NP-MRD: Showing NP-Card for (4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one (NP0205826)

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Record Information

Version

2.0

Created at

2022-09-05 01:49:58 UTC

Updated at

2022-09-05 01:49:58 UTC

NP-MRD ID

NP0205826

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one

Description

Viteoid II belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety. (4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one is found in Vitex cymosa and Vitex trifolia. (4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one was first documented in 2003 (PMID: 12895535). Based on a literature review a small amount of articles have been published on Viteoid II (PMID: 32816150) (PMID: 31429297).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052203492D          

 13 14  0  0  1  0            999 V2000
    3.2789    2.0625    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   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
    2.5645    0.8250    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
    1.5249    1.8646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7179    2.0361    0.0000 O   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   -0.2549    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  2  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0205826

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=C2[C@@H](CCOC2=O)[C@H](O)C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H12O4/c10-4-5-3-7(11)6-1-2-13-9(12)8(5)6/h6-7,10-11H,1-4H2/t6-,7+/m0/s1

> <INCHI_KEY>
QISJSHBLMHINFW-NKWVEPMBSA-N

> <FORMULA>
C9H12O4

> <MOLECULAR_WEIGHT>
184.191

> <EXACT_MASS>
184.073558866

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
18.282374118982062

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4aR,5R)-5-hydroxy-7-(hydroxymethyl)-1H,3H,4H,4aH,5H,6H-cyclopenta[c]pyran-1-one

> <JCHEM_LOGP>
-0.857485540333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.260126275375072

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.605620713766402

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7668624399153146

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
45.3561

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4aR,5R)-5-hydroxy-7-(hydroxymethyl)-3H,4H,4aH,5H,6H-cyclopenta[c]pyran-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  O   UNK     0       6.121   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       7.454   1.540   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.846   3.481   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.340   3.801   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.846  -1.941   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8   12                                                       
CONECT   12   11    6   13                                                  
CONECT   13   12                                                            
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

(4aR,5R)-5-hydroxy-7-(hydroxymethyl)-1H,3H,4H,4aH,5H,6H-cyclopenta[c]pyran-1-one

Traditional Name

(4aR,5R)-5-hydroxy-7-(hydroxymethyl)-3H,4H,4aH,5H,6H-cyclopenta[c]pyran-1-one

CAS Registry Number

Not Available

SMILES

OCC1=C2[C@@H](CCOC2=O)[C@H](O)C1

InChI Identifier

InChI=1S/C9H12O4/c10-4-5-3-7(11)6-1-2-13-9(12)8(5)6/h6-7,10-11H,1-4H2/t6-,7+/m0/s1

InChI Key

QISJSHBLMHINFW-NKWVEPMBSA-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
Vitex cymosa	LOTUS Database	35616633
Vitex trifolia	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactones

Sub Class

Delta valerolactones

Direct Parent

Delta valerolactones

Alternative Parents

Substituents

Delta valerolactone
Delta_valerolactone
Oxane
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Oxacycle
Alcohol
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Carbonyl group
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	-0.86	ChemAxon
pKa (Strongest Acidic)	14.61	ChemAxon
pKa (Strongest Basic)	-2.8	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	45.36 m³·mol⁻¹	ChemAxon
Polarizability	18.28 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

C00036654

Chemspider ID

8782900

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10607533

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gouda YG, Abdel-baky AM, Darwish FM, Mohamed KM, Kasai R, Yamasaki K: Iridoids from Kigelia pinnata DC. fruits. Phytochemistry. 2003 Aug;63(8):887-92. doi: 10.1016/s0031-9422(03)00262-0. [PubMed:12895535 ]
Yu H, Toume K, Kurokawa Y, Andoh T, Komatsu K: Iridoids isolated from Viticis Fructus inhibit paclitaxel-induced mechanical allodynia in mice. J Nat Med. 2021 Jan;75(1):48-55. doi: 10.1007/s11418-020-01441-6. Epub 2020 Aug 20. [PubMed:32816150 ]
Ma LL, Wang LL, Zhang YF, Jiang XF, Zhu XL, Pan K, Wan CX, Zhou ZB: A new chlorine-containing iridoid glycoside from Plantago maxima. Nat Prod Res. 2021 May;35(9):1491-1496. doi: 10.1080/14786419.2019.1655410. Epub 2019 Aug 20. [PubMed:31429297 ]
LOTUS database [Link]

Showing NP-Card for (4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one (NP0205826)

MOL for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)

3D MOL for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)

3D SDF for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)

3D-SDF for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)

PDB for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)

3D PDB for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)

SMILES for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)

INCHI for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)

Structure for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)

3D Structure for NP0205826 ((4ar,5r)-5-hydroxy-7-(hydroxymethyl)-3h,4h,4ah,5h,6h-cyclopenta[c]pyran-1-one)