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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 19:33:40 UTC

Update Date

2023-02-21 17:24:20 UTC

HMDB ID

HMDB0034663

Secondary Accession Numbers

HMDB34663

Metabolite Identification

Common Name

5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone

Description

5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 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). 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone has been detected, but not quantified in, nuts. This could make 5-hydroxy-2,3-dimethyl-1,4-naphthoquinone a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 05061307592D          

 15 16  0  0  0  0            999 V2000
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
    3.5724    2.0625    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    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    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
    1.4289    3.3000    0.0000 O   0  0  0  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
    2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  7  2  1  0  0  0  0
  7  6  2  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
 11  6  1  0  0  0  0
 11  8  1  0  0  0  0
 12  7  1  0  0  0  0
 12 10  1  0  0  0  0
 13  9  1  0  0  0  0
 14 11  2  0  0  0  0
 15 12  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034663

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=C(C)C(=O)C2=C(C=CC=C2O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H10O3/c1-6-7(2)12(15)10-8(11(6)14)4-3-5-9(10)13/h3-5,13H,1-2H3

> <INCHI_KEY>
WBPHCLSNRLPSPK-UHFFFAOYSA-N

> <FORMULA>
C12H10O3

> <MOLECULAR_WEIGHT>
202.206

> <EXACT_MASS>
202.062994186

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
20.543093456801273

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-hydroxy-2,3-dimethyl-1,4-dihydronaphthalene-1,4-dione

> <ALOGPS_LOGP>
2.31

> <JCHEM_LOGP>
2.6318536076666668

> <ALOGPS_LOGS>
-2.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.462599821673702

> <JCHEM_PKA_STRONGEST_BASIC>
-4.4412058622482045

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
56.87830000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.42e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy-2,3-dimethylnaphthalene-1,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
CONECT    1    6                                                            
CONECT    2    7                                                            
CONECT    3    4    5                                                       
CONECT    4    3    8                                                       
CONECT    5    3    9                                                       
CONECT    6    1    7   11                                                  
CONECT    7    2    6   12                                                  
CONECT    8    4   10   11                                                  
CONECT    9    5   10   13                                                  
CONECT   10    8    9   12                                                  
CONECT   11    6    8   14                                                  
CONECT   12    7   10   15                                                  
CONECT   13    9                                                            
CONECT   14   11                                                            
CONECT   15   12                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Methylplumbagin	HMDB

Chemical Formula

C₁₂H₁₀O₃

Average Molecular Weight

202.206

Monoisotopic Molecular Weight

202.062994186

IUPAC Name

5-hydroxy-2,3-dimethyl-1,4-dihydronaphthalene-1,4-dione

Traditional Name

5-hydroxy-2,3-dimethylnaphthalene-1,4-dione

CAS Registry Number

80596-51-6

SMILES

CC1=C(C)C(=O)C2=C(C=CC=C2O)C1=O

InChI Identifier

InChI=1S/C12H10O3/c1-6-7(2)12(15)10-8(11(6)14)4-3-5-9(10)13/h3-5,13H,1-2H3

InChI Key

WBPHCLSNRLPSPK-UHFFFAOYSA-N

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
Aryl ketone
Quinone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Vinylogous acid
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0034663)
Cytoplasm (HMDB: HMDB0034663)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0034663)

Source

Exogenous

Food

Food (HMDB: HMDB0034663)

Nut

Nuts (FooDB: FOOD00869)

Endogenous

Plant

Plant (HMDB: HMDB0034663)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0034663)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	120 - 121 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	401 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.84 g/L	ALOGPS
logP	2.31	ALOGPS
logP	2.63	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	9.46	ChemAxon
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	56.88 m³·mol⁻¹	ChemAxon
Polarizability	20.54 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	146.251	31661259
DarkChem	[M-H]-	145.995	31661259
DeepCCS	[M+H]+	146.363	30932474
DeepCCS	[M-H]-	144.005	30932474
DeepCCS	[M-2H]-	178.158	30932474
DeepCCS	[M+Na]+	152.962	30932474
AllCCS	[M+H]+	142.0	32859911
AllCCS	[M+H-H2O]+	137.8	32859911
AllCCS	[M+NH4]+	146.0	32859911
AllCCS	[M+Na]+	147.1	32859911
AllCCS	[M-H]-	143.6	32859911
AllCCS	[M+Na-2H]-	143.6	32859911
AllCCS	[M+HCOO]-	143.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone	CC1=C(C)C(=O)C2=C(C=CC=C2O)C1=O	2598.0	Standard polar	33892256
5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone	CC1=C(C)C(=O)C2=C(C=CC=C2O)C1=O	1738.1	Standard non polar	33892256
5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone	CC1=C(C)C(=O)C2=C(C=CC=C2O)C1=O	1686.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone,1TMS,isomer #1	CC1=C(C)C(=O)C2=C(O[Si](C)(C)C)C=CC=C2C1=O	1927.3	Semi standard non polar	33892256
5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone,1TBDMS,isomer #1	CC1=C(C)C(=O)C2=C(O[Si](C)(C)C(C)(C)C)C=CC=C2C1=O	2168.0	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone GC-MS (Non-derivatized) - 70eV, Positive	splash10-00di-0900000000-3cc8e487af56523385c1	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone GC-MS (1 TMS) - 70eV, Positive	splash10-0kmj-3390000000-3aea8eaf0ee9c2431fa3	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 10V, Positive-QTOF	splash10-0udi-0490000000-a39cc44509fd80c84aaf	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 20V, Positive-QTOF	splash10-0fek-3910000000-323621d3fb86d2886e8f	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 40V, Positive-QTOF	splash10-0udi-9500000000-22c19019f7c3ada9007a	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 10V, Negative-QTOF	splash10-0udi-0190000000-1eade8ed56c197adc1fb	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 20V, Negative-QTOF	splash10-0udi-1690000000-732d62c3cd9c58d92dc4	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 40V, Negative-QTOF	splash10-0006-4900000000-d2653a2a5aec14c1ea9e	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 10V, Negative-QTOF	splash10-0udi-0090000000-640af3b1d8cc9eeb5d6f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 20V, Negative-QTOF	splash10-0udi-0390000000-b3812549f172bb925ef3	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 40V, Negative-QTOF	splash10-00e9-0900000000-a50be4caaa589b1b51d9	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 10V, Positive-QTOF	splash10-0udi-0090000000-cf2deb9bcad1cbe5c298	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 20V, Positive-QTOF	splash10-0udi-0390000000-f791f0d5107cef118073	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone 40V, Positive-QTOF	splash10-0fkj-7900000000-dc5486209112780a3453	2021-09-23	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB013187

KNApSAcK ID

Not Available

Chemspider ID

8997270

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10821969

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1844961

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for 5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone (HMDB0034663)

MOL for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

3D MOL for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

3D SDF for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

3D-SDF for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

PDB for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

3D PDB for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

SMILES for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

INCHI for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

Structure for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

3D Structure for HMDB0034663 (5-Hydroxy-2,3-dimethyl-1,4-naphthoquinone)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra