NP-MRD: Showing NP-Card for (2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione (NP0258280)

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Record Information

Version

2.0

Created at

2022-09-07 23:39:43 UTC

Updated at

2022-09-07 23:39:43 UTC

NP-MRD ID

NP0258280

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione

Description

Deliquinone belongs to the class of organic compounds known as ketones. These are organic compounds in which a carbonyl group is bonded to two carbon atoms R2C=O (neither R may be a hydrogen atom). Ketones that have one or more alpha-hydrogen atoms undergo keto-enol tautomerization, the tautomer being an enol. (2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione is found in Russula delica and Russula japonica. (2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione was first documented in 2019 (PMID: 31322348). Based on a literature review very few articles have been published on Deliquinone (PMID: 30633535).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 37  0  0  0  0  0  0  0  0999 V2000
    3.0110   -0.5308    2.0096 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8200   -0.2827    1.1352 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9247    0.6998    0.2498 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1600    1.4934    0.1498 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7928    1.3954   -1.2267 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1096    0.0440   -1.4957 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7693    0.9365   -0.5948 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7952    1.8620   -1.4679 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4806    0.1376   -0.4974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587   -0.8260    0.3849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8890   -1.5228    0.3500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7428   -0.4824   -0.3629 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8255   -1.1948   -1.1057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2715    0.5435    0.6246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0573   -0.0518    1.6078 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7507    0.2169   -1.2603 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6082   -1.0836    1.2552 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5525   -2.0178    2.1206 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2481    0.3339    2.6337 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7412   -1.3713    2.7104 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8726   -0.9187    1.4230 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9113    1.2200    0.9152 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9063    2.5590    0.3258 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1680    1.8326   -2.0074 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7671    1.9250   -1.2287 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7220   -0.2675   -0.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2710   -1.7214    1.3570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7737   -2.4250   -0.2778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1490   -0.6739   -2.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4906   -2.2377   -1.3332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7183   -1.2780   -0.4594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9208    1.2641    0.0882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4150    1.0909    1.0375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8891    0.4587    1.7656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0544    1.2610   -1.4741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6219   -0.3879   -2.1759 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  1  0
  5  6  1  0
  3  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  6
 12 14  1  0
 14 15  1  0
 12 16  1  0
 10 17  1  0
 17 18  2  0
 17  2  1  0
 16  9  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
 11 27  1  0
 11 28  1  0
 13 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 14 33  1  0
 15 34  1  0
 16 35  1  0
 16 36  1  0
M  END


  Mrv1652309082201392D          

 18 19  0  0  1  0            999 V2000
    4.0668    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   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    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 O   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
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0407    2.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0407    0.9709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2122    0.1639    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    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  1  0  0  0  0
  5  6  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  6  0  0  0
 14 15  1  0  0  0  0
 12 16  1  0  0  0  0
  9 16  1  0  0  0  0
 10 17  1  0  0  0  0
  2 17  1  0  0  0  0
 17 18  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0258280

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(CCO)C(=O)C2=C(C[C@@](C)(CO)C2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H18O4/c1-8-9(3-4-15)13(18)11-6-14(2,7-16)5-10(11)12(8)17/h15-16H,3-7H2,1-2H3/t14-/m1/s1

> <INCHI_KEY>
ZJUSBIHJNNDXNV-CQSZACIVSA-N

> <FORMULA>
C14H18O4

> <MOLECULAR_WEIGHT>
250.294

> <EXACT_MASS>
250.12050906

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
27.104229854904037

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-2,3,4,7-tetrahydro-1H-indene-4,7-dione

> <JCHEM_LOGP>
0.9013436390000003

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.339132859734246

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.91205619922481

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3382632163798078

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
68.58409999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       7.591   4.383   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.591   1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.925   2.073   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      10.259   1.303   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.924  -0.237   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.076   3.873   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.076   1.812   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.396   0.306   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.924   5.923   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    3    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   16                                                  
CONECT   10    9   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14   16                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14                                                            
CONECT   16   12    9                                                       
CONECT   17   10    2   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₄H₁₈O₄

Average Mass

250.2940 Da

Monoisotopic Mass

250.12051 Da

IUPAC Name

(2R)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-2,3,4,7-tetrahydro-1H-indene-4,7-dione

Traditional Name

(2R)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione

CAS Registry Number

Not Available

SMILES

CC1=C(CCO)C(=O)C2=C(C[C@@](C)(CO)C2)C1=O

InChI Identifier

InChI=1S/C14H18O4/c1-8-9(3-4-15)13(18)11-6-14(2,7-16)5-10(11)12(8)17/h15-16H,3-7H2,1-2H3/t14-/m1/s1

InChI Key

ZJUSBIHJNNDXNV-CQSZACIVSA-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
Russula delica	LOTUS Database	35616633
Russula japonica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as ketones. These are organic compounds in which a carbonyl group is bonded to two carbon atoms R2C=O (neither R may be a hydrogen atom). Ketones that have one or more alpha-hydrogen atoms undergo keto-enol tautomerization, the tautomer being an enol.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Ketones

Alternative Parents

Substituents

Ketone
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	0.9	ChemAxon
pKa (Strongest Acidic)	15.91	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	68.58 m³·mol⁻¹	ChemAxon
Polarizability	27.1 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

78442018

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

100927704

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Melot R, Craveiro MV, Baudoin O: Total Synthesis of (Nor)illudalane Sesquiterpenes Based on a C(sp(3))-H Activation Strategy. J Org Chem. 2019 Oct 18;84(20):12933-12945. doi: 10.1021/acs.joc.9b01669. Epub 2019 Jul 29. [PubMed:31322348 ]
Melot R, Craveiro MV, Burgi T, Baudoin O: Divergent Enantioselective Synthesis of (Nor)illudalane Sesquiterpenes via Pd(0)-Catalyzed Asymmetric C(sp(3))-H Activation. Org Lett. 2019 Feb 1;21(3):812-815. doi: 10.1021/acs.orglett.8b04086. Epub 2019 Jan 11. [PubMed:30633535 ]
LOTUS database [Link]

Showing NP-Card for (2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione (NP0258280)

MOL for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)

3D MOL for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)

3D SDF for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)

3D-SDF for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)

PDB for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)

3D PDB for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)

SMILES for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)

INCHI for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)

Structure for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)

3D Structure for NP0258280 ((2r)-5-(2-hydroxyethyl)-2-(hydroxymethyl)-2,6-dimethyl-1,3-dihydroindene-4,7-dione)