Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 17:10:49 UTC

Update Date

2022-09-22 17:44:26 UTC

HMDB ID

HMDB0256646

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Plumbagin

Description

Plumbagin, also known as 2-methyljuglone or plumbagone, 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). Plumbagin has been detected, but not quantified in, several different foods, such as black walnuts (Juglans nigra), common walnuts (Juglans regia), japanese persimmons (Diospyros kaki), and persimmons (Diospyros). This could make plumbagin a potential biomarker for the consumption of these foods. Plumbagin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Plumbagin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Plumbagin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Plumbagin is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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


  Mrv0541 02241221002D          

 14 15  0  0  0  0            999 V2000
   -0.2061    0.4742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2095   -0.3504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5119    0.8830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9173    0.8865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5051   -0.7696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9173   -0.7662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2265    0.4707    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5153    1.7110    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6319    0.4742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2231   -0.3573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5016   -1.5942    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6319   -0.3504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9173   -1.5908    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9446    0.8761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  2  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  5 11  2  0  0  0  0
  6 12  2  0  0  0  0
  6 13  1  0  0  0  0
  7 14  1  0  0  0  0
  7 10  2  0  0  0  0
  9 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256646

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H8O3/c1-6-5-9(13)10-7(11(6)14)3-2-4-8(10)12/h2-5,12H,1H3

> <INCHI_KEY>
VCMMXZQDRFWYSE-UHFFFAOYSA-N

> <FORMULA>
C11H8O3

> <MOLECULAR_WEIGHT>
188.1794

> <EXACT_MASS>
188.047344122

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
18.524919928857557

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
2.15

> <JCHEM_LOGP>
2.236303118333333

> <ALOGPS_LOGS>
-2.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.322065994425337

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.48140387107231

> <JCHEM_PKA_STRONGEST_BASIC>
-4.439359188090946

> <JCHEM_POLAR_SURFACE_AREA>
54.370000000000005

> <JCHEM_REFRACTIVITY>
52.52119999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.23e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
plumbagin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -0.385   0.885   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.391  -0.654   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.956   1.648   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.712   1.655   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.943  -1.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.712  -1.430   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.289   0.879   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.962   3.194   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -3.046   0.885   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.283  -0.667   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.936  -2.976   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -3.046  -0.654   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.712  -2.969   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.630   1.635   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10   11                                                  
CONECT    6    2   12   13                                                  
CONECT    7    3   14   10                                                  
CONECT    8    3                                                            
CONECT    9    4   12                                                       
CONECT   10    5    7                                                       
CONECT   11    5                                                            
CONECT   12    6    9                                                       
CONECT   13    6                                                            
CONECT   14    7                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-Methyl-5-hydroxy-1,4-naphthoquinone	ChEBI
2-Methyljuglone	ChEBI
5-Hydroxy-2-methyl-1,4-naphthalenedione	ChEBI
5-Hydroxy-2-methyl-1,4-naphthoquinone	ChEBI
Plumbaein	ChEBI
Plumbagine	ChEBI
Plumbagone	ChEBI

Chemical Formula

C₁₁H₈O₃

Average Molecular Weight

188.1794

Monoisotopic Molecular Weight

188.047344122

IUPAC Name

5-hydroxy-2-methyl-1,4-dihydronaphthalene-1,4-dione

Traditional Name

plumbagin

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C11H8O3/c1-6-5-9(13)10-7(11(6)14)3-2-4-8(10)12/h2-5,12H,1H3

InChI Key

VCMMXZQDRFWYSE-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

phenols (CHEBI:8273 )
naphthoquinone (CHEBI:8273 )
a small molecule (CPD-4461 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0256646)

Food

Fruit

Tropical fruit

Persimmon (FooDB: FOOD00594)
Japanese persimmon (FooDB: FOOD00073)

Nut

Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)

Process

Not Available

Role

Industrial application

Manufacturing industry

Material processing agent

Solid material processing agent

Protective agent

Antioxidant (HMDB: HMDB0256646)
Antioxidant (HMDB: HMDB0256646)

Coloring agent

Fluorescent agent

Immunological adjuvant (HMDB: HMDB0256646)
Diuretic (HMDB: HMDB0256646)

Agriculture

Pesticide

Pesticide (HMDB: HMDB0256646)

Abortifacient (HMDB: HMDB0256646)
Anticoagulant (HMDB: HMDB0256646)
Central nervous system stimulant (HMDB: HMDB0256646)
Vasodilator agent (HMDB: HMDB0256646)

Pharmaceutical industry

Antineoplastic agent

Antitumor (HMDB: HMDB0256646)

Biological role

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	2.15	ALOGPS
logP	2.24	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	9.48	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	52.52 m³·mol⁻¹	ChemAxon
Polarizability	18.52 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
DeepCCS	[M+H]+	138.511	30932474
DeepCCS	[M-H]-	136.145	30932474
DeepCCS	[M-2H]-	171.422	30932474
DeepCCS	[M+Na]+	146.524	30932474
AllCCS	[M+H]+	138.8	32859911
AllCCS	[M+H-H2O]+	134.4	32859911
AllCCS	[M+NH4]+	143.0	32859911
AllCCS	[M+Na]+	144.1	32859911
AllCCS	[M-H]-	138.7	32859911
AllCCS	[M+Na-2H]-	138.8	32859911
AllCCS	[M+HCOO]-	139.0	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	6.02 minutes	32390414
Predicted by Siyang on May 30, 2022	12.7888 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.99 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2000.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	406.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	138.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	251.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	183.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	416.1 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	687.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	143.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	990.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	419.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1302.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	422.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	421.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	578.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	290.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	141.8 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Plumbagin	CC1=CC(=O)C2=C(C=CC=C2O)C1=O	2551.7	Standard polar	33892256
Plumbagin	CC1=CC(=O)C2=C(C=CC=C2O)C1=O	1648.2	Standard non polar	33892256
Plumbagin	CC1=CC(=O)C2=C(C=CC=C2O)C1=O	1579.8	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 - Plumbagin GC-MS (Non-derivatized) - 70eV, Positive	splash10-08ms-0900000000-a31fcbec96f4d1a2db51	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Plumbagin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Plumbagin GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Plumbagin GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	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 - Plumbagin 10V, Positive-QTOF	splash10-000i-0900000000-d3e2b63eb92a4cbdd9c0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plumbagin 20V, Positive-QTOF	splash10-000i-0900000000-81aea83b5c9c64b35bab	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plumbagin 40V, Positive-QTOF	splash10-00di-2900000000-151b7c1cd4ff07d54e32	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plumbagin 10V, Negative-QTOF	splash10-000i-0900000000-c275c16c4766821f0f85	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plumbagin 20V, Negative-QTOF	splash10-000i-0900000000-ecf0c8fffcd45b0b9849	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Plumbagin 40V, Negative-QTOF	splash10-000i-5900000000-d13a80e451eeb2f932b6	2016-08-03	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Plumbagin

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

8273

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1275251

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Plumbagin (HMDB0256646)

MOL for HMDB0256646 (Plumbagin)

3D MOL for HMDB0256646 (Plumbagin)

3D SDF for HMDB0256646 (Plumbagin)

3D-SDF for HMDB0256646 (Plumbagin)

PDB for HMDB0256646 (Plumbagin)

3D PDB for HMDB0256646 (Plumbagin)

SMILES for HMDB0256646 (Plumbagin)

INCHI for HMDB0256646 (Plumbagin)

Structure for HMDB0256646 (Plumbagin)

3D Structure for HMDB0256646 (Plumbagin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra