NP-MRD: Showing NP-Card for 7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one (NP0164652)

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Record Information

Version

2.0

Created at

2022-09-02 23:34:50 UTC

Updated at

2022-09-02 23:34:50 UTC

NP-MRD ID

NP0164652

Secondary Accession Numbers

None

Natural Product Identification

Common Name

7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one

Description

7-(Hydroxymethyl)-5-methoxy-1H,3H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring. 7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one is found in Scrophularia buergeriana. 7-(Hydroxymethyl)-5-methoxy-1H,3H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 28 29  0  0  0  0  0  0  0  0999 V2000
   -2.3846    2.5583   -0.0023 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4340    1.8914    0.7703 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7259    1.0692   -0.0754 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7543    1.3769   -0.0305 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4560    0.2709   -0.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9367    0.1773   -0.2768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4534    1.4478   -0.0407 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4975   -0.8515   -0.4533 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9421   -2.1543    0.1129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1820   -3.0151    0.1353 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4350   -2.5614   -0.2473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2131   -3.3318   -0.8586 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8784   -1.1736    0.0532 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6765   -0.3702    0.3869 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0891    1.8596   -0.5070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9249    3.2946    0.6335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8293    3.1528   -0.7641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0587    1.1271   -1.1127 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1295    2.3799    0.1559 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3312   -0.4710    0.5529 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2682   -0.2278   -1.2675 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3110    1.5203   -0.5277 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1964   -0.9475   -1.5155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7477   -2.6504   -0.4551 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2201   -1.9873    1.1823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5239   -0.7460   -0.7230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5046   -1.2460    0.9905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3840   -0.3921    1.4532 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14  3  1  0
 14  8  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  6
  4 19  1  0
  6 20  1  0
  6 21  1  0
  7 22  1  0
  8 23  1  6
  9 24  1  0
  9 25  1  0
 13 26  1  0
 13 27  1  0
 14 28  1  1
M  END


  Mrv1533004181503192D          

 14 15  0  0  0  0            999 V2000
    1.4358   -2.7631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 O   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  0  0  0  0  0  0  0  0  0  0
    0.8838    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768    0.9256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  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 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  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  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
  3 14  1  0  0  0  0
  8 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0164652

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1C=C(CO)C2COC(=O)CC12

> <INCHI_IDENTIFIER>
InChI=1S/C10H14O4/c1-13-9-2-6(4-11)8-5-14-10(12)3-7(8)9/h2,7-9,11H,3-5H2,1H3

> <INCHI_KEY>
JSLPGGGPWKHMKK-UHFFFAOYSA-N

> <FORMULA>
C10H14O4

> <MOLECULAR_WEIGHT>
198.218

> <EXACT_MASS>
198.089208931

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
19.974737362900807

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7-(hydroxymethyl)-5-methoxy-1H,3H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one

> <ALOGPS_LOGP>
-0.05

> <JCHEM_LOGP>
-0.682107719333333

> <ALOGPS_LOGS>
-1.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.135532195073129

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7395182178750135

> <JCHEM_POLAR_SURFACE_AREA>
55.76

> <JCHEM_REFRACTIVITY>
50.091100000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.67e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-(hydroxymethyl)-5-methoxy-1H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 18-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-APR-15         0                                  
HETATM    1  C   UNK     0       2.680  -5.158   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.650  -4.013   0.000  0.00  0.00           O+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  C   UNK     0       1.650   1.408   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.143   1.728   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.258  -0.533   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       7.591  -2.843   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  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   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    3    8                                                  
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₄O₄

Average Mass

198.2180 Da

Monoisotopic Mass

198.08921 Da

IUPAC Name

7-(hydroxymethyl)-5-methoxy-1H,3H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one

Traditional Name

7-(hydroxymethyl)-5-methoxy-1H,4H,4aH,5H,7aH-cyclopenta[c]pyran-3-one

CAS Registry Number

Not Available

SMILES

COC1C=C(CO)C2COC(=O)CC12

InChI Identifier

InChI=1S/C10H14O4/c1-13-9-2-6(4-11)8-5-14-10(12)3-7(8)9/h2,7-9,11H,3-5H2,1H3

InChI Key

JSLPGGGPWKHMKK-UHFFFAOYSA-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 terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Iridoid-skeleton
Bicyclic monoterpenoid
Monoterpenoid
Delta valerolactone
Delta_valerolactone
Oxane
Carboxylic acid ester
Lactone
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Oxacycle
Ether
Dialkyl ether
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
Organooxygen compound
Primary 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
logP	-0.05	ALOGPS
logP	-0.68	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	15.14	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	55.76 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	50.09 m³·mol⁻¹	ChemAxon
Polarizability	19.97 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

130145400

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one (NP0164652)

MOL for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D MOL for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D SDF for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D-SDF for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

PDB for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D PDB for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

SMILES for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

INCHI for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

Structure for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D Structure for NP0164652 (7-(hydroxymethyl)-5-methoxy-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)