NP-MRD: Showing NP-Card for Nodularin (NP0137296)

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Record Information

Version

2.0

Created at

2022-05-30 16:48:06 UTC

Updated at

2022-05-30 16:48:06 UTC

NP-MRD ID

NP0137296

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nodularin

Description

Nodularin-R belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. Nodularin-R is a cyanotoxin and poses a health risk for wild and domestic animals as well as humans. Nodularin-R is a very strong basic compound (based on its pKa). Nodularin-R is a potentially toxic compound. This enzyme removes phosphate from a protein, a common step in many biochemical pathways. Microcystins also activate the enzyme phosphorylase b, which plays a very important role in the affairs of the hepatocyte. The cells die and this destroys the finer blood vessels of the liver leading to massive hepatic bleeding. This cyanobacterium forms blooms in brackish water bodies throughout the world. These toxins can break down slowly at high temperature (40 °C or 104 o F ) at either very low (<1) or high (>9) pH. The half-life, the time it takes for one-half of the toxin to degrade, at pH 1 and 40 oC is 3 weeks; at typical ambient conditions half-life is 10 weeks.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241205472D          

 59 60  0  0  0  0            999 V2000
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  3 11  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv0541 02241205472D          

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M  END
> <DATABASE_ID>
NP0137296

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(CC1=CC=CC=C1)C(C)C=C(C)C=CC1NC(=O)C(CCCN=C(N)N)NC(=O)C(C)C(NC(=O)C(=CC)N(C)C(=O)CCC(NC(=O)C1C)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C41H60N8O10/c1-8-31-38(54)48-34(40(57)58)26(5)36(52)46-29(15-12-20-44-41(42)43)37(53)45-28(25(4)35(51)47-30(39(55)56)18-19-33(50)49(31)6)17-16-23(2)21-24(3)32(59-7)22-27-13-10-9-11-14-27/h8-11,13-14,16-17,21,24-26,28-30,32,34H,12,15,18-20,22H2,1-7H3,(H,45,53)(H,46,52)(H,47,51)(H,48,54)(H,55,56)(H,57,58)(H4,42,43,44)

> <INCHI_KEY>
IXBQSRWSVIBXNC-UHFFFAOYSA-N

> <FORMULA>
C41H60N8O10

> <MOLECULAR_WEIGHT>
824.9627

> <EXACT_MASS>
824.44324018

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
88.05616351277486

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
9-{3-[(diaminomethylidene)amino]propyl}-2-ethylidene-12-(6-methoxy-3,5-dimethyl-7-phenylhepta-1,3-dien-1-yl)-1,6,13-trimethyl-3,7,10,14,19-pentaoxo-1,4,8,11,15-pentaazacyclononadecane-5,16-dicarboxylic acid

> <ALOGPS_LOGP>
1.58

> <JCHEM_LOGP>
-1.234330456315228

> <ALOGPS_LOGS>
-5.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.6993859409472005

