NP-MRD: Showing NP-Card for (3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid (NP0250310)

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Record Information

Version

2.0

Created at

2022-09-07 13:06:00 UTC

Updated at

2022-09-07 13:06:00 UTC

NP-MRD ID

NP0250310

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid

Description

[(3R)-3-cyano-2-methylidene-3-{[(2R,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxy]sulfonic acid belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. (3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid is found in Cardiospermum grandiflorum. Based on a literature review very few articles have been published on [(3R)-3-cyano-2-methylidene-3-{[(2R,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxy]sulfonic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309072215062D          

 23 23  0  0  1  0            999 V2000
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414    4.2355    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164    5.6645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    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  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  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
    0.0000    0.0000    0.0000 C   0  0  2  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    0.8250    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
  1  2  2  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  2  0  0  0  0
  5  7  2  0  0  0  0
  5  8  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  3  0  0  0  0
  9 12  1  1  0  0  0
 13 12  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 13 22  1  0  0  0  0
 22 23  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0250310

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H]1O[C@@H](O[C@@H](C#N)C(=C)COS(O)(=O)=O)[C@@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C11H17NO10S/c1-5(4-20-23(17,18)19)6(2-12)21-11-10(16)9(15)8(14)7(3-13)22-11/h6-11,13-16H,1,3-4H2,(H,17,18,19)/t6-,7-,8+,9-,10-,11+/m0/s1

> <INCHI_KEY>
XRVSCIZCEJNBIO-OJHQEIPXSA-N

> <FORMULA>
C11H17NO10S

> <MOLECULAR_WEIGHT>
355.31

> <EXACT_MASS>
355.057316925

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
30.935538524262945

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(3R)-3-cyano-2-methylidene-3-{[(2R,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxy]sulfonic acid

> <JCHEM_LOGP>
-4.734919269217005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.208336098042667

> <JCHEM_PKA_STRONGEST_ACIDIC>
-2.1317724335011343

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981084263674

> <JCHEM_POLAR_SURFACE_AREA>
186.77

> <JCHEM_REFRACTIVITY>
70.69500000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-cyano-2-methylidene-3-{[(2R,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.334   8.470   0.000  0.00  0.00           O+0
HETATM    5  S   UNK     0      -2.667   9.240   0.000  0.00  0.00           S+0
HETATM    6  O   UNK     0      -4.001  10.010   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -3.437   7.906   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.897  10.574   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -2.667   3.080   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5                                                            
CONECT    9    2   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14   22                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   13   23                                                  
CONECT   23   22                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

View in JSmol

Synonyms

Value	Source
[(3R)-3-Cyano-2-methylidene-3-{[(2R,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxy]sulfonate	Generator
[(3R)-3-Cyano-2-methylidene-3-{[(2R,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxy]sulphonate	Generator
[(3R)-3-Cyano-2-methylidene-3-{[(2R,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxy]sulphonic acid	Generator

Chemical Formula

C₁₁H₁₇NO₁₀S

Average Mass

355.3100 Da

Monoisotopic Mass

355.05732 Da

IUPAC Name

[(3R)-3-cyano-2-methylidene-3-{[(2R,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxy]sulfonic acid

Traditional Name

(3R)-3-cyano-2-methylidene-3-{[(2R,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid

CAS Registry Number

Not Available

SMILES

OC[C@@H]1O[C@@H](O[C@@H](C#N)C(=C)COS(O)(=O)=O)[C@@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C11H17NO10S/c1-5(4-20-23(17,18)19)6(2-12)21-11-10(16)9(15)8(14)7(3-13)22-11/h6-11,13-16H,1,3-4H2,(H,17,18,19)/t6-,7-,8+,9-,10-,11+/m0/s1

InChI Key

XRVSCIZCEJNBIO-OJHQEIPXSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cardiospermum grandiflorum	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
Hexose monosaccharide
O-glycosyl compound
Monosaccharide
Oxane
Sulfuric acid ester
Alkyl sulfate
Sulfate-ester
Sulfuric acid monoester
Organic sulfuric acid or derivatives
Secondary alcohol
Acetal
Carbonitrile
Nitrile
Oxacycle
Organoheterocyclic compound
Polyol
Alcohol
Hydrocarbon derivative
Organic nitrogen compound
Organonitrogen compound
Organopnictogen compound
Organic oxide
Primary 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	-4.7	ChemAxon
pKa (Strongest Acidic)	-2.1	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	186.77 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	70.7 m³·mol⁻¹	ChemAxon
Polarizability	30.94 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

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

162999162

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid (NP0250310)

MOL for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)

3D MOL for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)

3D SDF for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)

3D-SDF for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)

PDB for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)

3D PDB for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)

SMILES for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)

INCHI for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)

Structure for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)

3D Structure for NP0250310 ((3r)-3-cyano-2-methylidene-3-{[(2r,3s,4s,5s,6s)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propoxysulfonic acid)