NP-MRD: Showing NP-Card for epitetraphyllin b (NP0198732)

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Record Information

Version

1.0

Created at

2022-09-04 17:13:33 UTC

Updated at

2022-09-04 17:13:34 UTC

NP-MRD ID

NP0198732

Secondary Accession Numbers

None

Natural Product Identification

Common Name

epitetraphyllin b

Description

Volkenin belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. epitetraphyllin b is found in Adenia gracilis, Adenia volkensii, Androsiphonia adenostegia, Mathurina penduliflora, Passiflora foetida, Passiflora tetrandra, Turnera diffusa and Turnera ulmifolia. It was first documented in 2001 (PMID: 11152950). Based on a literature review very few articles have been published on volkenin.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
   -3.7489   -0.9108   -3.0780 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9770   -0.7044   -2.2515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0016   -0.4464   -1.2391 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7320   -0.5473   -1.5824 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2946   -0.4154   -0.7565 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0947    0.7325   -0.9841 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7167    1.0313    0.2139 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4623    2.3364    0.1747 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6627    3.4221   -0.1036 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6428   -0.0287    0.7145 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0513    0.3318    1.9981 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9213   -1.3790    0.7725 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7821   -2.4093    1.0475 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2455   -1.5518   -0.5990 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6780   -2.8021   -0.6074 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2790   -1.2813   -0.0333 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9429   -0.6350    0.8883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2242    0.7528    0.4495 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.5332    0.8691   -0.0234 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2345    0.9651   -0.6640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1377   -0.2183    0.2713 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8897    1.1241    0.9765 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3171    2.2483   -0.5440 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9326    2.4842    1.1707 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2249    3.7229    0.7181 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5610   -0.1039    0.0933 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9301   -0.1005    2.1678 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1152   -1.2795    1.5074 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3747   -3.0110    1.7458 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1164   -1.4779   -1.3174 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4427   -3.0321   -1.5415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9421   -2.3297    0.0302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2290   -1.1029    1.8412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0633    1.4708    1.2846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4833    1.2616   -0.9411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6208    1.6387   -1.4551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3073    1.3756   -0.2242 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3 20  1  0
 20 18  1  0
 18 19  1  0
 18 17  1  0
 17 16  2  0
  3  2  1  6
  2  1  3  0
  5 14  1  0
 14 15  1  0
 14 12  1  0
 12 13  1  0
 12 10  1  0
 10 11  1  0
 10  7  1  0
 16  3  1  0
  9 25  1  0
  8 23  1  0
  8 24  1  0
  7 22  1  1
  5 21  1  1
 20 36  1  0
 20 37  1  0
 18 34  1  1
 19 35  1  0
 17 33  1  0
 16 32  1  0
 14 30  1  6
 15 31  1  0
 12 28  1  1
 13 29  1  0
 10 26  1  6
 11 27  1  0
M  END


  Mrv1652309042219132D          

 20 21  0  0  1  0            999 V2000
    0.4176    0.4239    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1344   -0.1892    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6865   -0.8023    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2385   -0.1892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0455   -0.3607    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3004   -1.1454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1074   -1.3169    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3623   -2.1015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1693   -2.2730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6594   -0.7038    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.4664   -0.8753    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4045    0.0808    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9565    0.6939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5975    0.2524    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3425    1.0370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0190   -1.2872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2740   -2.0718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0990   -2.0718    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5839   -2.7393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3539   -1.2872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  1  0  0  0
  5  4  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
  5 14  1  0  0  0  0
 14 15  1  1  0  0  0
  3 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
  3 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0198732

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@]2(C[C@@H](O)C=C2)C#N)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C12H17NO7/c13-5-12(2-1-6(15)3-12)20-11-10(18)9(17)8(16)7(4-14)19-11/h1-2,6-11,14-18H,3-4H2/t6-,7+,8+,9-,10+,11-,12-/m0/s1

