NP-MRD: Showing NP-Card for Dysinosin D (NP0076486)

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Record Information

Version

2.0

Created at

2022-04-28 21:39:43 UTC

Updated at

2022-04-28 21:39:43 UTC

NP-MRD ID

NP0076486

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dysinosin D

Description

(2S,3aR,5S,6S,7aS)-N-[2-(1-carbamimidoyl-2,5-dihydro-1H-pyrrol-3-yl)ethyl]-1-[(2R)-2-{[(2R)-1,3-dihydroxy-2-methoxypropylidene]amino}-3-methylbutanoyl]-5,6-dihydroxy-octahydro-1H-indole-2-carboximidic acid belongs to the class of organic compounds known as n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom. Dysinosin D is found in Lamellodysidea chlorea. Based on a literature review very few articles have been published on (2S,3aR,5S,6S,7aS)-N-[2-(1-carbamimidoyl-2,5-dihydro-1H-pyrrol-3-yl)ethyl]-1-[(2R)-2-{[(2R)-1,3-dihydroxy-2-methoxypropylidene]amino}-3-methylbutanoyl]-5,6-dihydroxy-octahydro-1H-indole-2-carboximidic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282223392D          

 38 40  0  0  1  0            999 V2000
    0.9400   -0.8911    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.6361    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    1.3815    0.4679    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5531   -0.3391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8664    1.1354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3815    1.8028    0.0000 C   0  0  1  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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
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  8  9  1  0  0  0  0
  4  9  1  1  0  0  0
  8 10  1  1  0  0  0
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 18 19  1  0  0  0  0
 15 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
  7 23  1  0  0  0  0
 23 24  2  0  0  0  0
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 29 30  1  0  0  0  0
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 33 34  1  0  0  0  0
 32 35  1  6  0  0  0
 35 36  1  0  0  0  0
  2 37  1  1  0  0  0
  1 38  1  6  0  0  0
M  END

     RDKit          3D

 80 82  0  0  0  0  0  0  0  0999 V2000
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  2  1  1  0
M  END


  Mrv1652304282223392D          

 38 40  0  0  1  0            999 V2000
    0.9400   -0.8911    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.6361    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    4.3414   -0.2936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9289   -1.0081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1664   -0.2936    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5789   -1.0081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4039   -1.0081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5789    0.4209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4039    0.4209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4578   -1.1882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1115   -1.6981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  1  0  0  0
  8 10  1  1  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 15 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
  7 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 25 29  1  6  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 32 35  1  6  0  0  0
 35 36  1  0  0  0  0
  2 37  1  1  0  0  0
  1 38  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0076486

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@H](CO)C(=O)N[C@H](C(C)C)C(=O)N1[C@H]2C[C@H](O)[C@@H](O)C[C@H]2C[C@H]1C(=O)NCCC1=CCN(C1)C(N)=N

> <INCHI_IDENTIFIER>
InChI=1S/C25H42N6O7/c1-13(2)21(29-23(36)20(12-32)38-3)24(37)31-16-10-19(34)18(33)9-15(16)8-17(31)22(35)28-6-4-14-5-7-30(11-14)25(26)27/h5,13,15-21,32-34H,4,6-12H2,1-3H3,(H3,26,27)(H,28,35)(H,29,36)/t15-,16+,17+,18+,19+,20-,21-/m1/s1

> <INCHI_KEY>
SVXQGBWHWPVWRI-LCERPBOYSA-N

> <FORMULA>
C25H42N6O7

> <MOLECULAR_WEIGHT>
538.646

> <EXACT_MASS>
538.311497716

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
56.937285771189295

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3aR,5S,6S,7aS)-N-[2-(1-carbamimidoyl-2,5-dihydro-1H-pyrrol-3-yl)ethyl]-5,6-dihydroxy-1-[(2R)-2-[(2R)-3-hydroxy-2-methoxypropanamido]-3-methylbutanoyl]-octahydro-1H-indole-2-carboxamide

> <ALOGPS_LOGP>
-1.63

> <JCHEM_LOGP>
-3.4742358987569415

> <ALOGPS_LOGS>
-3.01

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.802184109004287

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.265906855981898

> <JCHEM_PKA_STRONGEST_BASIC>
11.476108388406637

> <JCHEM_POLAR_SURFACE_AREA>
201.53999999999996

> <JCHEM_REFRACTIVITY>
149.1618

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.22e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3aR,5S,6S,7aS)-N-[2-(1-carbamimidoyl-2,5-dihydropyrrol-3-yl)ethyl]-5,6-dihydroxy-1-[(2R)-2-[(2R)-3-hydroxy-2-methoxypropanamido]-3-methylbutanoyl]-octahydroindole-2-carboxamide

