NP-MRD: Showing NP-Card for (1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid (NP0324210)

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Record Information

Version

2.0

Created at

2022-09-12 04:08:56 UTC

Updated at

2022-09-12 04:08:56 UTC

NP-MRD ID

NP0324210

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid

Description

Negundoside 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. (1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid is found in Vitex altissima and Vitex negundo. (1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid was first documented in 2013 (PMID: 23954198). Based on a literature review a small amount of articles have been published on Negundoside (PMID: 26726748) (PMID: 35072759) (PMID: 34466412) (PMID: 31155557).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122206082D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309122206082D          

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M  END
> <DATABASE_ID>
NP0324210

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@]1(O)CC[C@H]2[C@@H]1[C@H](O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1OC(=O)C1=CC=C(O)C=C1)OC=C2C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C23H28O12/c1-23(31)7-6-12-13(19(28)29)9-32-21(15(12)23)35-22-18(17(27)16(26)14(8-24)33-22)34-20(30)10-2-4-11(25)5-3-10/h2-5,9,12,14-18,21-22,24-27,31H,6-8H2,1H3,(H,28,29)/t12-,14-,15-,16-,17+,18-,21+,22+,23+/m1/s1

> <INCHI_KEY>
RFCSGMIUBXUYSE-KLZCBZFCSA-N

> <FORMULA>
C23H28O12

> <MOLECULAR_WEIGHT>
496.465

> <EXACT_MASS>
496.158076342

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
47.7469946094139

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4aS,7S,7aS)-1-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylic acid

> <JCHEM_LOGP>
0.15204466633333263

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.49035271897782

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.217091623282402

> <JCHEM_PKA_STRONGEST_BASIC>
-2.969944072569172

> <JCHEM_POLAR_SURFACE_AREA>
192.44

> <JCHEM_REFRACTIVITY>
114.31400000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4aS,7S,7aS)-1-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1H,4aH,5H,6H,7aH-cyclopenta[c]pyran-4-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       0.792  -3.319   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.752  -3.956   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   1.777   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       3.590   2.547   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       6.258   2.547   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.258  -2.073   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.924  -4.383   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.258  -5.153   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       7.591  -4.383   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.925  -5.153   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.259  -4.383   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      11.592  -5.153   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       8.925  -6.693   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      10.259  -7.463   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       7.591  -7.463   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       7.591  -9.003   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       6.258  -6.693   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       4.924  -7.463   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.924  -9.003   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       6.258  -9.773   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       3.590  -9.773   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.590 -11.313   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.257 -12.083   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.923 -11.313   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -0.411 -12.083   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.923  -9.773   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.257  -9.003   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4   35                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   35                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   35                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   24                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   15   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   34                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   28                                                       
CONECT   35   13    6    2                                                  
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₂₈O₁₂

Average Mass

496.4650 Da

Monoisotopic Mass

496.15808 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@]1(O)CC[C@H]2[C@@H]1[C@H](O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1OC(=O)C1=CC=C(O)C=C1)OC=C2C(O)=O

InChI Identifier

InChI=1S/C23H28O12/c1-23(31)7-6-12-13(19(28)29)9-32-21(15(12)23)35-22-18(17(27)16(26)14(8-24)33-22)34-20(30)10-2-4-11(25)5-3-10/h2-5,9,12,14-18,21-22,24-27,31H,6-8H2,1H3,(H,28,29)/t12-,14-,15-,16-,17+,18-,21+,22+,23+/m1/s1

InChI Key

RFCSGMIUBXUYSE-KLZCBZFCSA-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
Vitex altissima	LOTUS Database	35616633
Vitex negundo	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
Hexose monosaccharide
P-hydroxybenzoic acid alkyl ester
P-hydroxybenzoic acid ester
O-glycosyl compound
Iridoid-skeleton
Glycosyl compound
Monoterpenoid
Aromatic monoterpenoid
Benzoate ester
Bicyclic monoterpenoid
Benzoic acid or derivatives
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
Phenol
Oxane
Benzenoid
Monocyclic benzene moiety
Monosaccharide
Dicarboxylic acid or derivatives
Vinylogous ester
Cyclic alcohol
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Acetal
Organoheterocyclic compound
Oxacycle
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Primary alcohol
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00043759

Chemspider ID

8111189

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9935561

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhou ZL, Yin WQ, Yang YM, He CH, Li XN, Zhou CP, Guo H: New Iridoid Glycosides with Antidepressant Activity Isolated from Cyperus rotundus. Chem Pharm Bull (Tokyo). 2016;64(1):73-7. doi: 10.1248/cpb.c15-00686. [PubMed:26726748 ]
Mehta K, Bhagwat DP, Devraj, Sehgal P, Mittal G, Suchal K: Vitex negundo protects against cerebral ischemia-reperfusion injury in mouse via attenuating behavioral deficits and oxidative damage. Psychopharmacology (Berl). 2022 Feb;239(2):573-587. doi: 10.1007/s00213-021-06050-z. Epub 2022 Jan 24. [PubMed:35072759 ]
Meena AK, Rekha P, Perumal A, Ilavarasan R, Singh R, Srikant N, Dhiman KS: Identification and estimation of bioactive constituents Negundoside, Berberine chloride, and Marmelosin by HPLC and HPTLC for development of quality control protocols for Ayurvedic medicated oil formulation. Futur J Pharm Sci. 2021;7(1):171. doi: 10.1186/s43094-021-00322-3. Epub 2021 Aug 26. [PubMed:34466412 ]
Sogame M, Naraki Y, Sasaki T, Seki M, Yokota K, Masada S, Hakamatsuka T: Quality Assessment of Medicinal Product and Dietary Supplements Containing Vitex agnus-castus by HPLC Fingerprint and Quantitative Analyses. Chem Pharm Bull (Tokyo). 2019;67(6):527-533. doi: 10.1248/cpb.c18-00725. [PubMed:31155557 ]
Singh PP, Bhunia D, Verma YK, Sidiq T, Khajuria A, Guptha A, Pallavi MP, Vamshi SS, Qazi GN, Kumar HM: Synthesis of novel lipidated iridoid glycosides as vaccine adjuvants: 6-O-palmitoyl Agnuside elicit strong Th1 and Th2 response to ovalbumin in mice. Int Immunopharmacol. 2013 Nov;17(3):593-600. doi: 10.1016/j.intimp.2013.07.018. Epub 2013 Aug 14. [PubMed:23954198 ]
LOTUS database [Link]

Showing NP-Card for (1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid (NP0324210)

MOL for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D MOL for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D SDF for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D-SDF for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

PDB for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D PDB for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

SMILES for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

INCHI for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

Structure for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)

3D Structure for NP0324210 ((1s,4as,7s,7as)-1-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-3-(4-hydroxybenzoyloxy)-6-(hydroxymethyl)oxan-2-yl]oxy}-7-hydroxy-7-methyl-1h,4ah,5h,6h,7ah-cyclopenta[c]pyran-4-carboxylic acid)