NP-MRD: Showing NP-Card for Radicinin (NP0061486)

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Record Information

Version

2.0

Created at

2022-04-28 06:15:58 UTC

Updated at

2022-04-28 06:15:58 UTC

NP-MRD ID

NP0061486

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Radicinin

Description

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. Radicinin is found in Alternaria chrysanthemi, Alternariaster helianthi and Curvularia sp. AB 2090A-11 (NRRL 22559). Radicinin was first documented in 2019 (PMID: 31484319). Based on a literature review a small amount of articles have been published on Radicinin (PMID: 34155352) (PMID: 32510948) (PMID: 31438466) (PMID: 31370299).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 30  0  0  0  0  0  0  0  0999 V2000
    5.1931    0.0063   -1.6900 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7613   -0.0477   -1.2750 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3779    0.1769   -0.0357 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9845    0.1270    0.3808 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9316   -0.1491   -0.4297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3682   -0.1722    0.0693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5695    0.0893    1.3974 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5262    0.3616    2.1700 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3775    0.6063    3.3945 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7211    0.3709    1.6550 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9004    0.0763    1.9585 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0787    0.1855    3.1825 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0627   -0.0683    1.0694 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9606    0.9689    1.3813 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7433    0.0414   -0.3846 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.8147   -0.7259   -1.1565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4573   -0.4474   -0.7196 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3103    0.5756   -2.6402 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8042    0.4923   -0.9004 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6049   -1.0136   -1.8276 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0281   -0.2785   -2.0217 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801    0.4050    0.6657 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0950   -0.3521   -1.4638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6157   -1.0215    1.2673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2352    1.4772    0.5799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7695    1.1007   -0.7234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4411   -1.1280   -2.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2299   -1.5158   -0.4792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6488    0.0081   -1.3208 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


  Mrv1652304282208152D          

 17 18  0  0  1  0            999 V2000
    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 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   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
   -1.4289   -0.0000    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 O   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
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  6  8  1  1  0  0  0
  5  9  1  6  0  0  0
  2 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  1 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0061486

> <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-DCJAWTJCSA-N

> <FORMULA>
C12H12O5

> <MOLECULAR_WEIGHT>
236.223

> <EXACT_MASS>
236.068473486

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
23.36226528266322

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
1.08

> <JCHEM_LOGP>
0.9796128363333336

> <ALOGPS_LOGS>
-1.56

> <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

> <ALOGPS_SOLUBILITY>
6.45e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S)-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                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.334  -0.770   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  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
CONECT    1    2    7   14                                                  
CONECT    2    1    3   10                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    9                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    1                                                       
CONECT    8    6                                                            
CONECT    9    5                                                            
CONECT   10    2   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13    1                                                       
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Value	Source
3,4-Dihydro-3-hydroxy-2-methyl-7-propenyl-2H,5H- pyrano(4,3-b)pyran-4,5-dione	MeSH
Radicinin, (2alpha,3beta,7(+)-(+-))-isomer	MeSH

Chemical Formula

C₁₂H₁₂O₅

Average Mass

236.2230 Da

Monoisotopic Mass

236.06847 Da

IUPAC Name

(2S,3S)-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,3S)-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-DCJAWTJCSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Alternaria chrysanthemi	Fungi	KNApSAcK
Alternariaster helianthi	LOTUS Database	35616633
Curvularia sp. AB 2090A-11 (NRRL 22559)	Fungi	KNApSAcK

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	1.08	ALOGPS
logP	0.98	ChemAxon
logS	-1.6	ALOGPS
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	23.36 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

C00016655

Chemspider ID

4529404

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Radicinin

METLIN ID

Not Available

PubChem Compound

5381458

PDB ID

Not Available

ChEBI ID

183741

Good Scents ID

Not Available

References

General References

Al Subeh ZY, Raja HA, Obike JC, Pearce CJ, Croatt MP, Oberlies NH: Media and strain studies for the scaled production of cis-enone resorcylic acid lactones as feedstocks for semisynthesis. J Antibiot (Tokyo). 2021 Aug;74(8):496-507. doi: 10.1038/s41429-021-00432-3. Epub 2021 Jun 21. [PubMed:34155352 ]
Brandenburg CA, Castro CA, Blacutt AA, Costa EA, Brinton KC, Corral DW, Drozd CL, Roper MC, Rolshausen PE, Maloney KN, Lockner JW: Synthesis of Deoxyradicinin, an Inhibitor of Xylella fastidiosa and Liberibacter crescens, a Culturable Surrogate for Candidatus Liberibacter asiaticus. J Nat Prod. 2020 Jun 26;83(6):1810-1816. doi: 10.1021/acs.jnatprod.9b01207. Epub 2020 Jun 8. [PubMed:32510948 ]
Marsico G, Ciccone MS, Masi M, Freda F, Cristofaro M, Evidente A, Superchi S, Scafato P: Synthesis and Herbicidal Activity Against Buffelgrass (Cenchrus ciliaris) of (+/-)-3-deoxyradicinin. Molecules. 2019 Sep 3;24(17). pii: molecules24173193. doi: 10.3390/molecules24173193. [PubMed:31484319 ]
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 ]

Showing NP-Card for Radicinin (NP0061486)

MOL for NP0061486 (Radicinin)

3D MOL for NP0061486 (Radicinin)

3D SDF for NP0061486 (Radicinin)

3D-SDF for NP0061486 (Radicinin)

PDB for NP0061486 (Radicinin)

3D PDB for NP0061486 (Radicinin)

SMILES for NP0061486 (Radicinin)

INCHI for NP0061486 (Radicinin)

Structure for NP0061486 (Radicinin)

3D Structure for NP0061486 (Radicinin)