Epirhynchophylline (NP0331710)

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Record Information

Version

2.0

Created at

2023-07-13 15:40:04 UTC

Updated at

2024-09-03 04:16:36 UTC

NP-MRD ID

NP0331710

Natural Product DOI

https://doi.org/10.57994/0725

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-Epirhynchophylline

Description

ZINC223283690 belongs to the class of organic compounds known as indolizidines. These are polycyclic compounds containing an indolizidine, which is a bicyclic heterocycle containing a saturated six-member ring fused to a saturated five-member ring, one of the bridging atoms being nitrogen. 3-Epirhynchophylline was first documented in 2020 (PMID: 32597657). Based on a literature review very few articles have been published on ZINC223283690.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309282217272D          

 29 32  0  0  1  0            999 V2000
    2.0425    3.0840    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2974    2.2994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0820    2.0445    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0820    1.2195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6951    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5236   -0.1395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7390   -0.3945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1259    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2974    0.9645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8125    1.6320    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3276    0.9645    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4991    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8860   -0.3945    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0575   -1.2014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8421   -1.4564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0137   -2.2634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7983   -2.5183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4552   -0.9043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444   -1.7535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3402   -1.4985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9533   -2.0506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1014   -0.1395    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5117   -0.6916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2963   -0.4366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5429    1.2195    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5429    2.0445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3276    2.2994    0.0000 C   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  1  0  0  0  0
  4  5  2  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
 10  9  1  1  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  2  0  0  0  0
 14 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 13 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 22 25  1  0  0  0  0
 11 26  1  6  0  0  0
 11 27  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 10 29  1  0  0  0  0
M  END


  Mrv1652309282217272D          

 29 32  0  0  1  0            999 V2000
    2.0425    3.0840    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2974    2.2994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0820    2.0445    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0820    1.2195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6951    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5236   -0.1395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7390   -0.3945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1259    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2974    0.9645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8125    1.6320    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3276    0.9645    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4991    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8860   -0.3945    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0575   -1.2014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8421   -1.4564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0137   -2.2634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7983   -2.5183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4552   -0.9043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444   -1.7535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3402   -1.4985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9533   -2.0506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1014   -0.1395    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5117   -0.6916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2963   -0.4366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5429    1.2195    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5429    2.0445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3276    2.2994    0.0000 C   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  1  0  0  0  0
  4  5  2  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
 10  9  1  1  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  2  0  0  0  0
 14 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 13 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 22 25  1  0  0  0  0
 11 26  1  6  0  0  0
 11 27  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 10 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331710

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C[C@@H]([C@@H](CC)CN1CC[C@]21C(=O)NC2=CC=CC=C12)C(=C/OC)\C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C22H28N2O4/c1-4-14-12-24-10-9-22(17-7-5-6-8-18(17)23-21(22)26)19(24)11-15(14)16(13-27-2)20(25)28-3/h5-8,13-15,19H,4,9-12H2,1-3H3,(H,23,26)/b16-13+/t14-,15-,19+,22+/m0/s1

> <INCHI_KEY>
DAXYUDFNWXHGBE-BRSGZFOASA-N

> <FORMULA>
C22H28N2O4

> <MOLECULAR_WEIGHT>
384.476

> <EXACT_MASS>
384.20490739

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
41.593783034106494

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (2E)-2-[(3R,6'R,7'S,8'aR)-6'-ethyl-2-oxo-1,2,3',5',6',7',8',8'a-octahydro-2'H-spiro[indole-3,1'-indolizine]-7'-yl]-3-methoxyprop-2-enoate

> <ALOGPS_LOGP>
2.85

> <JCHEM_LOGP>
2.6094639083333337

> <ALOGPS_LOGS>
-3.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.16702338486493

> <JCHEM_PKA_STRONGEST_BASIC>
10.712527798380334

> <JCHEM_POLAR_SURFACE_AREA>
67.86999999999999

> <JCHEM_REFRACTIVITY>
108.00599999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.40e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2E)-2-[(3R,6'R,7'S,8'aR)-6'-ethyl-2-oxo-3',5',6',7',8',8'a-hexahydro-1H,2'H-spiro[indole-3,1'-indolizine]-7'-yl]-3-methoxyprop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-SEP-22         0                                  
HETATM    1  O   UNK     0       3.813   5.757   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.289   4.292   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       5.753   3.816   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       5.753   2.276   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.898   1.246   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.577  -0.260   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.113  -0.736   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.968   0.294   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.289   1.800   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.383   3.046   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.478   1.800   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.798   0.294   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.654  -0.736   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.974  -2.243   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.439  -2.719   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.759  -4.225   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.223  -4.701   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.583  -1.688   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.830  -3.273   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.635  -2.797   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -1.779  -3.828   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.189  -0.260   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.955  -1.291   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.420  -0.815   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.131   1.246   0.000  0.00  0.00           C+0
HETATM   26  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   27  N   UNK     0       1.013   2.276   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0       1.013   3.816   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.478   4.292   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9    2   11   29                                             
CONECT   11   10   12   26   27                                             
CONECT   12   11   13                                                       
CONECT   13   12   14   22                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15                                                            
CONECT   19   14   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   13   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   22   27                                                       
CONECT   26   11                                                            
CONECT   27   11   25   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28   10                                                       
MASTER        0    0    0    0    0    0    0    0   29    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₂₈N₂O₄