> <INCHI_KEY>
JRCWYCAEAZEYNW-WTMYBKBASA-N

> <FORMULA>
C12H17NO7

> <MOLECULAR_WEIGHT>
287.268

> <EXACT_MASS>
287.100501891

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
27.07084343516314

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,4R)-4-hydroxy-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclopent-2-ene-1-carbonitrile

> <JCHEM_LOGP>
-2.680250793333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.187995762787704

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.206697891243529

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9133000556887545

> <JCHEM_POLAR_SURFACE_AREA>
143.4

> <JCHEM_REFRACTIVITY>
64.626

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
volkenin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  N   UNK     0       0.780   0.791   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -0.251  -0.353   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.281  -1.498   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.312  -0.353   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -3.818  -0.673   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.294  -2.138   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -5.800  -2.458   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -6.276  -3.923   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -7.783  -4.243   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -6.831  -1.314   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -8.337  -1.634   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -6.355   0.151   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -7.385   1.295   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -4.849   0.471   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.373   1.936   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -0.035  -2.403   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.511  -3.867   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.051  -3.867   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.957  -5.113   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -2.527  -2.403   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   16   20                                             
CONECT    4    3    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    3   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18    3                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₇NO₇

Average Mass

287.2680 Da

Monoisotopic Mass

287.10050 Da

IUPAC Name

(1R,4R)-4-hydroxy-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}cyclopent-2-ene-1-carbonitrile

Traditional Name

volkenin

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@]2(C[C@@H](O)C=C2)C#N)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C12H17NO7/c13-5-12(2-1-6(15)3-12)20-11-10(18)9(17)8(16)7(4-14)19-11/h1-2,6-11,14-18H,3-4H2/t6-,7+,8+,9-,10+,11-,12-/m0/s1

InChI Key

JRCWYCAEAZEYNW-WTMYBKBASA-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
Adenia gracilis	LOTUS Database	35616633
Adenia volkensii	LOTUS Database	35616633
Androsiphonia adenostegia	LOTUS Database	35616633
Mathurina penduliflora	LOTUS Database	35616633
Passiflora foetida	LOTUS Database	35616633
Tetrapathaea tetrandra	LOTUS Database	35616633
Turnera diffusa	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
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

beta-D-glucoside (CHEBI:10018 )
monosaccharide derivative (CHEBI:10018 )
aliphatic nitrile (CHEBI:10018 )
cyanogenic glycoside (CHEBI:10018 )
Cyanogenic glucosides derived from nonprotein amino acid (C08344 )

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	-2.7	ChemAxon
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	143.4 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	64.63 m³·mol⁻¹	ChemAxon
Polarizability	27.07 Å³	ChemAxon
Number of Rings	2	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

C00001459

Chemspider ID

158135

KEGG Compound ID

C08344

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

181811

PDB ID

Not Available

ChEBI ID

10018

Good Scents ID

Not Available

References

General References

Clausen V V, Wellendorph P, Ekpe P, Jaroszewski JW: Tetraphyllin B, volkenin and cyclopentenylglycine in Androsiphonia adenostegia. Biochem Syst Ecol. 2001 Mar;29(3):317-319. doi: 10.1016/s0305-1978(00)00051-x. [PubMed:11152950 ]
LOTUS database [Link]

Showing NP-Card for epitetraphyllin b (NP0198732)

MOL for NP0198732 (epitetraphyllin b)

3D MOL for NP0198732 (epitetraphyllin b)

3D SDF for NP0198732 (epitetraphyllin b)

3D-SDF for NP0198732 (epitetraphyllin b)

PDB for NP0198732 (epitetraphyllin b)

3D PDB for NP0198732 (epitetraphyllin b)

SMILES for NP0198732 (epitetraphyllin b)

INCHI for NP0198732 (epitetraphyllin b)

Structure for NP0198732 (epitetraphyllin b)

3D Structure for NP0198732 (epitetraphyllin b)