NP-MRD: Showing NP-Card for (6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid (NP0199685)

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Record Information

Version

2.0

Created at

2022-09-04 18:22:18 UTC

Updated at

2022-09-04 18:22:18 UTC

NP-MRD ID

NP0199685

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

CHEMBL528546 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. (6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid is found in Chimarrhis turbinata. Based on a literature review very few articles have been published on CHEMBL528546.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042220222D          

 37 41  0  0  1  0            999 V2000
    5.3194    0.6825    0.0000 C   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


  Mrv1652309042220222D          

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 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 10 18  1  0  0  0  0
 13 18  1  0  0  0  0
  4 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 19 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
  3 25  1  0  0  0  0
 25 26  1  6  0  0  0
 27 26  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  6  0  0  0
 30 31  1  0  0  0  0
 29 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  0  0  0  0
 34 35  1  6  0  0  0
 34 36  1  0  0  0  0
 27 36  1  0  0  0  0
 36 37  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0199685

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2OC=C(C(C[C@@H]3NCCC4=C3NC3=CC=CC=C43)C2C=C)C(O)=O)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H32N2O9/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/h2-6,11-12,15,18-19,21-23,25-32H,1,7-10H2,(H,33,34)/t12?,15?,18-,19+,21+,22-,23+,25-,26-/m0/s1

> <INCHI_KEY>
CMMIVMFGFIBAGC-IEUFSHIYSA-N

> <FORMULA>
C26H32N2O9

> <MOLECULAR_WEIGHT>
516.547

> <EXACT_MASS>
516.210780618

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
53.412890111561296

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.331280750924213

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.207521348311491

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.265253437485975

> <JCHEM_PKA_STRONGEST_BASIC>
9.343306863188246

> <JCHEM_POLAR_SURFACE_AREA>
173.73

> <JCHEM_REFRACTIVITY>
129.92870000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(6S)-5-ethenyl-4-[(1S)-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2S,3R,4S,5S,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                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       9.930   1.274   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.899   0.130   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.375  -1.335   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.344  -2.479   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.838  -2.159   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.362  -0.695   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       7.393   0.450   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       6.917   1.914   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.410   2.235   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.610  -1.280   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.173   0.450   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.810   2.235   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.820  -3.944   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.790  -5.089   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       8.266  -6.553   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       6.284  -4.768   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      10.327  -4.264   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      11.357  -3.120   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      10.881  -1.655   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      11.912  -0.511   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      13.418  -0.831   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      14.449   0.314   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      15.955  -0.007   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      16.985   1.138   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      16.509   2.602   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      16.431  -1.471   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      17.937  -1.791   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      15.400  -2.616   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      15.876  -4.080   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      13.894  -2.296   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      12.864  -3.440   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   25                                                  
CONECT    4    3    5   19                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10    6   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   10   13                                                  
CONECT   19    4   20   23                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   19   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24    3   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   36                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   29   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   27   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₂N₂O₉

Average Mass

516.5470 Da

Monoisotopic Mass

516.21078 Da

IUPAC Name

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

Traditional Name

(6S)-5-ethenyl-4-[(1S)-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2S,3R,4S,5S,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(C[C@@H]3NCCC4=C3NC3=CC=CC=C43)C2C=C)C(O)=O)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C26H32N2O9/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/h2-6,11-12,15,18-19,21-23,25-32H,1,7-10H2,(H,33,34)/t12?,15?,18-,19+,21+,22-,23+,25-,26-/m0/s1

InChI Key

CMMIVMFGFIBAGC-IEUFSHIYSA-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
Chimarrhis turbinata	LOTUS Database	35616633

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
3-alkylindole
Indole
Indole or derivatives
Alkaloid or derivatives
Aralkylamine
Sugar acid
Oxane
Monosaccharide
Benzenoid
Pyrrole
Vinylogous ester
Heteroaromatic compound
Secondary alcohol
Amino acid or derivatives
Amino acid
Acetal
Carboxylic acid derivative
Carboxylic acid
Secondary aliphatic amine
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Secondary amine
Polyol
Organic oxide
Organic nitrogen compound
Hydrocarbon derivative
Organic oxygen compound
Organopnictogen compound
Carbonyl group
Alcohol
Primary alcohol
Amine
Organonitrogen compound
Organooxygen compound
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	-2.3	ChemAxon
pKa (Strongest Acidic)	4.27	ChemAxon
pKa (Strongest Basic)	9.34	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	173.73 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	129.93 m³·mol⁻¹	ChemAxon
Polarizability	53.41 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

24721592

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44575750

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid (NP0199685)

MOL for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)

3D MOL for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)

3D SDF for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)

3D-SDF for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)

PDB for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)

3D PDB for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)

SMILES for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)

INCHI for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)

Structure for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)

3D Structure for NP0199685 ((6s)-5-ethenyl-4-[(1s)-1h,2h,3h,4h,9h-pyrido[3,4-b]indol-1-ylmethyl]-6-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5,6-dihydro-4h-pyran-3-carboxylic acid)