NP-MRD: Showing NP-Card for Hermitamide B (NP0003361)

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Record Information

Version

1.0

Created at

2020-12-09 00:38:43 UTC

Updated at

2021-07-15 16:46:13 UTC

NP-MRD ID

NP0003361

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hermitamide B

Provided By

NPAtlas

Description

(4E,7S)-N-[2-(1H-indol-3-yl)ethyl]-7-methoxytetradec-4-enimidic acid belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position. Hermitamide B is found in Lyngbya majuscula. It was first documented in 2000 (PMID: 10924172). Based on a literature review very few articles have been published on (4E,7S)-N-[2-(1H-indol-3-yl)ethyl]-7-methoxytetradec-4-enimidic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242117473D          

 67 68  0  0  0  0            999 V2000
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    4.0414    0.1792    1.1710 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652306242117473D          

 67 68  0  0  0  0            999 V2000
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 29 67  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0003361

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]N(C(=O)C([H])([H])C([H])([H])C(\[H])=C(/[H])C([H])([H])[C@@]([H])(OC([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H])C([H])([H])C([H])([H])C1=C([H])N([H])C2=C([H])C([H])=C([H])C([H])=C12

> <INCHI_IDENTIFIER>
InChI=1S/C25H38N2O2/c1-3-4-5-6-8-13-22(29-2)14-9-7-10-17-25(28)26-19-18-21-20-27-24-16-12-11-15-23(21)24/h7,9,11-12,15-16,20,22,27H,3-6,8,10,13-14,17-19H2,1-2H3,(H,26,28)/b9-7+/t22-/m0/s1

> <INCHI_KEY>
OHYDYQKPXIXRBQ-GLJAUCNMSA-N

> <FORMULA>
C25H38N2O2

> <MOLECULAR_WEIGHT>
398.591

> <EXACT_MASS>
398.293328472

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
49.23164723430199

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4E,7S)-N-[2-(1H-indol-3-yl)ethyl]-7-methoxytetradec-4-enamide

> <ALOGPS_LOGP>
6.81

> <JCHEM_LOGP>
5.790561535

> <ALOGPS_LOGS>
-6.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.445900807362968

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.835517553685328

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3473517398912698

> <JCHEM_POLAR_SURFACE_AREA>
54.120000000000005

> <JCHEM_REFRACTIVITY>
122.59190000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.39e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4E,7S)-N-[2-(1H-indol-3-yl)ethyl]-7-methoxytetradec-4-enamide

