NP-MRD: Showing NP-Card for (2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione (NP0296274)

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Record Information

Version

2.0

Created at

2022-09-10 05:45:16 UTC

Updated at

2022-09-10 05:45:16 UTC

NP-MRD ID

NP0296274

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione

Description

3-Epi-Radicinin belongs to the class of organic compounds known as aryl alkyl ketones. These are ketones have the generic structure RC(=O)R', where R = aryl group and R'=alkyl group. (2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione was first documented in 2012 (PMID: 22177540). Based on a literature review a small amount of articles have been published on 3-epi-Radicinin (PMID: 31438466) (PMID: 31370299) (PMID: 28422495).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 30  0  0  0  0  0  0  0  0999 V2000
   -5.5721   -0.7142   -0.2636 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1493   -0.5163   -0.7017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1524   -0.4201    0.1533 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7937   -0.2283   -0.3413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7380   -0.1257    0.5405 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5670    0.0568    0.1135 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7814    0.1336   -1.2337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2978    0.0265   -2.0753 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1098    0.0961   -3.3211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5211   -0.1467   -1.6164 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1533    0.3254   -1.6848 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3399    0.5501   -2.9082 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2999    0.2561   -0.7185 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6302   -1.0675   -0.4302 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8324    0.8857    0.5891 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8357    0.6599    1.6914 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6505    0.1638    0.9741 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2698   -0.3213   -1.0323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7937   -1.7532   -0.0131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7255   -0.0888    0.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9181   -0.4481   -1.7560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3803   -0.4878    1.2057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8942   -0.1846    1.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1637    0.8378   -1.1016 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1552   -1.3784    0.3858 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6064    1.9637    0.4361 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3684    0.2466    2.6116 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6839    0.0235    1.3751 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2479    1.6553    1.9934 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  7 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 15 17  1  0
 10  4  1  0
 17  6  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  3 22  1  0
  5 23  1  0
 13 24  1  6
 14 25  1  0
 15 26  1  6
 16 27  1  0
 16 28  1  0
 16 29  1  0
M  END


  Mrv1652309102207452D          

 17 18  0  0  1  0            999 V2000
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  4 10  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
  6 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0296274

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C\C1=CC2=C(C(=O)O1)C(=O)[C@H](O)[C@H](C)O2

> <INCHI_IDENTIFIER>
InChI=1S/C12H12O5/c1-3-4-7-5-8-9(12(15)17-7)11(14)10(13)6(2)16-8/h3-6,10,13H,1-2H3/b4-3+/t6-,10+/m0/s1

> <INCHI_KEY>
SDKXGAICTNHFCN-HOESVWFNSA-N

> <FORMULA>
C12H12O5

> <MOLECULAR_WEIGHT>
236.223

> <EXACT_MASS>
236.068473486

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
23.37893177740712

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R)-3-hydroxy-2-methyl-7-[(1E)-prop-1-en-1-yl]-2H,3H,4H,5H-pyrano[4,3-b]pyran-4,5-dione

> <JCHEM_LOGP>
0.9796128363333336

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.341364831540417

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9615006458533353

> <JCHEM_POLAR_SURFACE_AREA>
72.83

> <JCHEM_REFRACTIVITY>
62.16840000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R)-3-hydroxy-2-methyl-7-[(1E)-prop-1-en-1-yl]-2H,3H-pyrano[4,3-b]pyran-4,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   17                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    4                                                       
CONECT   11    7   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    6                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₂O₅

Average Mass

236.2230 Da

Monoisotopic Mass

236.06847 Da

IUPAC Name

(2S,3R)-3-hydroxy-2-methyl-7-[(1E)-prop-1-en-1-yl]-2H,3H,4H,5H-pyrano[4,3-b]pyran-4,5-dione

Traditional Name

(2S,3R)-3-hydroxy-2-methyl-7-[(1E)-prop-1-en-1-yl]-2H,3H-pyrano[4,3-b]pyran-4,5-dione

CAS Registry Number

Not Available

SMILES

C\C=C\C1=CC2=C(C(=O)O1)C(=O)[C@H](O)[C@H](C)O2

InChI Identifier

InChI=1S/C12H12O5/c1-3-4-7-5-8-9(12(15)17-7)11(14)10(13)6(2)16-8/h3-6,10,13H,1-2H3/b4-3+/t6-,10+/m0/s1

InChI Key

SDKXGAICTNHFCN-HOESVWFNSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aryl alkyl ketones. These are ketones have the generic structure RC(=O)R', where R = aryl group and R'=alkyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Aryl alkyl ketones

Alternative Parents

Substituents

Aryl alkyl ketone
Pyranone
Alkyl aryl ether
Pyran
Heteroaromatic compound
Vinylogous ester
Secondary alcohol
Lactone
Oxacycle
Organoheterocyclic compound
Ether
Organic oxide
Hydrocarbon derivative
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	0.98	ChemAxon
pKa (Strongest Acidic)	12.34	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	72.83 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	62.17 m³·mol⁻¹	ChemAxon
Polarizability	23.38 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

78436286

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

92140716

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Santoro E, Mazzeo G, Marsico G, Masi M, Longhi G, Superchi S, Evidente A, Abbate S: Assignment Through Chiroptical Methods of The Absolute Configuration of Fungal Dihydropyranpyran-4-5-Diones Phytotoxins, Potential Herbicides for Buffelgrass (Cenchrus ciliaris) Biocontrol. Molecules. 2019 Aug 21;24(17). pii: molecules24173022. doi: 10.3390/molecules24173022. [PubMed:31438466 ]
Masi M, Freda F, Clement S, Cimmino A, Cristofaro M, Meyer S, Evidente A: Phytotoxic Activity and Structure-Activity Relationships of Radicinin Derivatives against the Invasive Weed Buffelgrass (Cenchrus ciliaris). Molecules. 2019 Jul 31;24(15). pii: molecules24152793. doi: 10.3390/molecules24152793. [PubMed:31370299 ]
Masi M, Meyer S, Clement S, Cimmino A, Cristofaro M, Evidente A: Cochliotoxin, a Dihydropyranopyran-4,5-dione, and Its Analogues Produced by Cochliobolus australiensis Display Phytotoxic Activity against Buffelgrass (Cenchrus ciliaris). J Nat Prod. 2017 May 26;80(5):1241-1247. doi: 10.1021/acs.jnatprod.6b00696. Epub 2017 Apr 19. [PubMed:28422495 ]
Suzuki M, Sakuno E, Ishihara A, Tamura J, Nakajima H: Conversions of deoxyradicinin to radicinin and of radicinin to 3-epi-radicinin in the phytopathogenic fungus Bipolaris coicis. Phytochemistry. 2012 Mar;75:14-20. doi: 10.1016/j.phytochem.2011.11.010. Epub 2011 Dec 16. [PubMed:22177540 ]
LOTUS database [Link]

Showing NP-Card for (2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione (NP0296274)

MOL for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)

3D MOL for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)

3D SDF for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)

3D-SDF for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)

PDB for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)

3D PDB for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)

SMILES for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)

INCHI for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)

Structure for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)

3D Structure for NP0296274 ((2s,3r)-3-hydroxy-2-methyl-7-[(1e)-prop-1-en-1-yl]-2h,3h-pyrano[4,3-b]pyran-4,5-dione)