NP-MRD: Showing NP-Card for [(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate (NP0173769)

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Record Information

Version

2.0

Created at

2022-09-03 10:56:58 UTC

Updated at

2022-09-03 10:56:58 UTC

NP-MRD ID

NP0173769

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate

Description

[(3S,4R,5R)-5-{[(2R,3S,4S,5R,6R)-6-[(R)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. [(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate is found in Psydrax livida. Based on a literature review very few articles have been published on [(3S,4R,5R)-5-{[(2R,3S,4S,5R,6R)-6-[(R)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032212562D          

 38 41  0  0  1  0            999 V2000
    4.1618    1.3791    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309032212562D          

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 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 19 24  1  0  0  0  0
 13 25  1  0  0  0  0
 10 25  1  0  0  0  0
 25 26  1  1  0  0  0
  7 27  1  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  0  0  0  0
 29 30  1  1  0  0  0
 29 31  1  0  0  0  0
  5 31  1  0  0  0  0
 31 32  1  6  0  0  0
  3 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 33 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0173769

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1[C@H](OC[C@H]2O[C@@H](O[C@@H](C#N)C3=CC=CC=C3)[C@H](O)[C@@H](O)[C@@H]2O)OC[C@]1(O)COC(=O)C1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C26H29NO11/c27-11-17(15-7-3-1-4-8-15)37-24-21(30)20(29)19(28)18(38-24)12-34-25-22(31)26(33,14-36-25)13-35-23(32)16-9-5-2-6-10-16/h1-10,17-22,24-25,28-31,33H,12-14H2/t17-,18+,19+,20-,21+,22-,24+,25+,26+/m0/s1

> <INCHI_KEY>
VQRFNQHZPFHUSV-BYQUYGEWSA-N

> <FORMULA>
C26H29NO11

> <MOLECULAR_WEIGHT>
531.514

> <EXACT_MASS>
531.174060758

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
52.2580521393974

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(3S,4R,5R)-5-{[(2R,3S,4S,5R,6R)-6-[(R)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate

> <ALOGPS_LOGP>
0.51

> <JCHEM_LOGP>
0.40174965433333243

> <ALOGPS_LOGS>
-2.36

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.309973445492254

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.692607115123645

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648669483277434

> <JCHEM_POLAR_SURFACE_AREA>
188.16

> <JCHEM_REFRACTIVITY>
126.58860000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.31e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3S,4R,5R)-5-{[(2R,3S,4S,5R,6R)-6-[(R)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  N   UNK     0       7.769   2.574   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       6.237   2.413   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.706   2.252   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.079   0.845   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.548   0.684   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.642   1.930   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.111   1.769   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.794   3.015   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.326   2.854   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -3.231   4.100   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -4.771   4.100   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -5.247   5.565   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.001   6.470   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -5.031   7.614   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -2.971   7.614   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.464   7.294   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -0.434   8.439   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.073   8.119   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -0.910   9.903   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.416  10.224   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.892  11.688   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.861  12.833   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.355  12.512   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.121  11.048   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -2.755   5.565   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -1.291   6.041   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -0.515   0.363   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -2.047   0.202   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.390  -0.883   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -0.237  -2.290   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.921  -0.722   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       2.826  -1.968   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.800   3.498   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.269   3.337   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.364   4.583   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       1.990   5.990   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       3.522   6.151   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.427   4.905   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   33                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   31                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   27                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   25                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15   25                                             
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   19                                                       
CONECT   25   13   10   26                                                  
CONECT   26   25                                                            
CONECT   27    7   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29    5   32                                                  
CONECT   32   31                                                            
CONECT   33    3   34   38                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   33                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Value	Source
[(3S,4R,5R)-5-{[(2R,3S,4S,5R,6R)-6-[(R)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoic acid	Generator

Chemical Formula

C₂₆H₂₉NO₁₁

Average Mass

531.5140 Da

Monoisotopic Mass

531.17406 Da

IUPAC Name

[(3S,4R,5R)-5-{[(2R,3S,4S,5R,6R)-6-[(R)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate

Traditional Name

[(3S,4R,5R)-5-{[(2R,3S,4S,5R,6R)-6-[(R)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate

CAS Registry Number

Not Available

SMILES

O[C@H]1[C@H](OC[C@H]2O[C@@H](O[C@@H](C#N)C3=CC=CC=C3)[C@H](O)[C@@H](O)[C@@H]2O)OC[C@]1(O)COC(=O)C1=CC=CC=C1

InChI Identifier

InChI=1S/C26H29NO11/c27-11-17(15-7-3-1-4-8-15)37-24-21(30)20(29)19(28)18(38-24)12-34-25-22(31)26(33,14-36-25)13-35-23(32)16-9-5-2-6-10-16/h1-10,17-22,24-25,28-31,33H,12-14H2/t17-,18+,19+,20-,21+,22-,24+,25+,26+/m0/s1

InChI Key

VQRFNQHZPFHUSV-BYQUYGEWSA-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

Species Name	Source	Reference
Psydrax livida	LOTUS Database	35616633

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
Disaccharide
O-glycosyl compound
Benzoate ester
Benzoic acid or derivatives
Benzoyl
Monocyclic benzene moiety
Oxane
Benzenoid
Tetrahydrofuran
Tertiary alcohol
Secondary alcohol
Carboxylic acid ester
Polyol
Organoheterocyclic compound
Nitrile
Carbonitrile
Monocarboxylic acid or derivatives
Oxacycle
Acetal
Carboxylic acid derivative
Alcohol
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen 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	0.51	ALOGPS
logP	0.4	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	11.69	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	188.16 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	126.59 m³·mol⁻¹	ChemAxon
Polarizability	52.26 Å³	ChemAxon
Number of Rings	4	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

162996561

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate (NP0173769)

MOL for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D MOL for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D SDF for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D-SDF for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

PDB for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D PDB for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

SMILES for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

INCHI for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

Structure for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D Structure for NP0173769 ([(3s,4r,5r)-5-{[(2r,3s,4s,5r,6r)-6-[(r)-cyano(phenyl)methoxy]-3,4,5-trihydroxyoxan-2-yl]methoxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)