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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 29 67  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       9.147  -1.775  -0.050  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.228  -0.786  -0.794  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.862  -1.346  -0.746  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.778  -0.477  -1.368  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.725   0.870  -0.656  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.366   0.690   0.745  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.041   0.179   1.171  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.886   1.077   0.977  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.408   1.521  -0.342  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.944   0.317  -1.089  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.667   0.314  -1.452  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.128  -0.650  -2.153  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.248  -1.157  -1.256  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.121  -0.129  -0.669  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.624   1.025  -0.334  0.00  0.00           O+0
HETATM   16  N   UNK     0      -3.506  -0.418  -0.479  0.00  0.00           N+0
HETATM   17  C   UNK     0      -4.756  -0.667  -0.303  0.00  0.00           C+0
HETATM   18  C   UNK     0      -5.271  -1.051   1.177  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.829  -1.089   0.854  0.00  0.00           C+0
HETATM   20  C   UNK     0      -7.543  -2.121   0.525  0.00  0.00           C+0
HETATM   21  N   UNK     0      -8.813  -1.708   0.219  0.00  0.00           N+0
HETATM   22  C   UNK     0      -8.786  -0.277   0.403  0.00  0.00           C+0
HETATM   23  C   UNK     0      -9.813   0.614   0.288  0.00  0.00           C+0
HETATM   24  C   UNK     0      -9.434   1.974   0.670  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.197   2.324   1.093  0.00  0.00           C+0
HETATM   26  C   UNK     0      -7.245   1.357   1.149  0.00  0.00           C+0
HETATM   27  C   UNK     0      -7.543   0.071   0.805  0.00  0.00           C+0
HETATM   28  O   UNK     0       1.803   0.652   1.800  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.548   1.540   2.826  0.00  0.00           C+0
HETATM   30  H   UNK     0      10.092  -1.762  -0.580  0.00  0.00           H+0
HETATM   31  H   UNK     0       8.647  -2.746   0.039  0.00  0.00           H+0
HETATM   32  H   UNK     0       9.307  -1.386   1.003  0.00  0.00           H+0
HETATM   33  H   UNK     0       8.534  -0.732  -1.867  0.00  0.00           H+0
HETATM   34  H   UNK     0       8.379   0.185  -0.363  0.00  0.00           H+0
HETATM   35  H   UNK     0       6.577  -1.565   0.280  0.00  0.00           H+0
HETATM   36  H   UNK     0       6.880  -2.342  -1.269  0.00  0.00           H+0
HETATM   37  H   UNK     0       4.792  -0.964  -1.256  0.00  0.00           H+0
HETATM   38  H   UNK     0       5.990  -0.295  -2.424  0.00  0.00           H+0
HETATM   39  H   UNK     0       5.093   1.549  -1.200  0.00  0.00           H+0
HETATM   40  H   UNK     0       6.765   1.356  -0.733  0.00  0.00           H+0
HETATM   41  H   UNK     0       5.458   1.734   1.271  0.00  0.00           H+0
HETATM   42  H   UNK     0       6.134   0.041   1.295  0.00  0.00           H+0
HETATM   43  H   UNK     0       3.898  -0.795   0.561  0.00  0.00           H+0
HETATM   44  H   UNK     0       4.058  -0.215   2.221  0.00  0.00           H+0
HETATM   45  H   UNK     0       3.189   2.078   1.513  0.00  0.00           H+0
HETATM   46  H   UNK     0       1.486   2.183  -0.047  0.00  0.00           H+0
HETATM   47  H   UNK     0       3.039   2.220  -0.864  0.00  0.00           H+0
HETATM   48  H   UNK     0       2.505  -0.541  -1.364  0.00  0.00           H+0
HETATM   49  H   UNK     0       0.130   1.282  -1.178  0.00  0.00           H+0
HETATM   50  H   UNK     0      -0.508  -0.236  -3.124  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.497  -1.590  -2.404  0.00  0.00           H+0
HETATM   52  H   UNK     0      -0.611  -1.593  -0.357  0.00  0.00           H+0
HETATM   53  H   UNK     0      -1.747  -2.015  -1.665  0.00  0.00           H+0
HETATM   54  H   UNK     0      -3.700   0.956  -0.386  0.00  0.00           H+0
HETATM   55  H   UNK     0      -5.486   0.198  -0.539  0.00  0.00           H+0
HETATM   56  H   UNK     0      -5.276  -1.513  -0.865  0.00  0.00           H+0
HETATM   57  H   UNK     0      -5.134  -0.324   1.895  0.00  0.00           H+0
HETATM   58  H   UNK     0      -5.039  -2.041   1.407  0.00  0.00           H+0
HETATM   59  H   UNK     0      -7.171  -3.181   0.512  0.00  0.00           H+0
HETATM   60  H   UNK     0      -9.572  -2.255  -0.015  0.00  0.00           H+0
HETATM   61  H   UNK     0     -10.756   0.431  -0.089  0.00  0.00           H+0
HETATM   62  H   UNK     0     -10.248   2.675   0.560  0.00  0.00           H+0
HETATM   63  H   UNK     0      -7.973   3.369   1.447  0.00  0.00           H+0
HETATM   64  H   UNK     0      -6.229   1.588   1.351  0.00  0.00           H+0
HETATM   65  H   UNK     0       1.237   2.539   2.494  0.00  0.00           H+0
HETATM   66  H   UNK     0       0.734   1.110   3.449  0.00  0.00           H+0
HETATM   67  H   UNK     0       2.481   1.721   3.431  0.00  0.00           H+0
CONECT    1    2   30   31   32                                             
CONECT    2    1    3   33   34                                             
CONECT    3    2    4   35   36                                             
CONECT    4    3    5   37   38                                             
CONECT    5    4    6   39   40                                             
CONECT    6    5    7   41   42                                             
CONECT    7    6    8   43   44                                             
CONECT    8    7    9   28   45                                             
CONECT    9    8   10   46   47                                             
CONECT   10    9   11   48                                                  
CONECT   11   10   12   49                                                  
CONECT   12   11   13   50   51                                             
CONECT   13   12   14   52   53                                             
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   54                                                  
CONECT   17   16   18   55   56                                             
CONECT   18   17   19   57   58                                             
CONECT   19   18   20   27                                                  
CONECT   20   19   21   59                                                  
CONECT   21   20   22   60                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24   61                                                  
CONECT   24   23   25   62                                                  
CONECT   25   24   26   63                                                  
CONECT   26   25   27   64                                                  
CONECT   27   26   19   22                                                  
CONECT   28    8   29                                                       
CONECT   29   28   65   66   67                                             
CONECT   30    1                                                            
CONECT   31    1                                                            
CONECT   32    1                                                            
CONECT   33    2                                                            
CONECT   34    2                                                            
CONECT   35    3                                                            
CONECT   36    3                                                            
CONECT   37    4                                                            
CONECT   38    4                                                            
CONECT   39    5                                                            
CONECT   40    5                                                            
CONECT   41    6                                                            
CONECT   42    6                                                            
CONECT   43    7                                                            
CONECT   44    7                                                            
CONECT   45    8                                                            
CONECT   46    9                                                            
CONECT   47    9                                                            
CONECT   48   10                                                            
CONECT   49   11                                                            
CONECT   50   12                                                            
CONECT   51   12                                                            
CONECT   52   13                                                            
CONECT   53   13                                                            
CONECT   54   16                                                            
CONECT   55   17                                                            
CONECT   56   17                                                            
CONECT   57   18                                                            
CONECT   58   18                                                            
CONECT   59   20                                                            
CONECT   60   21                                                            
CONECT   61   23                                                            
CONECT   62   24                                                            
CONECT   63   25                                                            
CONECT   64   26                                                            
CONECT   65   29                                                            
CONECT   66   29                                                            
CONECT   67   29                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  136    0
END

