NP-MRD: Showing NP-Card for Nephilatoxin 2 (NP0068106)

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Record Information

Version

2.0

Created at

2022-04-28 13:06:28 UTC

Updated at

2022-04-28 13:06:28 UTC

NP-MRD ID

NP0068106

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nephilatoxin 2

Description

NPTX-801E, also known as NPTX 801E, belongs to the class of organic compounds known as asparagine and derivatives. Asparagine and derivatives are compounds containing asparagine or a derivative thereof resulting from reaction of asparagine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Nephilatoxin 2 is found in Nephila clavata. Nephilatoxin 2 was first documented in 1998 (PMID: 9637368). Based on a literature review very few articles have been published on NPTX-801E.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282215062D          

 57 58  0  0  1  0            999 V2000
   -2.1345    0.0320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4201   -0.3805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7056    0.0320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7056    0.8570    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0089   -0.3805    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7233    0.0320    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7233    0.8570    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4378    1.2695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1523    0.8570    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4378    2.0945    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4378   -0.3805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4378   -1.2055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8668   -0.3805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   20.0141   -0.3805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   21.4430   -0.3805    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   23.5864    0.0320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.3009   -0.3805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.2208    0.8525    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  2  0  0  0  0
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 13 14  1  0  0  0  0
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 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
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 22 23  1  0  0  0  0
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 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
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 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  1  0  0  0  0
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 37 38  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304282215062D          

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  1 49  2  0  0  0  0
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  1 52  1  0  0  0  0
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 51 56  2  0  0  0  0
 53 57  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0068106

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCCCNCCC(=O)NCCCCNCCC(=O)NCCCNCCC(=O)NCCCCCNC(=O)[C@H](CC(N)=O)NC(=O)CC1=CNC2=CC=CC(O)=C12

> <INCHI_IDENTIFIER>
InChI=1S/C39H67N11O7/c40-15-2-5-16-42-23-12-35(54)46-20-7-6-17-43-24-13-36(55)47-22-9-18-44-25-14-34(53)45-19-3-1-4-21-48-39(57)31(27-33(41)52)50-37(56)26-29-28-49-30-10-8-11-32(51)38(29)30/h8,10-11,28,31,42-44,49,51H,1-7,9,12-27,40H2,(H2,41,52)(H,45,53)(H,46,54)(H,47,55)(H,48,57)(H,50,56)/t31-/m0/s1

> <INCHI_KEY>
FCDDOXZNNGKUHJ-HKBQPEDESA-N

> <FORMULA>
C39H67N11O7

> <MOLECULAR_WEIGHT>
802.035

> <EXACT_MASS>
801.522493541

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
124

> <JCHEM_AVERAGE_POLARIZABILITY>
91.74733529343018

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-N-(5-{3-[(3-{3-[(4-{3-[(4-aminobutyl)amino]propanamido}butyl)amino]propanamido}propyl)amino]propanamido}pentyl)-2-[2-(4-hydroxy-1H-indol-3-yl)acetamido]butanediamide

> <ALOGPS_LOGP>
0.50

> <JCHEM_LOGP>
-4.840295503033878

> <ALOGPS_LOGS>
-4.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_PKA>
12.730712430741253

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.331877633506876

> <JCHEM_PKA_STRONGEST_BASIC>
10.517936241379125

> <JCHEM_POLAR_SURFACE_AREA>
286.72

> <JCHEM_REFRACTIVITY>
218.93499999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
34

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.22e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-N-(5-{3-[(3-{3-[(4-{3-[(4-aminobutyl)amino]propanamido}butyl)amino]propanamido}propyl)amino]propanamido}pentyl)-2-[2-(4-hydroxy-1H-indol-3-yl)acetamido]succinamide

> <JCHEM_VEBER_RULE>
0

$$$$

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      -3.984   0.060   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.651  -0.710   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.317   0.060   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.317   1.600   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       0.017  -0.710   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.350   0.060   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.350   1.600   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.684   2.370   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.018   1.600   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       2.684   3.910   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.684  -0.710   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.684  -2.250   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       4.018   0.060   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       5.351  -0.710   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.685   0.060   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.019  -0.710   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.352   0.060   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.686  -0.710   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      12.020   0.060   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      13.353  -0.710   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      13.353  -2.250   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      14.687   0.060   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      16.021  -0.710   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      17.354   0.060   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0      18.688  -0.710   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      20.022   0.060   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      21.355  -0.710   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0      22.689   0.060   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0      24.023  -0.710   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      24.023  -2.250   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      25.356   0.060   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      26.690  -0.710   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      28.024   0.060   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0      29.358  -0.710   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      30.691   0.060   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      32.025  -0.710   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      33.359   0.060   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0      34.692  -0.710   0.000  0.00  0.00           N+0
HETATM   39  C   UNK     0      36.026   0.060   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      36.026   1.600   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      37.360  -0.710   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      38.693   0.060   0.000  0.00  0.00           C+0
HETATM   43  N   UNK     0      40.027  -0.710   0.000  0.00  0.00           N+0
HETATM   44  C   UNK     0      41.361   0.060   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      42.694  -0.710   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      44.028   0.060   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      45.362  -0.710   0.000  0.00  0.00           C+0
HETATM   48  N   UNK     0      46.695   0.060   0.000  0.00  0.00           N+0
HETATM   49  C   UNK     0      -4.145   1.591   0.000  0.00  0.00           C+0
HETATM   50  N   UNK     0      -5.652   1.911   0.000  0.00  0.00           N+0
HETATM   51  C   UNK     0      -6.422   0.578   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -5.391  -0.567   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      -5.867  -2.031   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      -7.374  -2.351   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -8.404  -1.207   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -7.928   0.258   0.000  0.00  0.00           C+0
HETATM   57  O   UNK     0      -4.837  -3.176   0.000  0.00  0.00           O+0
CONECT    1    2   49   52                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    6   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47                                                            
CONECT   49    1   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52   56                                                  
CONECT   52   51    1   53                                                  
CONECT   53   52   54   57                                                  
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   51                                                       
CONECT   57   53                                                            
MASTER        0    0    0    0    0    0    0    0   57    0  116    0
END

