NP-MRD: Showing NP-Card for (1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol (NP0240433)

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Record Information

Version

2.0

Created at

2022-09-07 00:15:11 UTC

Updated at

2022-09-07 00:15:12 UTC

NP-MRD ID

NP0240433

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol

Description

Aucubigenin 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. (1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol is found in Aucuba japonica. (1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol was first documented in 2007 (PMID: 18338591). Based on a literature review a small amount of articles have been published on Aucubigenin (PMID: 28199906) (PMID: 19762008).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072202152D          

 13 14  0  0  1  0            999 V2000
    0.0768   -2.3215    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8838    0.7541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6378   -2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    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
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13  3  1  6  0  0  0
  7 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0240433

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=C[C@@H](O)[C@@H]2C=CO[C@@H](O)[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C9H12O4/c10-4-5-3-7(11)6-1-2-13-9(12)8(5)6/h1-3,6-12H,4H2/t6-,7+,8+,9+/m0/s1

> <INCHI_KEY>
BACWCXKATFIVFS-JQCXWYLXSA-N

> <FORMULA>
C9H12O4

> <MOLECULAR_WEIGHT>
184.191

> <EXACT_MASS>
184.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
17.92244265733859

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,4aR,5S,7aS)-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-1,5-diol

> <JCHEM_LOGP>
-1.411034256666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.393727925108418

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.032608655418606

> <JCHEM_PKA_STRONGEST_BASIC>
-2.741441652457315

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
46.76349999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4aR,5S,7aS)-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-1,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       0.143  -4.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+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  O   UNK     0       1.650   1.408   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.258  -2.073   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.924  -4.383   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   13                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   13                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    3    7                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₂O₄

Average Mass

184.1910 Da

Monoisotopic Mass

184.07356 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

OCC1=C[C@@H](O)[C@@H]2C=CO[C@@H](O)[C@H]12

InChI Identifier

InChI=1S/C9H12O4/c10-4-5-3-7(11)6-1-2-13-9(12)8(5)6/h1-3,6-12H,4H2/t6-,7+,8+,9+/m0/s1

InChI Key

BACWCXKATFIVFS-JQCXWYLXSA-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
Aucuba 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
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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

Not Available

Chemspider ID

143116

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

163040

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Lv PY, Feng H, Huang WH, Tian YY, Wang YQ, Qin YH, Li XH, Hu K, Zhou HH, Ouyang DS: Aucubin and its hydrolytic derivative attenuate activation of hepatic stellate cells via modulation of TGF-beta stimulation. Environ Toxicol Pharmacol. 2017 Mar;50:234-239. doi: 10.1016/j.etap.2017.02.012. Epub 2017 Feb 8. [PubMed:28199906 ]
Li Y, Zhao Y, Zhang YM, Wang MJ, Sun WJ: X-ray crystal structure of iridoid glucoside aucubin and its aglycone. Carbohydr Res. 2009 Nov 2;344(16):2270-3. doi: 10.1016/j.carres.2009.08.021. Epub 2009 Aug 24. [PubMed:19762008 ]
Kang Z, Wu WH, Wang JJ, Ouyang DS: [Research advances in pharmacology of aucubin and aucubigenin]. Zhongguo Zhong Yao Za Zhi. 2007 Dec;32(24):2585-7. [PubMed:18338591 ]
LOTUS database [Link]

Showing NP-Card for (1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol (NP0240433)

MOL for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)

3D MOL for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)

3D SDF for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)

3D-SDF for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)

PDB for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)

3D PDB for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)

SMILES for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)

INCHI for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)

Structure for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)

3D Structure for NP0240433 ((1r,4ar,5s,7as)-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-1,5-diol)