NP-MRD: Showing NP-Card for linamarin (NP0163919)

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Record Information

Version

2.0

Created at

2022-09-02 22:41:31 UTC

Updated at

2025-07-16 00:03:49 UTC

NP-MRD ID

NP0163919

Natural Product DOI

https://doi.org/10.57994/4326

Secondary Accession Numbers

None

Natural Product Identification

Common Name

linamarin

Description

2-Methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propanenitrile belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. linamarin is found in Hevea brasiliensis, Hevea guianensis, Hevea pauciflora, Linum grandiflorum, Linum usitatissimum, Lotus corniculatus, Lotus creticus, Lotus parviflorus, Manihot esculenta, Passiflora foetida, Passiflora lutea, Passiflora morifolia, Passiflora subpeltata, Trifolium repens, Turnera angustifolia and Turnera ulmifolia. 2-Methyl-2-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propanenitrile is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 34  0  0  0  0  0  0  0  0999 V2000
    2.6357    1.0770   -0.0649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6154   -0.4491   -0.1071 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8464   -1.0351    0.5521 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4895   -0.8763   -1.4950 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3824   -1.2023   -2.5982 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5172   -0.8683    0.6024 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3112   -0.4166    0.1174 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2767    0.3504    1.1494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2548    1.1220    0.5686 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0746    1.7842    1.6815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0814    2.5786    1.1266 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1329    0.4021   -0.3968 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8618    0.8117   -1.6960 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0431   -1.1012   -0.2925 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5147   -1.6291   -1.4965 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6316   -1.5910   -0.1009 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1782   -2.3877   -1.1306 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4773    1.4908   -1.0987 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6095    1.4365    0.3008 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8231    1.4830    0.5672 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5112   -1.4363   -0.2389 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3509   -0.3109    1.2030 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5518   -1.9317    1.1707 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3694    0.2169   -0.7675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7309    1.9746    0.0479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4720    1.0312    2.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4291    2.4691    2.2674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0034    3.5308    1.3769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1871    0.6883   -0.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6883    1.0679   -2.1816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7000   -1.5114    0.5043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4039   -1.2396   -1.7173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5772   -2.1980    0.8339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2493   -3.3302   -0.9017 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
  9 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  2  4  1  0
  4  5  3  0
 16  7  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  3 23  1  0
  7 24  1  6
  9 25  1  6
 10 26  1  0
 10 27  1  0
 11 28  1  0
 12 29  1  1
 13 30  1  0
 14 31  1  1
 15 32  1  0
 16 33  1  1
 17 34  1  0
M  END


  Mrv1533004251504432D          

 17 17  0  0  0  0            999 V2000
    0.4125    3.1895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    1.7605    0.0000 C   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  0  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  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
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  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  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    0.8250    0.0000 C   0  0  0  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
   -0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 N   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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
  5 14  1  0  0  0  0
 14 15  1  0  0  0  0
  2 16  1  0  0  0  0
 16 17  3  0  0  0  0
M  END
> <DATABASE_ID>
NP0163919

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)(OC1OC(CO)C(O)C(O)C1O)C#N

> <INCHI_IDENTIFIER>
InChI=1S/C10H17NO6/c1-10(2,4-11)17-9-8(15)7(14)6(13)5(3-12)16-9/h5-9,12-15H,3H2,1-2H3

> <INCHI_KEY>
QLTCHMYAEJEXBT-UHFFFAOYSA-N

> <FORMULA>
C10H17NO6

> <MOLECULAR_WEIGHT>
247.247

> <EXACT_MASS>
247.105587271

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
23.802563583172105

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.15

> <JCHEM_LOGP>
-1.7519504109999997

> <ALOGPS_LOGS>
-0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.199265755493812

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.208435937637255

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810842497378927

> <JCHEM_POLAR_SURFACE_AREA>
123.17000000000002

> <JCHEM_REFRACTIVITY>
54.945699999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.68e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
linamarin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       0.770   5.954   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.770   3.286   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.334   5.390   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -2.667   6.160   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4   16                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   14                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    7   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    5   15                                                  
CONECT   15   14                                                            
CONECT   16    2   17                                                       
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₇NO₆

Average Mass

247.2470 Da

Monoisotopic Mass

247.10559 Da

IUPAC Name

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

Traditional Name

linamarin

CAS Registry Number

Not Available

SMILES

CC(C)(OC1OC(CO)C(O)C(O)C1O)C#N

InChI Identifier

InChI=1S/C10H17NO6/c1-10(2,4-11)17-9-8(15)7(14)6(13)5(3-12)16-9/h5-9,12-15H,3H2,1-2H3

InChI Key

QLTCHMYAEJEXBT-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, D2O, experimental)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, D2O, experimental)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, D2O, experimental)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D2O, experimental)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600.0 MHz, D₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

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

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600.0, D₂O, simulated)	rjm4kd@umsystem.edu	Sumner lab, University of Missouri	Ronald Myers	2025-07-14	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Hevea brasiliensis	LOTUS Database	35616633
Hevea guianensis	LOTUS Database	35616633
Hevea pauciflora	LOTUS Database	35616633
Linum grandiflorum	LOTUS Database	35616633
Linum usitatissimum	LOTUS Database	35616633
Lotus corniculatus	LOTUS Database	35616633
Lotus creticus	LOTUS Database	35616633
Lotus parviflorus	LOTUS Database	35616633
Manihot esculenta	LOTUS Database	35616633
Passiflora foetida	LOTUS Database	35616633
Passiflora lutea L.	LOTUS Database	35616633
Passiflora morifolia Mast.	LOTUS Database	35616633
Passiflora subpeltata	LOTUS Database	35616633
Trifolium repens	LOTUS Database	35616633
Turnera angustifolia	LOTUS Database	35616633
Turnera ulmifolia	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
Secondary alcohol
Organoheterocyclic compound
Polyol
Nitrile
Carbonitrile
Acetal
Oxacycle
Primary alcohol
Alcohol
Organonitrogen compound
Cyanide
Organopnictogen compound
Organic nitrogen compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

a small molecule (LINAMARIN )

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	-1.2	ALOGPS
logP	-1.8	ChemAxon
logS	-0.57	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	3	ChemAxon
Refractivity	54.95 m³·mol⁻¹	ChemAxon
Polarizability	23.8 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

4457489

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for linamarin (NP0163919)

MOL for NP0163919 (linamarin)

3D MOL for NP0163919 (linamarin)

3D SDF for NP0163919 (linamarin)

3D-SDF for NP0163919 (linamarin)

PDB for NP0163919 (linamarin)

3D PDB for NP0163919 (linamarin)

SMILES for NP0163919 (linamarin)

INCHI for NP0163919 (linamarin)

Structure for NP0163919 (linamarin)

3D Structure for NP0163919 (linamarin)