RDKit          3D

67 68  0  0  0  0  0  0  0  0999 V2000
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  8 28  1  0
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  1 30  1  0
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  1 32  1  0
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 29 65  1  0
 29 66  1  0
 29 67  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(4E,7S)-N-[2-(1H-indol-3-yl)Ethyl]-7-methoxytetradec-4-enimidate	Generator

Chemical Formula

C₂₅H₃₈N₂O₂

Average Mass

398.5910 Da

Monoisotopic Mass

398.29333 Da

IUPAC Name

(4E,7S)-N-[2-(1H-indol-3-yl)ethyl]-7-methoxytetradec-4-enamide

Traditional Name

(4E,7S)-N-[2-(1H-indol-3-yl)ethyl]-7-methoxytetradec-4-enamide

CAS Registry Number

Not Available

SMILES

CCCCCCC[C@@H](C\C=C\CCC(=O)NCCC1=CNC2=CC=CC=C12)OC

InChI Identifier

InChI=1S/C25H38N2O2/c1-3-4-5-6-8-13-22(29-2)14-9-7-10-17-25(28)26-19-18-21-20-27-24-16-12-11-15-23(21)24/h7,9,11-12,15-16,20,22,27H,3-6,8,10,13-14,17-19H2,1-2H3,(H,26,28)/b9-7+/t22-/m0/s1

InChI Key

OHYDYQKPXIXRBQ-GLJAUCNMSA-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
Lyngbya majuscula	NPAtlas	10924172

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

3-alkylindoles

Alternative Parents

Substituents

3-alkylindole
Fatty amide
N-acyl-amine
Fatty acyl
Benzenoid
Substituted pyrrole
Pyrrole
Heteroaromatic compound
Carboxamide group
Secondary carboxylic acid amide
Carboxylic acid derivative
Dialkyl ether
Ether
Azacycle
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
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	6.81	ALOGPS
logP	5.79	ChemAxon
logS	-6.9	ALOGPS
pKa (Strongest Acidic)	15.84	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	54.12 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	122.59 m³·mol⁻¹	ChemAxon
Polarizability	49.23 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

NPAtlas ID

NPA013791

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8561615

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10386173

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Tan LT, Okino T, Gerwick WH: Hermitamides A and B, toxic malyngamide-type natural products from the marine cyanobacterium Lyngbya majuscula. J Nat Prod. 2000 Jul;63(7):952-5. doi: 10.1021/np000037x. [PubMed:10924172 ]

Showing NP-Card for Hermitamide B (NP0003361)

MOL for NP0003361 (Hermitamide B)

3D MOL for NP0003361 (Hermitamide B)

3D SDF for NP0003361 (Hermitamide B)

3D-SDF for NP0003361 (Hermitamide B)

PDB for NP0003361 (Hermitamide B)

3D PDB for NP0003361 (Hermitamide B)

SMILES for NP0003361 (Hermitamide B)

INCHI for NP0003361 (Hermitamide B)

Structure for NP0003361 (Hermitamide B)

3D Structure for NP0003361 (Hermitamide B)