NP-MRD: Showing NP-Card for (2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione (NP0152185)

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Record Information

Version

2.0

Created at

2022-09-02 08:36:42 UTC

Updated at

2022-09-02 08:36:43 UTC

NP-MRD ID

NP0152185

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione

Description

Diomuscinone belongs to the class of organic compounds known as naphthoquinones. Naphthoquinones are compounds containing a naphthohydroquinone moiety, which consists of a benzene ring linearly fused to a bezene-1,4-dione (quinone). (2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione is found in Dionaea muscipula and Diospyros wallichii. (2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione was first documented in 2022 (PMID: 35263101). Based on a literature review very few articles have been published on Diomuscinone.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 28 29  0  0  0  0  0  0  0  0999 V2000
   -2.1297   -1.3806    0.6368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4935   -0.1382    0.0594 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6008    0.8995   -0.1428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5809    0.4423   -1.0094 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9297   -0.4621   -1.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4311   -1.0652   -1.0880 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7961   -2.1595   -1.5340 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3949   -0.3079   -0.3102 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7511   -0.3245   -0.5487 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2366   -1.0896   -1.5767 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6229    0.4342    0.2514 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1642    1.2104    1.2861 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8050    1.2268    1.5240 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9379    0.4804    0.7387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5027    0.4731    0.9651 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8974    1.0423    2.0271 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0440   -1.5852    0.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4605   -1.1711    1.6746 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4393   -2.2377    0.5877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9931    1.1511    0.8628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0729    1.8071   -0.5383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3508    1.0325   -0.9401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8206    0.4727   -1.8765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5828   -1.1380   -1.8468 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8315   -1.6612   -2.2357 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6809    0.4095    0.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8283    1.8029    1.9136 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4181    1.8361    2.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 15  2  1  0
 14  8  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
 10 25  1  0
 11 26  1  0
 12 27  1  0
 13 28  1  0
M  END


  Mrv1652309022210362D          

 16 17  0  0  1  0            999 V2000
   -0.0980   -1.0942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4323   -2.0127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3802   -2.1560    0.0000 O   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
    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  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    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
    2.1434   -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
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  1  0  0  0
  3  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
  8 14  1  0  0  0  0
 14 15  1  0  0  0  0
  2 15  1  0  0  0  0
 15 16  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0152185

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@]1(CO)CC(=O)C2=C(O)C=CC=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H12O4/c1-12(6-13)5-9(15)10-7(11(12)16)3-2-4-8(10)14/h2-4,13-14H,5-6H2,1H3/t12-/m1/s1

> <INCHI_KEY>
NZGUHHPFWBHXCA-GFCCVEGCSA-N

> <FORMULA>
C12H12O4

> <MOLECULAR_WEIGHT>
220.224

> <EXACT_MASS>
220.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
21.841053967395

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R)-5-hydroxy-2-(hydroxymethyl)-2-methyl-1,2,3,4-tetrahydronaphthalene-1,4-dione

> <ALOGPS_LOGP>
1.40

> <JCHEM_LOGP>
1.3014134166666667

> <ALOGPS_LOGS>
-1.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.386775601101764

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.230529852998874

> <JCHEM_PKA_STRONGEST_BASIC>
-2.827054019676516

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
57.94430000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.88e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3H-naphthalene-1,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.183  -2.043   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.807  -3.757   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.710  -4.025   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       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5   15                                             
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   14                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    8   15                                                  
CONECT   15   14    2   16                                                  
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₂O₄

Average Mass

220.2240 Da

Monoisotopic Mass

220.07356 Da

IUPAC Name

(2R)-5-hydroxy-2-(hydroxymethyl)-2-methyl-1,2,3,4-tetrahydronaphthalene-1,4-dione

Traditional Name

(2R)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3H-naphthalene-1,4-dione

CAS Registry Number

Not Available

SMILES

C[C@]1(CO)CC(=O)C2=C(O)C=CC=C2C1=O

InChI Identifier

InChI=1S/C12H12O4/c1-12(6-13)5-9(15)10-7(11(12)16)3-2-4-8(10)14/h2-4,13-14H,5-6H2,1H3/t12-/m1/s1

InChI Key

NZGUHHPFWBHXCA-GFCCVEGCSA-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
Dionaea muscipula	LOTUS Database	35616633
Diospyros wallichii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthoquinones. Naphthoquinones are compounds containing a naphthohydroquinone moiety, which consists of a benzene ring linearly fused to a bezene-1,4-dione (quinone).

Kingdom

Super Class

Class

Sub Class

Direct Parent

Alternative Parents

Substituents

Naphthoquinone
Tetralin
Aryl alkyl ketone
Aryl ketone
Quinone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Vinylogous acid
Ketone
Alcohol
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic 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	1.4	ALOGPS
logP	1.3	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	8.23	ChemAxon
pKa (Strongest Basic)	-2.8	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	1	ChemAxon
Refractivity	57.94 m³·mol⁻¹	ChemAxon
Polarizability	21.84 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

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

101337388

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Chen ZH, Sun RZ, Yao F, Hu XD, Xiang LX, Cong H, Liu WB: Enantioselective Nickel-Catalyzed Reductive Aryl/Alkenyl-Cyano Cyclization Coupling to All-Carbon Quaternary Stereocenters. J Am Chem Soc. 2022 Mar 23;144(11):4776-4782. doi: 10.1021/jacs.2c01237. Epub 2022 Mar 9. [PubMed:35263101 ]
LOTUS database [Link]

Showing NP-Card for (2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione (NP0152185)

MOL for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)

3D MOL for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)

3D SDF for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)

3D-SDF for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)

PDB for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)

3D PDB for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)

SMILES for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)

INCHI for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)

Structure for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)

3D Structure for NP0152185 ((2r)-5-hydroxy-2-(hydroxymethyl)-2-methyl-3h-naphthalene-1,4-dione)