> <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       1.755  -1.663   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -1.187   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.030   0.319   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.114   1.349   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.579   0.873   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.899  -0.633   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       3.484   2.119   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.579   3.365   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.114   2.889   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.055   4.830   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.561   5.150   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       2.024   5.974   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.500   7.439   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.470   8.583   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.946  10.048   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.040  11.294   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.946  12.540   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       3.410  12.064   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       3.410  10.524   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.656  12.969   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       4.495  14.501   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       6.063  12.343   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       5.024   2.119   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.794   3.453   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.794   0.786   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.024  -0.548   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.484  -0.548   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.794  -1.882   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       7.334   0.786   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       8.104  -0.548   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       7.334  -1.882   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       9.644  -0.548   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      10.414  -1.882   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      11.954  -1.882   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      10.414   0.786   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      11.954   0.786   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -0.854  -2.218   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       2.075  -3.170   0.000  0.00  0.00           O+0
CONECT    1    2    6   38                                                  
CONECT    2    1    3   37                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   23                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   19                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18   15                                                       
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23    7   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   29                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   25   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   32   36                                                       
CONECT   36   35                                                            
CONECT   37    2                                                            
CONECT   38    1                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   80    0
END

View in JSmol

Synonyms

Value	Source
(2S,3AR,5S,6S,7as)-N-[2-(1-carbamimidoyl-2,5-dihydro-1H-pyrrol-3-yl)ethyl]-1-[(2R)-2-{[(2R)-1,3-dihydroxy-2-methoxypropylidene]amino}-3-methylbutanoyl]-5,6-dihydroxy-octahydro-1H-indole-2-carboximidate	Generator

Chemical Formula

C₂₅H₄₂N₆O₇

Average Mass

538.6460 Da

Monoisotopic Mass

538.31150 Da

IUPAC Name

(2S,3aR,5S,6S,7aS)-N-[2-(1-carbamimidoyl-2,5-dihydro-1H-pyrrol-3-yl)ethyl]-5,6-dihydroxy-1-[(2R)-2-[(2R)-3-hydroxy-2-methoxypropanamido]-3-methylbutanoyl]-octahydro-1H-indole-2-carboxamide

Traditional Name

(2S,3aR,5S,6S,7aS)-N-[2-(1-carbamimidoyl-2,5-dihydropyrrol-3-yl)ethyl]-5,6-dihydroxy-1-[(2R)-2-[(2R)-3-hydroxy-2-methoxypropanamido]-3-methylbutanoyl]-octahydroindole-2-carboxamide

CAS Registry Number

Not Available

SMILES

CO[C@H](CO)C(=O)N[C@H](C(C)C)C(=O)N1[C@H]2C[C@H](O)[C@@H](O)C[C@H]2C[C@H]1C(=O)NCCC1=CCN(C1)C(N)=N

InChI Identifier

InChI=1S/C25H42N6O7/c1-13(2)21(29-23(36)20(12-32)38-3)24(37)31-16-10-19(34)18(33)9-15(16)8-17(31)22(35)28-6-4-14-5-7-30(11-14)25(26)27/h5,13,15-21,32-34H,4,6-12H2,1-3H3,(H3,26,27)(H,28,35)(H,29,36)/t15-,16+,17+,18+,19+,20-,21-/m1/s1

InChI Key

SVXQGBWHWPVWRI-LCERPBOYSA-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
Lamellodysidea chlorea	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-alpha amino acids and derivatives. N-acyl-alpha amino acids and derivatives are compounds containing an alpha amino acid (or a derivative thereof) which bears an acyl group at its terminal nitrogen atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

N-acyl-alpha amino acids and derivatives

Alternative Parents

Substituents

Valine or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Indole or derivatives
N-acylpyrrolidine
Tertiary carboxylic acid amide
Pyrroline
Pyrrolidine
Cyclic alcohol
Secondary alcohol
Guanidine
Carboxamide group
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Ether
Dialkyl ether
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Imine
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	-1.6	ALOGPS
logP	-3.5	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	12.27	ChemAxon
pKa (Strongest Basic)	11.48	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	201.54 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	149.16 m³·mol⁻¹	ChemAxon
Polarizability	56.94 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

163106064

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Dysinosin D (NP0076486)

MOL for NP0076486 (Dysinosin D)

3D MOL for NP0076486 (Dysinosin D)

3D SDF for NP0076486 (Dysinosin D)

3D-SDF for NP0076486 (Dysinosin D)

PDB for NP0076486 (Dysinosin D)

3D PDB for NP0076486 (Dysinosin D)

SMILES for NP0076486 (Dysinosin D)

INCHI for NP0076486 (Dysinosin D)

Structure for NP0076486 (Dysinosin D)

3D Structure for NP0076486 (Dysinosin D)