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.0955487389992187

> <JCHEM_PKA_STRONGEST_BASIC>
10.845274204744426

> <JCHEM_POLAR_SURFACE_AREA>
284.93999999999994

> <JCHEM_REFRACTIVITY>
220.68680000000018

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.05e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-{3-[(diaminomethylidene)amino]propyl}-2-ethylidene-12-(6-methoxy-3,5-dimethyl-7-phenylhepta-1,3-dien-1-yl)-1,6,13-trimethyl-3,7,10,14,19-pentaoxo-1,4,8,11,15-pentaazacyclononadecane-5,16-dicarboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0     -14.530   5.606   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0     -13.196   4.836   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0     -11.863   5.606   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -10.529   4.836   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -10.529   3.296   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -9.195   2.526   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -9.195   0.986   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -10.529   0.216   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -11.863   0.986   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0     -11.863   2.526   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0     -11.863   7.146   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -10.529   7.916   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -13.196   7.916   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -13.196   9.456   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -11.863  10.226   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -14.530  10.226   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -14.530  11.766   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -15.864  12.536   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0     -16.138  11.021   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0     -17.663  10.813   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0     -18.392   9.457   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0     -18.333  12.200   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -19.412  11.101   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -20.903  11.487   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -21.982  10.388   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0     -23.473  10.773   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0     -24.552   9.675   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0     -26.043  10.060   0.000  0.00  0.00           N+0
HETATM   29  N   UNK     0     -24.140   8.191   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0     -19.863  12.905   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0     -20.071  14.431   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0     -18.854  15.374   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0     -21.496  15.014   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -22.714  14.071   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -21.704  16.540   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0     -23.130  17.123   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0     -23.337  18.649   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0     -24.763  19.232   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0     -22.120  19.592   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -22.328  21.118   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -23.753  21.701   0.000  0.00  0.00           C+0
HETATM   42  N   UNK     0     -20.694  19.009   0.000  0.00  0.00           N+0
HETATM   43  C   UNK     0     -20.487  17.483   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -19.477  19.952   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0     -19.685  21.478   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0     -18.051  19.369   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -17.844  17.843   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -16.418  17.260   0.000  0.00  0.00           C+0
HETATM   49  N   UNK     0     -16.211  15.734   0.000  0.00  0.00           N+0
HETATM   50  C   UNK     0     -14.785  15.151   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0     -13.567  16.094   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0     -14.577  13.625   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -13.139  13.073   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -15.201  18.203   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0     -13.775  17.620   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0     -15.409  19.729   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0     -22.922  15.597   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0     -23.650  14.240   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0     -24.347  16.180   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    3   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   52                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   30                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   22   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   57                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40   42                                                  
CONECT   40   39   41                                                       
CONECT   41   40                                                            
CONECT   42   39   43   44                                                  
CONECT   43   42                                                            
CONECT   44   42   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49   54                                                  
CONECT   49   48   50                                                       
CONECT   50   49   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50   18   53                                                  
CONECT   53   52                                                            
CONECT   54   48   55   56                                                  
CONECT   55   54                                                            
CONECT   56   54                                                            
CONECT   57   35   58   59                                                  
CONECT   58   57                                                            
CONECT   59   57                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  120    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₁H₆₀N₈O₁₀

Average Mass

824.9627 Da

Monoisotopic Mass

824.44324 Da

IUPAC Name

9-{3-[(diaminomethylidene)amino]propyl}-2-ethylidene-12-(6-methoxy-3,5-dimethyl-7-phenylhepta-1,3-dien-1-yl)-1,6,13-trimethyl-3,7,10,14,19-pentaoxo-1,4,8,11,15-pentaazacyclononadecane-5,16-dicarboxylic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

COC(CC1=CC=CC=C1)C(C)C=C(C)C=CC1NC(=O)C(CCCN=C(N)N)NC(=O)C(C)C(NC(=O)C(=CC)N(C)C(=O)CCC(NC(=O)C1C)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C41H60N8O10/c1-8-31-38(54)48-34(40(57)58)26(5)36(52)46-29(15-12-20-44-41(42)43)37(53)45-28(25(4)35(51)47-30(39(55)56)18-19-33(50)49(31)6)17-16-23(2)21-24(3)32(59-7)22-27-13-10-9-11-14-27/h8-11,13-14,16-17,21,24-26,28-30,32,34H,12,15,18-20,22H2,1-7H3,(H,45,53)(H,46,52)(H,47,51)(H,48,54)(H,55,56)(H,57,58)(H4,42,43,44)

InChI Key

IXBQSRWSVIBXNC-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
Gamma-glutamyl alpha peptide
Macrolactam
Beta amino acid or derivatives
Alpha-amino acid or derivatives
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Benzenoid
Tertiary carboxylic acid amide
Carboxamide group
Guanidine
Lactam
Secondary carboxylic acid amide
Carboxylic acid
Dialkyl ether
Ether
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Hydrocarbon derivative
Organic oxygen compound
Organopnictogen compound
Carbonyl group
Organic oxide
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	1.58	ALOGPS
logP	-1.2	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	3.1	ChemAxon
pKa (Strongest Basic)	10.85	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	284.94 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	220.69 m³·mol⁻¹	ChemAxon
Polarizability	88.06 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

Nodularin

METLIN ID

Not Available

PubChem Compound

104970

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Nodularin (NP0137296)

MOL for NP0137296 (Nodularin)

3D MOL for NP0137296 (Nodularin)

3D SDF for NP0137296 (Nodularin)

3D-SDF for NP0137296 (Nodularin)

PDB for NP0137296 (Nodularin)

3D PDB for NP0137296 (Nodularin)

SMILES for NP0137296 (Nodularin)

INCHI for NP0137296 (Nodularin)

Structure for NP0137296 (Nodularin)

3D Structure for NP0137296 (Nodularin)