Average Mass

384.4760 Da

Monoisotopic Mass

384.20491 Da

IUPAC Name

methyl (2E)-2-[(3R,6'R,7'S,8'aR)-6'-ethyl-2-oxo-1,2,3',5',6',7',8',8'a-octahydro-2'H-spiro[indole-3,1'-indolizine]-7'-yl]-3-methoxyprop-2-enoate

Traditional Name

methyl (2E)-2-[(3R,6'R,7'S,8'aR)-6'-ethyl-2-oxo-3',5',6',7',8',8'a-hexahydro-1H,2'H-spiro[indole-3,1'-indolizine]-7'-yl]-3-methoxyprop-2-enoate

CAS Registry Number

Not Available

SMILES

[H][C@]12C[C@@H]([C@@H](CC)CN1CC[C@]21C(=O)NC2=CC=CC=C12)C(=C/OC)\C(=O)OC

InChI Identifier

InChI=1S/C22H28N2O4/c1-4-14-12-24-10-9-22(17-7-5-6-8-18(17)23-21(22)26)19(24)11-15(14)16(13-27-2)20(25)28-3/h5-8,13-15,19H,4,9-12H2,1-3H3,(H,23,26)/b16-13+/t14-,15-,19+,22+/m0/s1

InChI Key

DAXYUDFNWXHGBE-BRSGZFOASA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CDCl3, experimental)	n_oberli@uncg.edu	Not Available	Not Available	2023-07-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl3, experimental)	n_oberli@uncg.edu	Not Available	Not Available	2023-07-13	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Mitragyna speciosa		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolizidines. These are polycyclic compounds containing an indolizidine, which is a bicyclic heterocycle containing a saturated six-member ring fused to a saturated five-member ring, one of the bridging atoms being nitrogen.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indolizidines

Sub Class

Not Available

Direct Parent

Indolizidines

Alternative Parents

Substituents

Indole or derivatives
Dihydroindole
Indolizidine
Aralkylamine
Piperidine
N-alkylpyrrolidine
Benzenoid
Pyrrolidine
Methyl ester
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Vinylogous ester
Tertiary aliphatic amine
Tertiary amine
Secondary carboxylic acid amide
Carboxamide group
Amino acid or derivatives
Lactam
Carboxylic acid ester
Azacycle
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Amine
Organic oxygen compound
Organic nitrogen compound
Organic oxide
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Carbonyl group
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	2.85	ALOGPS
logP	2.61	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	13.17	ChemAxon
pKa (Strongest Basic)	10.71	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	67.87 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	108.01 m³·mol⁻¹	ChemAxon
Polarizability	41.59 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

90468042

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Flores-Bocanegra L, Raja HA, Graf TN, Augustinovic M, Wallace ED, Hematian S, Kellogg JJ, Todd DA, Cech NB, Oberlies NH: The Chemistry of Kratom [Mitragyna speciosa]: Updated Characterization Data and Methods to Elucidate Indole and Oxindole Alkaloids. J Nat Prod. 2020 Jul 24;83(7):2165-2177. doi: 10.1021/acs.jnatprod.0c00257. Epub 2020 Jun 29. [PubMed:32597657 ]
DOI: 10.1021/acs.jnatprod.0c00257

Showing NP-Card for 3-Epirhynchophylline (NP0331710)

MOL for NP0331710 (3-Epirhynchophylline)

3D MOL for NP0331710 (3-Epirhynchophylline)

3D SDF for NP0331710 (3-Epirhynchophylline)

3D-SDF for NP0331710 (3-Epirhynchophylline)

PDB for NP0331710 (3-Epirhynchophylline)

3D PDB for NP0331710 (3-Epirhynchophylline)

SMILES for NP0331710 (3-Epirhynchophylline)

INCHI for NP0331710 (3-Epirhynchophylline)

Structure for NP0331710 (3-Epirhynchophylline)

3D Structure for NP0331710 (3-Epirhynchophylline)