View in JSmol

Synonyms

Value	Source
HO-Indole-asn-cad-pta-orn-arg	MeSH
NPTX 801E	MeSH

Chemical Formula

C₃₉H₆₇N₁₁O₇

Average Mass

802.0350 Da

Monoisotopic Mass

801.52249 Da

IUPAC Name

(2S)-N-(5-{3-[(3-{3-[(4-{3-[(4-aminobutyl)amino]propanamido}butyl)amino]propanamido}propyl)amino]propanamido}pentyl)-2-[2-(4-hydroxy-1H-indol-3-yl)acetamido]butanediamide

Traditional Name

(2S)-N-(5-{3-[(3-{3-[(4-{3-[(4-aminobutyl)amino]propanamido}butyl)amino]propanamido}propyl)amino]propanamido}pentyl)-2-[2-(4-hydroxy-1H-indol-3-yl)acetamido]succinamide

CAS Registry Number

Not Available

SMILES

NCCCCNCCC(=O)NCCCCNCCC(=O)NCCCNCCC(=O)NCCCCCNC(=O)[C@H](CC(N)=O)NC(=O)CC1=CNC2=CC=CC(O)=C12

InChI Identifier

InChI=1S/C39H67N11O7/c40-15-2-5-16-42-23-12-35(54)46-20-7-6-17-43-24-13-36(55)47-22-9-18-44-25-14-34(53)45-19-3-1-4-21-48-39(57)31(27-33(41)52)50-37(56)26-29-28-49-30-10-8-11-32(51)38(29)30/h8,10-11,28,31,42-44,49,51H,1-7,9,12-27,40H2,(H2,41,52)(H,45,53)(H,46,54)(H,47,55)(H,48,57)(H,50,56)/t31-/m0/s1

InChI Key

FCDDOXZNNGKUHJ-HKBQPEDESA-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
Nephila clavata	Animalia	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as asparagine and derivatives. Asparagine and derivatives are compounds containing asparagine or a derivative thereof resulting from reaction of asparagine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Asparagine and derivatives

Alternative Parents

Substituents

Asparagine or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Beta amino acid or derivatives
Hydroxyindole
3-alkylindole
Indole
Indole or derivatives
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Fatty amide
N-acyl-amine
Fatty acyl
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Primary carboxylic acid amide
Secondary carboxylic acid amide
Carboxamide group
Secondary amine
Secondary aliphatic amine
Organoheterocyclic compound
Azacycle
Primary amine
Primary aliphatic amine
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organonitrogen compound
Organooxygen compound
Carbonyl group
Organic oxygen compound
Amine
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	0.5	ALOGPS
logP	-4.8	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	9.33	ChemAxon
pKa (Strongest Basic)	10.52	ChemAxon
Physiological Charge	4	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	12	ChemAxon
Polar Surface Area	286.72 Å²	ChemAxon
Rotatable Bond Count	34	ChemAxon
Refractivity	218.94 m³·mol⁻¹	ChemAxon
Polarizability	91.75 Å³	ChemAxon
Number of Rings	2	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

102318070

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Palma MS, Itagaki Y, Fujita T, Naoki H, Nakajima T: Structural characterization of a new acylpolyaminetoxin from the venom of Brazilian garden spider Nephilengys cruentata. Toxicon. 1998 Mar;36(3):485-93. doi: 10.1016/s0041-0101(97)00139-6. [PubMed:9637368 ]

Showing NP-Card for Nephilatoxin 2 (NP0068106)

MOL for NP0068106 (Nephilatoxin 2)

3D MOL for NP0068106 (Nephilatoxin 2)

3D SDF for NP0068106 (Nephilatoxin 2)

3D-SDF for NP0068106 (Nephilatoxin 2)

PDB for NP0068106 (Nephilatoxin 2)

3D PDB for NP0068106 (Nephilatoxin 2)

SMILES for NP0068106 (Nephilatoxin 2)

INCHI for NP0068106 (Nephilatoxin 2)

Structure for NP0068106 (Nephilatoxin 2)

3D Structure for NP0068106 (Nephilatoxin 2)