NP-MRD: Showing NP-Card for Epidermin (NP0086476)

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Record Information

Version

2.0

Created at

2022-04-29 06:46:09 UTC

Updated at

2022-04-29 06:46:09 UTC

NP-MRD ID

NP0086476

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Epidermin

Description

3-Methyl-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxybutanenitrile belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. Epidermin is found in Hordeum vulgare . Based on a literature review very few articles have been published on 3-methyl-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxybutanenitrile.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 37  0  0  0  0  0  0  0  0999 V2000
    3.2985    1.0647    1.1969 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2468    0.7536    0.1235 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9575    2.1103   -0.5289 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9272   -0.0949   -0.9009 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4458   -1.3461   -0.3476 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8646   -2.3371    0.0719 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1842    0.2215    0.7543 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0980   -0.1392    0.0101 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9720    0.6666    0.4780 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9853    0.5181   -0.4618 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1317    1.4714   -0.2223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7395    2.8014   -0.2772 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5411   -0.8816   -0.4840 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6713   -1.2573   -1.8213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7249   -1.8502    0.3191 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2165   -1.9190    1.6266 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2650   -1.5545    0.3539 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4119   -2.4756   -0.4802 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1089    1.6761    0.7978 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7243    1.5615    2.0202 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6151    0.0773    1.5874 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5088    2.8206    0.1646 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9517    2.4959   -0.8543 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3694    1.9146   -1.4423 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7970    0.4334   -1.3425 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2756   -0.3744   -1.7510 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2095    0.0448   -1.0774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5485    0.7834   -1.4423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8627    1.2991   -1.0439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6797    1.2276    0.7204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3261    3.3169    0.3138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5666   -0.8887   -0.0604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9100   -2.2195   -1.8431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8792   -2.8581   -0.1174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8922   -2.6344    1.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1193   -1.7632    1.3732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2015   -2.6651   -1.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  3  0
  2  7  1  1
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  8  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  3 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
  8 27  1  6
 10 28  1  6
 11 29  1  0
 11 30  1  0
 12 31  1  0
 13 32  1  1
 14 33  1  0
 15 34  1  6
 16 35  1  0
 17 36  1  1
 18 37  1  0
M  END


  Mrv1652304292208462D          

 18 18  0  0  1  0            999 V2000
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   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
   -1.0164    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  3  0  0  0  0
  9 17  1  0  0  0  0
  2 17  1  0  0  0  0
 17 18  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0086476

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)(CC#N)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C11H19NO6/c1-11(2,3-4-12)18-10-9(16)8(15)7(14)6(5-13)17-10/h6-10,13-16H,3,5H2,1-2H3/t6-,7-,8+,9-,10+/m1/s1

> <INCHI_KEY>
GDSYPXWUHMRTHT-SPFKKGSWSA-N

> <FORMULA>
C11H19NO6

> <MOLECULAR_WEIGHT>
261.274

> <EXACT_MASS>
261.121237336

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.893063231892057

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methyl-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanenitrile

> <ALOGPS_LOGP>
-0.84

> <JCHEM_LOGP>
-1.81931611

> <ALOGPS_LOGS>
-0.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.199927149088346

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210144379389055

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083674959522

> <JCHEM_POLAR_SURFACE_AREA>
123.17

> <JCHEM_REFRACTIVITY>
59.4949

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.56e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methyl-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanenitrile

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.897   1.334   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.437  -1.334   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.001   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -6.668  -0.770   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10   17                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17    9    2   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₉NO₆

Average Mass

261.2740 Da

Monoisotopic Mass

261.12124 Da

IUPAC Name

3-methyl-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanenitrile

Traditional Name

3-methyl-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}butanenitrile

CAS Registry Number

Not Available

SMILES

CC(C)(CC#N)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C11H19NO6/c1-11(2,3-4-12)18-10-9(16)8(15)7(14)6(5-13)17-10/h6-10,13-16H,3,5H2,1-2H3/t6-,7-,8+,9-,10+/m1/s1

InChI Key

GDSYPXWUHMRTHT-SPFKKGSWSA-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
Hordeum vulgare	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Cyanogenic glycosides

Alternative Parents

Substituents

Cyanogenic glycoside
Hexose monosaccharide
O-glycosyl compound
Monosaccharide
Oxane
Secondary alcohol
Polyol
Organoheterocyclic compound
Oxacycle
Nitrile
Carbonitrile
Acetal
Primary alcohol
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	-0.84	ALOGPS
logP	-1.8	ChemAxon
logS	-0.67	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	123.17 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	59.49 m³·mol⁻¹	ChemAxon
Polarizability	25.89 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

C00056760

Chemspider ID

103884963

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14559841

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Epidermin (NP0086476)

MOL for NP0086476 (Epidermin)

3D MOL for NP0086476 (Epidermin)

3D SDF for NP0086476 (Epidermin)

3D-SDF for NP0086476 (Epidermin)

PDB for NP0086476 (Epidermin)

3D PDB for NP0086476 (Epidermin)

SMILES for NP0086476 (Epidermin)

INCHI for NP0086476 (Epidermin)

Structure for NP0086476 (Epidermin)

3D Structure for NP0086476 (Epidermin)