NP-MRD: Showing NP-Card for Speciogynine (NP0331709)

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Record Information

Version

1.0

Created at

2023-07-12 22:57:34 UTC

Updated at

2024-05-12 18:38:50 UTC

NP-MRD ID

NP0331709

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Speciogynine

Description

It was first documented in 2020 (PMID: 33408731).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 08302317422D          

 31 36  0  0  1  0            999 V2000
    1.8249   -2.3730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6054   -1.5777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7374   -1.4576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1018   -0.7895    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1925   -1.5602    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6892   -0.0330    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4300   -0.3961    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3740    0.4270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8899   -1.0810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4037   -0.2791    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4833   -0.8368    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1608   -0.1298    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5899    0.6629    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8674    1.4399    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2191    0.9990    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3425    1.8147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1053   -0.7131    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8762    0.4521    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1799    1.2191    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7497    0.3998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2620   -1.0512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3199   -0.2283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1205   -0.0291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5082    0.6991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3327    0.7275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7204    1.4557    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2836    2.1556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7696    0.0276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3819   -0.7006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5574   -0.7290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0267   -1.3607    0.0000 N   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
  4  3  1  0  0  0  0
  4  5  1  6  0  0  0
  6  4  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  8  1  1  0  0  0
  7  9  1  1  0  0  0
  4 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  0  0  0  0
  6 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 10 17  1  6  0  0  0
 10 18  1  0  0  0  0
 18 15  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
  2 21  1  0  0  0  0
 21 22  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 25 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 23 30  1  0  0  0  0
 30 31  1  0  0  0  0
 21 31  1  0  0  0  0
M  END


  Mrv2104 08302317422D          

 31 36  0  0  1  0            999 V2000
    1.8249   -2.3730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6054   -1.5777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7374   -1.4576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1018   -0.7895    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1925   -1.5602    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6892   -0.0330    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4300   -0.3961    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3740    0.4270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8899   -1.0810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4037   -0.2791    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4833   -0.8368    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1608   -0.1298    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5899    0.6629    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8674    1.4399    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2191    0.9990    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3425    1.8147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1053   -0.7131    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8762    0.4521    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1799    1.2191    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7497    0.3998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2620   -1.0512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3199   -0.2283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1205   -0.0291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5082    0.6991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3327    0.7275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7204    1.4557    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2836    2.1556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7696    0.0276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3819   -0.7006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5574   -0.7290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0267   -1.3607    0.0000 N   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
  4  3  1  0  0  0  0
  4  5  1  6  0  0  0
  6  4  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  6  8  1  1  0  0  0
  7  9  1  1  0  0  0
  4 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 13 12  1  0  0  0  0
  6 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 10 17  1  6  0  0  0
 10 18  1  0  0  0  0
 18 15  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
  2 21  1  0  0  0  0
 21 22  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 25 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 23 30  1  0  0  0  0
 30 31  1  0  0  0  0
 21 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331709

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12CC3=C(NC4=CC=C(OC)C=C34)C(=O)C[C@]3([H])[C@@]1([H])CO[C@]([H])(N2C)[C@]31O[C@@H]1C

> <INCHI_IDENTIFIER>
InChI=1S/C21H24N2O4/c1-10-21(27-10)15-8-18(24)19-13(7-17-14(15)9-26-20(21)23(17)2)12-6-11(25-3)4-5-16(12)22-19/h4-6,10,14-15,17,20,22H,7-9H2,1-3H3/t10-,14-,15-,17+,20+,21-/m1/s1

> <INCHI_KEY>
BDSWMRIFIBSETF-HGEBQDRNSA-N

> <FORMULA>
C21H24N2O4

> <MOLECULAR_WEIGHT>
368.433

> <EXACT_MASS>
368.173607261

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
39.58988897740596

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1'S,2S,3R,14'R,16'S,19'R)-6'-methoxy-3,20'-dimethyl-17'-oxa-10',20'-diazaspiro[oxirane-2,15'-pentacyclo[14.3.1.0^{3,11}.0^{4,9}.0^{14,19}]icosane]-3'(11'),4',6',8'-tetraen-12'-one

