NP-MRD: Showing NP-Card for 7-deoxyloganetin (NP0225898)

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Record Information

Version

2.0

Created at

2022-09-06 04:45:52 UTC

Updated at

2022-09-06 04:45:52 UTC

NP-MRD ID

NP0225898

Secondary Accession Numbers

None

Natural Product Identification

Common Name

7-deoxyloganetin

Description

7-Deoxyloganetin belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. 7-deoxyloganetin is found in Lonicera japonica. 7-deoxyloganetin was first documented in 2011 (PMID: 21799001). Based on a literature review a small amount of articles have been published on 7-deoxyloganetin (PMID: 34975985) (PMID: 29454308) (PMID: 24066073).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 32  0  0  0  0  0  0  0  0999 V2000
    4.7090   -0.4842   -1.4492 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6703   -0.0523   -0.5794 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3454   -0.4255   -0.7860 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1227   -1.1608   -1.7785 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2717    0.0190    0.1102 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5063    0.7927    1.1546 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4389    1.1876    1.9787 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8466    1.4059    1.4307 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0676    2.7729    1.3581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0174    0.8101    0.0752 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3919    0.1302    0.0533 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8469    0.0141   -1.3703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1611   -1.2001    0.6985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6584   -1.3686    0.8561 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1173   -0.3915   -0.1337 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6315   -0.6914   -0.8332 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9754    0.3369   -2.1195 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4652   -1.4305   -1.9555 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5237    1.0994    1.3419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5692    0.9780    2.1856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8298    3.0272    0.7970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9149    1.5326   -0.7486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0847    0.7831    0.6156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3724    0.7906   -1.9921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9521    0.1803   -1.3766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6016   -0.9663   -1.7988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6893   -1.2504    1.6564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5305   -2.0215    0.0222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3427   -1.1873    1.8881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3799   -2.4280    0.6197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2861   -0.8022   -1.1471 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15  5  1  0
 15 10  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  6 19  1  0
  8 20  1  1
  9 21  1  0
 10 22  1  6
 11 23  1  1
 12 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 13 28  1  0
 14 29  1  0
 14 30  1  0
 15 31  1  6
M  END


  Mrv1652309062206452D          

 15 16  0  0  1  0            999 V2000
    2.5645    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  6  0  0  0
  5 15  1  0  0  0  0
 10 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0225898

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CO[C@@H](O)[C@@H]2[C@@H](C)CC[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C11H16O4/c1-6-3-4-7-8(10(12)14-2)5-15-11(13)9(6)7/h5-7,9,11,13H,3-4H2,1-2H3/t6-,7+,9+,11+/m0/s1

> <INCHI_KEY>
GGFAHFSRIITJIJ-NONSRLQASA-N

> <FORMULA>
C11H16O4

> <MOLECULAR_WEIGHT>
212.245

> <EXACT_MASS>
212.104858995

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
22.056133306454875

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (1R,4aS,7S,7aR)-1-hydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

> <JCHEM_LOGP>
1.2424549783333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.094619456891767

> <JCHEM_PKA_STRONGEST_BASIC>
-4.069613449555541

> <JCHEM_POLAR_SURFACE_AREA>
55.760000000000005

> <JCHEM_REFRACTIVITY>
53.468599999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1R,4aS,7S,7aR)-1-hydroxy-7-methyl-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

> <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  C   UNK     0       4.787   6.160   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.787   4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.121   3.850   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       7.454   4.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.454   0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   15                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   15                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    5   10                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol

Synonyms

Value	Source
Methyl 7-deoxyloganetate	ChEBI
Methyl 7-deoxyloganetic acid	Generator

Chemical Formula

C₁₁H₁₆O₄

Average Mass

212.2450 Da

Monoisotopic Mass

212.10486 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CO[C@@H](O)[C@@H]2[C@@H](C)CC[C@H]12

InChI Identifier

InChI=1S/C11H16O4/c1-6-3-4-7-8(10(12)14-2)5-15-11(13)9(6)7/h5-7,9,11,13H,3-4H2,1-2H3/t6-,7+,9+,11+/m0/s1

InChI Key

GGFAHFSRIITJIJ-NONSRLQASA-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 iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

Iridoid-skeleton
Bicyclic monoterpenoid
Methyl ester
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Vinylogous ester
Carboxylic acid ester
Hemiacetal
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

methyl ester (CHEBI:76849 )
lactol (CHEBI:76849 )
iridoid monoterpenoid (CHEBI:76849 )
cyclopentapyran (CHEBI:76849 )

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

Not Available

Chemspider ID

8438077

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10262598

PDB ID

Not Available

ChEBI ID

76849

Good Scents ID

Not Available

References

General References

Nagatoshi M, Terasaka K, Nagatsu A, Mizukami H: Iridoid-specific glucosyltransferase from Gardenia jasminoides. J Biol Chem. 2011 Sep 16;286(37):32866-74. doi: 10.1074/jbc.M111.242586. Epub 2011 Jul 28. [PubMed:21799001 ]
Qu Z, Jia Y, Duan Y, Chen H, Wang X, Zheng H, Liu H, Wang J, Zou D, Zhao H: Integrated Isoform Sequencing and Dynamic Transcriptome Analysis Reveals Diverse Transcripts Responsible for Low Temperature Stress at Anther Meiosis Stage in Rice. Front Plant Sci. 2021 Dec 17;12:795834. doi: 10.3389/fpls.2021.795834. eCollection 2021. [PubMed:34975985 ]
Jiao H, Liu X, Sun S, Wang P, Qiao X, Li J, Tang C, Wu J, Zhang S, Tao S: The unique evolutionary pattern of the Hydroxyproline-rich glycoproteins superfamily in Chinese white pear (Pyrus bretschneideri). BMC Plant Biol. 2018 Feb 17;18(1):36. doi: 10.1186/s12870-018-1252-2. [PubMed:29454308 ]
Bhat WW, Dhar N, Razdan S, Rana S, Mehra R, Nargotra A, Dhar RS, Ashraf N, Vishwakarma R, Lattoo SK: Molecular characterization of UGT94F2 and UGT86C4, two glycosyltransferases from Picrorhiza kurrooa: comparative structural insight and evaluation of substrate recognition. PLoS One. 2013 Sep 16;8(9):e73804. doi: 10.1371/journal.pone.0073804. eCollection 2013. [PubMed:24066073 ]
LOTUS database [Link]

Showing NP-Card for 7-deoxyloganetin (NP0225898)

MOL for NP0225898 (7-deoxyloganetin)

3D MOL for NP0225898 (7-deoxyloganetin)

3D SDF for NP0225898 (7-deoxyloganetin)

3D-SDF for NP0225898 (7-deoxyloganetin)

PDB for NP0225898 (7-deoxyloganetin)

3D PDB for NP0225898 (7-deoxyloganetin)

SMILES for NP0225898 (7-deoxyloganetin)

INCHI for NP0225898 (7-deoxyloganetin)

Structure for NP0225898 (7-deoxyloganetin)

3D Structure for NP0225898 (7-deoxyloganetin)