NP-MRD: Showing NP-Card for Lyalosidic acid (NP0071465)

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Record Information

Version

2.0

Created at

2022-04-28 16:50:44 UTC

Updated at

2022-04-28 16:50:44 UTC

NP-MRD ID

NP0071465

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lyalosidic acid

Description

(2R,3R,4R)-3-ethenyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-2-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-5-carboxylic acid belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. Lyalosidic acid is found in Ophiorrhiza japonica and Ophiorrhiza liukiuensis. Based on a literature review very few articles have been published on (2R,3R,4R)-3-ethenyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-2-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-5-carboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282218502D          

 37 41  0  0  1  0            999 V2000
    1.9339   -0.6855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.2410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2046   -1.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6024   -1.3283    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1544   -0.7152    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9614   -0.8867    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2163   -1.6713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4515    0.6825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.4084   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  3  4  1  0  0  0  0
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  6 10  1  0  0  0  0
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 13 20  1  6  0  0  0
 21 20  1  1  0  0  0
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  3 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
  2 37  1  0  0  0  0
M  END

     RDKit          3D

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    6.0856    0.1520   -0.6024 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652304282218502D          

 37 41  0  0  1  0            999 V2000
    1.9339   -0.6855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.9694    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 12 32  1  6  0  0  0
 32 33  2  0  0  0  0
  3 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
  2 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0071465

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@H]2OC=C([C@H](CC3=NC=CC4=C3NC3=C4C=CC=C3)[C@H]2C=C)C(O)=O)[C@H](O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28N2O9/c1-2-12-15(9-18-20-14(7-8-27-18)13-5-3-4-6-17(13)28-20)16(24(33)34)11-35-25(12)37-26-23(32)22(31)21(30)19(10-29)36-26/h2-8,11-12,15,19,21-23,25-26,28-32H,1,9-10H2,(H,33,34)/t12-,15-,19-,21+,22+,23-,25-,26+/m1/s1

> <INCHI_KEY>
UZLBTLIRYSYTRG-BKBZZBMWSA-N

> <FORMULA>
C26H28N2O9

> <MOLECULAR_WEIGHT>
512.515

> <EXACT_MASS>
512.17948049

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
51.904391642974986

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R)-3-ethenyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-2-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-5-carboxylic acid

> <ALOGPS_LOGP>
0.94

> <JCHEM_LOGP>
-0.8930480598528381

> <ALOGPS_LOGS>
-3.11

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.19010706239267

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.452239121320354

> <JCHEM_PKA_STRONGEST_BASIC>
5.700228148338306

> <JCHEM_POLAR_SURFACE_AREA>
174.58999999999997

> <JCHEM_REFRACTIVITY>
127.94

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.94e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5R,6R)-5-ethenyl-4-{9H-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4H-pyran-3-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  N   UNK     0       3.610  -1.280   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.173   0.450   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.810   2.235   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.382  -2.159   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.124  -2.479   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.155  -1.335   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.661  -1.655   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -4.137  -3.120   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -3.107  -4.264   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.600  -3.944   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.570  -5.089   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.936  -4.768   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.046  -6.553   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -4.692  -0.511   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -6.198  -0.831   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -6.674  -2.296   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -8.180  -2.616   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -9.211  -1.471   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.735  -0.007   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -7.229   0.314   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -9.765   1.138   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0     -11.272   0.818   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0     -10.717  -1.791   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -8.656  -4.080   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -5.643  -3.440   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -1.679   0.130   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -2.709   1.274   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       5.410   2.235   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.917   1.914   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.393   0.450   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.362  -0.695   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3   37                                                  
CONECT    3    2    4   34                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
CONECT   10    6   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   32                                                  
CONECT   13   12   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   11   17                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   13   21                                                       
CONECT   21   20   22   26                                                  
CONECT   22   21   23   31                                                  
CONECT   23   22   24   30                                                  
CONECT   24   23   25   29                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25   21                                                       
CONECT   27   25   28                                                       
CONECT   28   27                                                            
CONECT   29   24                                                            
CONECT   30   23                                                            
CONECT   31   22                                                            
CONECT   32   12   33                                                       
CONECT   33   32                                                            
CONECT   34    3   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36    2                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Value	Source
(2R,3R,4R)-3-Ethenyl-4-({9h-pyrido[3,4-b]indol-1-yl}methyl)-2-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-5-carboxylate	Generator

Chemical Formula

C₂₆H₂₈N₂O₉

Average Mass

512.5150 Da

Monoisotopic Mass

512.17948 Da

IUPAC Name

(2R,3R,4R)-3-ethenyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-2-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-pyran-5-carboxylic acid

Traditional Name

(4R,5R,6R)-5-ethenyl-4-{9H-pyrido[3,4-b]indol-1-ylmethyl}-6-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4H-pyran-3-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@H]2OC=C([C@H](CC3=NC=CC4=C3NC3=C4C=CC=C3)[C@H]2C=C)C(O)=O)[C@H](O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C26H28N2O9/c1-2-12-15(9-18-20-14(7-8-27-18)13-5-3-4-6-17(13)28-20)16(24(33)34)11-35-25(12)37-26-23(32)22(31)21(30)19(10-29)36-26/h2-8,11-12,15,19,21-23,25-26,28-32H,1,9-10H2,(H,33,34)/t12-,15-,19-,21+,22+,23-,25-,26+/m1/s1

InChI Key

UZLBTLIRYSYTRG-BKBZZBMWSA-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
Ophiorrhiza japonica	Plant	KNApSAcK
Ophiorrhiza liukiuensis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Harman
Pyridoindole
Beta-carboline
O-glycosyl compound
Secoiridoid-skeleton
Glycosyl compound
Monoterpenoid
Aromatic monoterpenoid
Alkaloid or derivatives
Indole or derivatives
Indole
Sugar acid
Benzenoid
Pyridine
Oxane
Monosaccharide
Heteroaromatic compound
Vinylogous ester
Pyrrole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	0.94	ALOGPS
logP	-0.89	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	4.45	ChemAxon
pKa (Strongest Basic)	5.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	174.59 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	127.94 m³·mol⁻¹	ChemAxon
Polarizability	51.9 Å³	ChemAxon
Number of Rings	5	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

163039055

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Lyalosidic acid (NP0071465)

MOL for NP0071465 (Lyalosidic acid)

3D MOL for NP0071465 (Lyalosidic acid)

3D SDF for NP0071465 (Lyalosidic acid)

3D-SDF for NP0071465 (Lyalosidic acid)

PDB for NP0071465 (Lyalosidic acid)

3D PDB for NP0071465 (Lyalosidic acid)

SMILES for NP0071465 (Lyalosidic acid)

INCHI for NP0071465 (Lyalosidic acid)

Structure for NP0071465 (Lyalosidic acid)

3D Structure for NP0071465 (Lyalosidic acid)