> <JCHEM_LOGP>
1.7491940589999997

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.525212311107353

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.684453995392873

> <JCHEM_PKA_STRONGEST_BASIC>
5.030952639691954

> <JCHEM_POLAR_SURFACE_AREA>
67.09

> <JCHEM_REFRACTIVITY>
99.36560000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1'S,2S,3R,14'R,16'S,19'R)-6'-methoxy-3,20'-dimethyl-17'-oxa-10',20'-diazaspiro[oxirane-2,15'-pentacyclo[14.3.1.0^{3,11}.0^{4,9}.0^{14,19}]icosane]-3'(11'),4',6',8'-tetraen-12'-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-AUG-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-AUG-23         0                                  
HETATM    1  O   UNK     0       3.406  -4.430   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.997  -2.945   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.377  -2.721   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.190  -1.474   0.000  0.00  0.00           C+0
HETATM    5  H   UNK     0      -0.359  -2.912   0.000  0.00  0.00           H+0
HETATM    6  C   UNK     0      -1.286  -0.062   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.669  -0.739   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.565   0.797   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -3.528  -2.018   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.754  -0.521   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.902  -1.562   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -2.167  -0.242   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.101   1.237   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0      -1.619   2.688   0.000  0.00  0.00           H+0
HETATM   15  N   UNK     0       0.409   1.865   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       0.639   3.388   0.000  0.00  0.00           C+0
HETATM   17  H   UNK     0       2.063  -1.331   0.000  0.00  0.00           H+0
HETATM   18  C   UNK     0       1.636   0.844   0.000  0.00  0.00           C+0
HETATM   19  H   UNK     0       2.202   2.276   0.000  0.00  0.00           H+0
HETATM   20  C   UNK     0       3.266   0.746   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.222  -1.962   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.331  -0.426   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.825  -0.054   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.549   1.305   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.088   1.358   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.812   2.717   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       7.996   4.024   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.903   0.052   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.179  -1.308   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.640  -1.361   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0       5.650  -2.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   21                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6   10                                             
CONECT    5    4                                                            
CONECT    6    4    7    8   13                                             
CONECT    7    6    8    9                                                  
CONECT    8    7    6                                                       
CONECT    9    7                                                            
CONECT   10    4   11   17   18                                             
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    6   14   15                                             
CONECT   14   13                                                            
CONECT   15   13   16   18                                                  
CONECT   16   15                                                            
CONECT   17   10                                                            
CONECT   18   10   15   19   20                                             
CONECT   19   18                                                            
CONECT   20   18   22                                                       
CONECT   21    2   22   31                                                  
CONECT   22   21   20   23                                                  
CONECT   23   22   24   30                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   28                                                  
CONECT   26   25   27                                                       
CONECT   27   26                                                            
CONECT   28   25   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   23   31                                                  
CONECT   31   30   21                                                       
MASTER        0    0    0    0    0    0    0    0   31    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₃₀N₂O₄

Average Mass

398.5030 Da

Monoisotopic Mass

398.22056 Da

IUPAC Name

(1'S,2S,3R,14'R,16'S,19'R)-6'-methoxy-3,20'-dimethyl-17'-oxa-10',20'-diazaspiro[oxirane-2,15'-pentacyclo[14.3.1.0^{3,11}.0^{4,9}.0^{14,19}]icosane]-3'(11'),4',6',8'-tetraen-12'-one

Traditional Name

(1'S,2S,3R,14'R,16'S,19'R)-6'-methoxy-3,20'-dimethyl-17'-oxa-10',20'-diazaspiro[oxirane-2,15'-pentacyclo[14.3.1.0^{3,11}.0^{4,9}.0^{14,19}]icosane]-3'(11'),4',6',8'-tetraen-12'-one

CAS Registry Number

Not Available

SMILES

CC[C@H]1CN2CCC3=C(NC4=CC=CC(OC)=C34)[C@@H]2C[C@@H]1\C(=C/OC)C(=O)OC

InChI Identifier

InChI=1S/C23H30N2O4/c1-5-14-12-25-10-9-15-21-18(7-6-8-20(21)28-3)24-22(15)19(25)11-16(14)17(13-27-2)23(26)29-4/h6-8,13-14,16,19,24H,5,9-12H2,1-4H3/b17-13+/t14-,16-,19-/m0/s1

InChI Key

LELBFTMXCIIKKX-CYSPOEIOSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	[¹H, ] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	n_oberli@uncg.edu	Not Available	Not Available	2023-07-13	View Spectrum
1D NMR	[¹³C, ] NMR Spectrum (2D, 126 MHz, CDCl3, experimental)	n_oberli@uncg.edu	Not Available	Not Available	2023-07-13	View Spectrum
1D NMR	[¹³C, ] NMR Spectrum (2D, 126 MHz, CDCl3, experimental)	n_oberli@uncg.edu	Not Available	Not Available	2023-07-12	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	n_oberli@uncg.edu	Not Available	Not Available	2023-07-12	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
speciosa		Not Available

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	1.75	ChemAxon
pKa (Strongest Acidic)	13.68	ChemAxon
pKa (Strongest Basic)	5.03	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	67.09 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	99.37 m³·mol⁻¹	ChemAxon
Polarizability	39.59 Å³	ChemAxon
Number of Rings	6	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

Not Available

References

General References

Kamble SH, Berthold EC, King TI, Raju Kanumuri SR, Popa R, Herting JR, Leon F, Sharma A, McMahon LR, Avery BA, McCurdy CR: Pharmacokinetics of Eleven Kratom Alkaloids Following an Oral Dose of Either Traditional or Commercial Kratom Products in Rats. J Nat Prod. 2021 Apr 23;84(4):1104-1112. doi: 10.1021/acs.jnatprod.0c01163. Epub 2021 Feb 23. [PubMed:33620222 ]
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 ]
Manwill PK, Flores-Bocanegra L, Khin M, Raja HA, Cech NB, Oberlies NH, Todd DA: Kratom (Mitragyna speciosa) Validation: Quantitative Analysis of Indole and Oxindole Alkaloids Reveals Chemotypes of Plants and Products. Planta Med. 2022 Apr 25. doi: 10.1055/a-1795-5876. [PubMed:35468648 ]
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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 ]

Showing NP-Card for Speciogynine (NP0331709)

MOL for NP0331709 (Speciogynine)

3D MOL for NP0331709 (Speciogynine)

3D SDF for NP0331709 (Speciogynine)

3D-SDF for NP0331709 (Speciogynine)

PDB for NP0331709 (Speciogynine)

3D PDB for NP0331709 (Speciogynine)

SMILES for NP0331709 (Speciogynine)

INCHI for NP0331709 (Speciogynine)

Structure for NP0331709 (Speciogynine)

3D Structure for NP0331709 (Speciogynine)