NP-MRD: Showing NP-Card for Tokaramide A (NP0070538)

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Record Information

Version

2.0

Created at

2022-04-28 15:55:44 UTC

Updated at

2022-04-28 15:55:44 UTC

NP-MRD ID

NP0070538

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Tokaramide A

Description

TOKARAMIDE A belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Tokaramide A is found in Theonella aff. mirabilis, Theonella cf mirabilis and Theonella mirabilis. Tokaramide A was first documented in 2012 (PMID: 22785468). Based on a literature review very few articles have been published on TOKARAMIDE A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282217552D          

 34 34  0  0  1  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.8592    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
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 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
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 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
  2 34  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282217552D          

 34 34  0  0  1  0            999 V2000
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    6.4302    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.8592    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.7171    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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  2 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0070538

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@H](NC(=O)[C@@H](NC(=O)C1=CC=C(O)C=C1)C(C)C)C(=O)N[C@@H](CCCNC(N)=N)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C23H36N6O5/c1-13(2)18(21(33)27-16(12-30)6-5-11-26-23(24)25)29-22(34)19(14(3)4)28-20(32)15-7-9-17(31)10-8-15/h7-10,12-14,16,18-19,31H,5-6,11H2,1-4H3,(H,27,33)(H,28,32)(H,29,34)(H4,24,25,26)/t16-,18-,19-/m0/s1

> <INCHI_KEY>
QIOXCWRQNDIISW-WDSOQIARSA-N

> <FORMULA>
C23H36N6O5

> <MOLECULAR_WEIGHT>
476.578

> <EXACT_MASS>
476.274718283

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
50.83312845847303

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-N-[(1S)-1-{[(2S)-5-carbamimidamido-1-oxopentan-2-yl]carbamoyl}-2-methylpropyl]-2-[(4-hydroxyphenyl)formamido]-3-methylbutanamide

> <ALOGPS_LOGP>
0.31

> <JCHEM_LOGP>
0.09817653220426908

> <ALOGPS_LOGS>
-3.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.43462955896624

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.468359910056723

> <JCHEM_PKA_STRONGEST_BASIC>
11.859714506251828

> <JCHEM_POLAR_SURFACE_AREA>
186.5

> <JCHEM_REFRACTIVITY>
137.6789

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.08e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-N-[(1S)-1-{[(2S)-5-carbamimidamido-1-oxopentan-2-yl]carbamoyl}-2-methylpropyl]-2-[(4-hydroxyphenyl)formamido]-3-methylbutanamide

> <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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       5.335   1.540   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0       9.336   2.310   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      12.003   3.850   0.000  0.00  0.00           O+0
HETATM   23  N   UNK     0      13.337   1.540   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0      14.670   2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      14.670   3.850   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      16.004   4.620   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      16.004   1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      17.338   2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      18.672   1.540   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      20.005   2.310   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      21.339   1.540   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      22.673   2.310   0.000  0.00  0.00           N+0
HETATM   33  N   UNK     0      21.339   0.000   0.000  0.00  0.00           N+0
HETATM   34  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   10   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   21                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   17   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27   24   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34    2                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₃₆N₆O₅

Average Mass

476.5780 Da

Monoisotopic Mass

476.27472 Da

IUPAC Name

(2S)-N-[(1S)-1-{[(2S)-5-carbamimidamido-1-oxopentan-2-yl]carbamoyl}-2-methylpropyl]-2-[(4-hydroxyphenyl)formamido]-3-methylbutanamide

Traditional Name

(2S)-N-[(1S)-1-{[(2S)-5-carbamimidamido-1-oxopentan-2-yl]carbamoyl}-2-methylpropyl]-2-[(4-hydroxyphenyl)formamido]-3-methylbutanamide

CAS Registry Number

Not Available

SMILES

CC(C)[C@H](NC(=O)[C@@H](NC(=O)C1=CC=C(O)C=C1)C(C)C)C(=O)N[C@@H](CCCNC(N)=N)C=O

InChI Identifier

InChI=1S/C23H36N6O5/c1-13(2)18(21(33)27-16(12-30)6-5-11-26-23(24)25)29-22(34)19(14(3)4)28-20(32)15-7-9-17(31)10-8-15/h7-10,12-14,16,18-19,31H,5-6,11H2,1-4H3,(H,27,33)(H,28,32)(H,29,34)(H4,24,25,26)/t16-,18-,19-/m0/s1

InChI Key

QIOXCWRQNDIISW-WDSOQIARSA-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
Theonella aff. mirabilis	-	KNApSAcK
Theonella cf mirabilis	-	KNApSAcK
Theonella mirabilis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
Valine or derivatives
Hippuric acid or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
Benzamide
Benzoic acid or derivatives
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Fatty acyl
Fatty amide
N-acyl-amine
Benzenoid
Guanidine
Carboxamide group
Secondary carboxylic acid amide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Carboximidamide
Organic oxide
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Aldehyde
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic 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	0.31	ALOGPS
logP	0.098	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	8.47	ChemAxon
pKa (Strongest Basic)	11.86	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	186.5 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	137.68 m³·mol⁻¹	ChemAxon
Polarizability	50.83 Å³	ChemAxon
Number of Rings	1	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

C00029135

Chemspider ID

8633111

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10457697

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Konno H: Synthesis of bioactive natural products as protein inhibitors. Biosci Biotechnol Biochem. 2012;76(7):1257-61. doi: 10.1271/bbb.120176. Epub 2012 Jul 7. [PubMed:22785468 ]

Showing NP-Card for Tokaramide A (NP0070538)

MOL for NP0070538 (Tokaramide A)

3D MOL for NP0070538 (Tokaramide A)

3D SDF for NP0070538 (Tokaramide A)

3D-SDF for NP0070538 (Tokaramide A)

PDB for NP0070538 (Tokaramide A)

3D PDB for NP0070538 (Tokaramide A)

SMILES for NP0070538 (Tokaramide A)

INCHI for NP0070538 (Tokaramide A)

Structure for NP0070538 (Tokaramide A)

3D Structure for NP0070538 (Tokaramide A)