NP-MRD: Showing NP-Card for [(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate (NP0317102)

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Record Information

Version

2.0

Created at

2022-09-11 16:45:03 UTC

Updated at

2022-09-11 16:45:03 UTC

NP-MRD ID

NP0317102

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate

Description

CHEMBL518566 belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton. [(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate is found in Scrophularia buergeriana. Based on a literature review very few articles have been published on CHEMBL518566.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112218452D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309112218452D          

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 20 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  1  0  0  0
 26 28  1  6  0  0  0
 29 26  1  1  0  0  0
 17 29  1  0  0  0  0
 21 29  1  0  0  0  0
 15 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  0  0  0  0
 13 34  1  0  0  0  0
 34 35  1  6  0  0  0
  6 36  1  0  0  0  0
 36 37  2  0  0  0  0
  3 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0317102

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(\C=C\C(=O)OC[C@H]2O[C@@H](O[C@@H]3OC=C[C@@]4(O)[C@H](O)C[C@](C)(O)[C@@H]34)[C@H](O)[C@@H](O)[C@@H]2O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H32O12/c1-24(31)11-16(26)25(32)9-10-34-23(21(24)25)37-22-20(30)19(29)18(28)15(36-22)12-35-17(27)8-5-13-3-6-14(33-2)7-4-13/h3-10,15-16,18-23,26,28-32H,11-12H2,1-2H3/b8-5+/t15-,16-,18-,19+,20-,21-,22+,23+,24+,25-/m1/s1

> <INCHI_KEY>
FLGNDYLGJFFGQZ-HWOKHOLDSA-N

> <FORMULA>
C25H32O12

> <MOLECULAR_WEIGHT>
524.519

> <EXACT_MASS>
524.18937647

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
52.18920600977252

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6S)-6-{[(1S,4aS,5R,7S,7aR)-4a,5,7-trihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(4-methoxyphenyl)prop-2-enoate

> <JCHEM_LOGP>
-1.082760473999999

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.778889556227067

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.11865777965756

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0465912412301828

> <JCHEM_POLAR_SURFACE_AREA>
184.6

> <JCHEM_REFRACTIVITY>
125.23480000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6S)-6-{[(1S,4aS,5R,7S,7aR)-4a,5,7-trihydroxy-7-methyl-1H,5H,6H,7aH-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(4-methoxyphenyl)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      22.125   8.470   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      22.125   6.930   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      20.791   6.160   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.791   4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      19.457   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.124   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      16.790   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.456   4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.123   3.850   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      14.123   2.310   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      12.789   4.620   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      11.455   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.122   4.620   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.788   3.850   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       7.454   4.620   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.121   3.850   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       7.454   1.540   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.626  -1.532   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.846  -1.941   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.989   2.786   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       3.949   3.423   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.454   6.160   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.121   6.930   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.788   6.930   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       8.788   8.470   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      10.122   6.160   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      11.455   6.930   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      18.124   6.160   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      19.457   6.930   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   37                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   36                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   34                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   30                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   29                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23   29                                             
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27   28   29                                             
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   26   17   21                                                  
CONECT   30   15   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   13   35                                                  
CONECT   35   34                                                            
CONECT   36    6   37                                                       
CONECT   37   36    3                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₂O₁₂

Average Mass

524.5190 Da

Monoisotopic Mass

524.18938 Da

IUPAC Name

[(2R,3S,4S,5R,6S)-6-{[(1S,4aS,5R,7S,7aR)-4a,5,7-trihydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(4-methoxyphenyl)prop-2-enoate

Traditional Name

[(2R,3S,4S,5R,6S)-6-{[(1S,4aS,5R,7S,7aR)-4a,5,7-trihydroxy-7-methyl-1H,5H,6H,7aH-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2E)-3-(4-methoxyphenyl)prop-2-enoate

CAS Registry Number

Not Available

SMILES

COC1=CC=C(\C=C\C(=O)OC[C@H]2O[C@@H](O[C@@H]3OC=C[C@@]4(O)[C@H](O)C[C@](C)(O)[C@@H]34)[C@H](O)[C@@H](O)[C@@H]2O)C=C1

InChI Identifier

InChI=1S/C25H32O12/c1-24(31)11-16(26)25(32)9-10-34-23(21(24)25)37-22-20(30)19(29)18(28)15(36-22)12-35-17(27)8-5-13-3-6-14(33-2)7-4-13/h3-10,15-16,18-23,26,28-32H,11-12H2,1-2H3/b8-5+/t15-,16-,18-,19+,20-,21-,22+,23+,24+,25-/m1/s1

InChI Key

FLGNDYLGJFFGQZ-HWOKHOLDSA-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
Scrophularia buergeriana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Iridoid O-glycosides

Alternative Parents

Substituents

Iridoid o-glycoside
Cinnamic acid ester
Cinnamic acid or derivatives
O-glycosyl compound
Iridoid-skeleton
Glycosyl compound
Bicyclic monoterpenoid
Monoterpenoid
Aromatic monoterpenoid
Anisole
Phenoxy compound
Styrene
Phenol ether
Methoxybenzene
Alkyl aryl ether
Fatty acid ester
Fatty acyl
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Alpha,beta-unsaturated carboxylic ester
Cyclic alcohol
Enoate ester
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Ether
Acetal
Carboxylic acid derivative
Organoheterocyclic compound
Oxacycle
Monocarboxylic acid or derivatives
Polyol
Organic oxide
Organic oxygen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
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	-1.1	ChemAxon
pKa (Strongest Acidic)	12.12	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	184.6 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	125.23 m³·mol⁻¹	ChemAxon
Polarizability	52.19 Å³	ChemAxon
Number of Rings	4	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

9159409

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10984208

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate (NP0317102)

MOL for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)

3D MOL for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)

3D SDF for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)

3D-SDF for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)

PDB for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)

3D PDB for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)

SMILES for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)

INCHI for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)

Structure for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)

3D Structure for NP0317102 ([(2r,3s,4s,5r,6s)-6-{[(1s,4as,5r,7s,7ar)-4a,5,7-trihydroxy-7-methyl-1h,5h,6h,7ah-cyclopenta[c]pyran-1-yl]oxy}-3,4,5-trihydroxyoxan-2-yl]methyl (2e)-3-(4-methoxyphenyl)prop-2-enoate)