NP-MRD: Showing NP-Card for (1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid (NP0221825)

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Record Information

Version

1.0

Created at

2022-09-05 23:30:14 UTC

Updated at

2022-09-05 23:30:14 UTC

NP-MRD ID

NP0221825

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid

Description

CHEBI:69638 Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. (1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid is found in Lonicera japonica. It was first documented in 2022 (PMID: 36075691). Based on a literature review a significant number of articles have been published on CHEBI:69638 (PMID: 36075690) (PMID: 36075689) (PMID: 36075688) (PMID: 36075687).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062201302D          

 34 38  0  0  1  0            999 V2000
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M  END

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M  END


  Mrv1652309062201302D          

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M  END
> <DATABASE_ID>
NP0221825

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2OC=C([C@H]3C[C@@H]4C[C@@H](OC=C4C4=CC=CC=C4)[C@@H]23)C(O)=O)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H28O10/c25-8-17-19(26)20(27)21(28)24(33-17)34-23-18-13(15(10-32-23)22(29)30)6-12-7-16(18)31-9-14(12)11-4-2-1-3-5-11/h1-5,9-10,12-13,16-21,23-28H,6-8H2,(H,29,30)/t12-,13-,16-,17-,18+,19-,20+,21-,23+,24+/m1/s1

> <INCHI_KEY>
SCTDPJFVWAWKPB-JBKQMOEBSA-N

> <FORMULA>
C24H28O10

> <MOLECULAR_WEIGHT>
476.478

> <EXACT_MASS>
476.168247102

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
46.50179859207795

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2S,3S,7S,9R)-10-phenyl-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0^{2,7}]trideca-5,10-diene-6-carboxylic acid

> <JCHEM_LOGP>
0.10879247566666672

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.207029987242203

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.344336087727439

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981084760188039

> <JCHEM_POLAR_SURFACE_AREA>
155.14000000000001

> <JCHEM_REFRACTIVITY>
114.51219999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,3S,7S,9R)-10-phenyl-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0^{2,7}]trideca-5,10-diene-6-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  O   UNK     0       4.956   5.376   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.231   4.513   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       7.616   5.185   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       6.120   2.977   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.395   2.113   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       7.285   0.577   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       5.899  -0.096   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.789  -1.632   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.064  -2.495   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.449  -1.823   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       9.724  -2.686   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.110  -2.014   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      12.385  -2.878   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       9.614  -4.223   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      10.889  -5.086   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.229  -4.895   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       8.118  -6.431   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.954  -4.031   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       5.568  -4.704   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.624   0.768   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.735   2.304   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.727   3.468   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.191   3.579   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.303   1.828   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.460  -0.240   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.924  -0.129   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       0.916   1.035   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.026   2.571   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.350   3.261   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.636   2.413   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.013   3.103   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.104   4.640   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.818   5.488   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -0.441   4.798   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   21                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   20                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   18                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    9   19                                                  
CONECT   19   18                                                            
CONECT   20    7   21   25                                                  
CONECT   21   20    4   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   20   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   23   29                                                  
CONECT   29   28   30   34                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   29                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₈O₁₀

Average Mass

476.4780 Da

Monoisotopic Mass

476.16825 Da

IUPAC Name

(1R,2S,3S,7S,9R)-10-phenyl-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0^{2,7}]trideca-5,10-diene-6-carboxylic acid

Traditional Name

(1R,2S,3S,7S,9R)-10-phenyl-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0^{2,7}]trideca-5,10-diene-6-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@H]2OC=C([C@H]3C[C@@H]4C[C@@H](OC=C4C4=CC=CC=C4)[C@@H]23)C(O)=O)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C24H28O10/c25-8-17-19(26)20(27)21(28)24(33-17)34-23-18-13(15(10-32-23)22(29)30)6-12-7-16(18)31-9-14(12)11-4-2-1-3-5-11/h1-5,9-10,12-13,16-21,23-28H,6-8H2,(H,29,30)/t12-,13-,16-,17-,18+,19-,20+,21-,23+,24+/m1/s1

InChI Key

SCTDPJFVWAWKPB-JBKQMOEBSA-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
Lonicera japonica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Hexose monosaccharide
O-glycosyl compound
Monocyclic benzene moiety
Monosaccharide
Oxane
Benzenoid
Vinylogous ester
Secondary alcohol
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Acetal
Organoheterocyclic compound
Oxacycle
Primary alcohol
Hydrocarbon derivative
Alcohol
Organic oxide
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

glycoside (CHEBI:69638 )

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	0.11	ChemAxon
pKa (Strongest Acidic)	4.34	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	155.14 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	114.51 m³·mol⁻¹	ChemAxon
Polarizability	46.5 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

Not Available

Chemspider ID

28490662

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

57395335

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Abioye AI, Sudfeld CR, Hughes MD, Aboud S, Muhihi A, Ulenga N, Nagu TJ, Wang M, Mugusi F, Fawzi WW: Iron status among HIV-infected adults during the first year of antiretroviral therapy in Tanzania. HIV Med. 2022 Sep 8. doi: 10.1111/hiv.13396. [PubMed:36075691 ]
Authors unspecified: Resources Round-up. Altern Lab Anim. 2022 Sep 8:2611929221121256. doi: 10.1177/02611929221121256. [PubMed:36075690 ]
Kim JU, Khan W, Arowoshola L, Ahmad M: Correspondence. Eur Heart J Qual Care Clin Outcomes. 2022 Aug 26. pii: 6677390. doi: 10.1093/ehjqcco/qcac051. [PubMed:36075689 ]
DaVault L: Field Amputations Facilitated by a Surgical Extraction Team. Am Surg. 2022 Sep 8:31348221114521. doi: 10.1177/00031348221114521. [PubMed:36075688 ]
Szanyi J, Walles JK, Tesfaye F, Gudeta AN, Bjorkman P: Intrauterine HIV exposure is associated with linear growth restriction among Ethiopian children in the first 18 months of life. Trop Med Int Health. 2022 Sep;27(9):823-830. doi: 10.1111/tmi.13805. Epub 2022 Aug 17. [PubMed:36075687 ]
LOTUS database [Link]

Showing NP-Card for (1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid (NP0221825)

MOL for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)

3D MOL for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)

3D SDF for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)

3D-SDF for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)

PDB for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)

3D PDB for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)

SMILES for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)

INCHI for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)

Structure for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)

3D Structure for NP0221825 ((1r,2s,3s,7s,9r)-10-phenyl-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,12-dioxatricyclo[7.3.1.0²,⁷]trideca-5,10-diene-6-carboxylic acid)