NP-MRD: Showing NP-Card for 5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one (NP0297361)

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Record Information

Version

2.0

Created at

2022-09-10 07:37:14 UTC

Updated at

2022-09-10 07:37:14 UTC

NP-MRD ID

NP0297361

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

5-Hydroxy-7-(hydroxymethyl)-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. 5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one is found in Pedicularis chinensis and Scrophularia buergeriana. 5-Hydroxy-7-(hydroxymethyl)-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


  Mrv1533004161503192D          

 13 14  0  0  0  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  0  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  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 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.1271    0.0000 O   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  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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  3 13  1  0  0  0  0
  7 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0297361

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=CC(O)C2CC(=O)OCC12

> <INCHI_IDENTIFIER>
InChI=1S/C9H12O4/c10-3-5-1-8(11)6-2-9(12)13-4-7(5)6/h1,6-8,10-11H,2-4H2

> <INCHI_KEY>
IGAJHBXTLAVHLX-UHFFFAOYSA-N

> <FORMULA>
C9H12O4

> <MOLECULAR_WEIGHT>
184.191

> <EXACT_MASS>
184.073558866

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
18.04167117197056

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.64

> <JCHEM_LOGP>
-1.3252342229999996

> <ALOGPS_LOGS>
-0.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.244328150912594

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.42135792833113

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7394731561324646

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
45.3399

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.73e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         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       7.591   0.237   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.258  -2.073   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+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   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    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

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OCC1=CC(O)C2CC(=O)OCC12

InChI Identifier

InChI=1S/C9H12O4/c10-3-5-1-8(11)6-2-9(12)13-4-7(5)6/h1,6-8,10-11H,2-4H2

InChI Key

IGAJHBXTLAVHLX-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
Pedicularis chinensis	LOTUS Database	35616633
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
Secondary alcohol
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Carbonyl group
Organooxygen compound
Alcohol
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	-0.64	ALOGPS
logP	-1.3	ChemAxon
logS	-0.59	ALOGPS
pKa (Strongest Acidic)	14.42	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	45.34 m³·mol⁻¹	ChemAxon
Polarizability	18.04 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

85294993

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one (NP0297361)

MOL for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D MOL for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D SDF for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D-SDF for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

PDB for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D PDB for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

SMILES for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

INCHI for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

Structure for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)

3D Structure for NP0297361 (5-hydroxy-7-(hydroxymethyl)-1h,4h,4ah,5h,7ah-cyclopenta[c]pyran-3-one)