Hmdb loader

Showing metabocard for Plumbagin (HMDB0256646)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:10:49 UTC
Update Date2022-09-22 17:44:26 UTC
HMDB IDHMDB0256646
Secondary Accession NumbersNone
Metabolite Identification
Common NamePlumbagin
DescriptionPlumbagin, 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0256646 (Plumbagin)

  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
Download

3D MOL for HMDB0256646 (Plumbagin)

HMDB0256646
     RDKit          3D
Plumbagin
 22 23  0  0  0  0  0  0  0  0999 V2000
    3.4243   -0.8949   -0.0196 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0286   -0.3814    0.0269 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8041    0.8809    0.3390 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4478    1.4687    0.4072 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3047    2.6674    0.7079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7265    0.6564    0.1250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0050    1.1888    0.1836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2943    2.4840    0.5002 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0956    0.3451   -0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8529   -0.9650   -0.4248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5811   -1.4887   -0.4816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4977   -0.6715   -0.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8636   -1.2055   -0.2577 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0895   -2.4215   -0.5577 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5183   -1.9248    0.3601 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8295   -0.8772   -1.0503 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0634   -0.2377    0.6033 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6662    1.5220    0.5577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7727    3.2712    0.7356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1098    0.7312   -0.0644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7084   -1.6156   -0.6456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3960   -2.5317   -0.7395 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 13  2  1  0
 12  6  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  8 19  1  0
  9 20  1  0
 10 21  1  0
 11 22  1  0
M  END
Download

3D SDF for HMDB0256646 (Plumbagin)

  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

$$$$
Download

3D-SDF for HMDB0256646 (Plumbagin)

HMDB0256646
     RDKit          3D
Plumbagin
 22 23  0  0  0  0  0  0  0  0999 V2000
    3.4243   -0.8949   -0.0196 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0286   -0.3814    0.0269 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8041    0.8809    0.3390 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4478    1.4687    0.4072 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3047    2.6674    0.7079 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7265    0.6564    0.1250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0050    1.1888    0.1836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2943    2.4840    0.5002 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0956    0.3451   -0.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8529   -0.9650   -0.4248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5811   -1.4887   -0.4816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4977   -0.6715   -0.2038 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8636   -1.2055   -0.2577 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0895   -2.4215   -0.5577 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5183   -1.9248    0.3601 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8295   -0.8772   -1.0503 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0634   -0.2377    0.6033 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6662    1.5220    0.5577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7727    3.2712    0.7356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1098    0.7312   -0.0644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7084   -1.6156   -0.6456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3960   -2.5317   -0.7395 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
  4  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 13  2  1  0
 12  6  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  8 19  1  0
  9 20  1  0
 10 21  1  0
 11 22  1  0
M  END
Download

PDB for HMDB0256646 (Plumbagin)

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
Download

3D PDB for HMDB0256646 (Plumbagin)

COMPND    HMDB0256646
HETATM    1  C1  UNL     1       3.424  -0.895  -0.020  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.029  -0.381   0.027  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.804   0.881   0.339  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.448   1.469   0.407  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.305   2.667   0.708  1.00  0.00           O  
HETATM    6  C5  UNL     1      -0.727   0.656   0.125  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.005   1.189   0.184  1.00  0.00           C  
HETATM    8  O2  UNL     1      -2.294   2.484   0.500  1.00  0.00           O  
HETATM    9  C7  UNL     1      -3.096   0.345  -0.102  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.853  -0.965  -0.425  1.00  0.00           C  
HETATM   11  C9  UNL     1      -1.581  -1.489  -0.482  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.498  -0.672  -0.204  1.00  0.00           C  
HETATM   13  C11 UNL     1       0.864  -1.205  -0.258  1.00  0.00           C  
HETATM   14  O3  UNL     1       1.089  -2.422  -0.558  1.00  0.00           O  
HETATM   15  H1  UNL     1       3.518  -1.925   0.360  1.00  0.00           H  
HETATM   16  H2  UNL     1       3.830  -0.877  -1.050  1.00  0.00           H  
HETATM   17  H3  UNL     1       4.063  -0.238   0.603  1.00  0.00           H  
HETATM   18  H4  UNL     1       2.666   1.522   0.558  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.773   3.271   0.736  1.00  0.00           H  
HETATM   20  H6  UNL     1      -4.110   0.731  -0.064  1.00  0.00           H  
HETATM   21  H7  UNL     1      -3.708  -1.616  -0.646  1.00  0.00           H  
HETATM   22  H8  UNL     1      -1.396  -2.532  -0.740  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3    3   13
CONECT    3    4   18
CONECT    4    5    5    6
CONECT    6    7    7   12
CONECT    7    8    9
CONECT    8   19
CONECT    9   10   10   20
CONECT   10   11   21
CONECT   11   12   12   22
CONECT   12   13
CONECT   13   14   14
END
Download

SMILES for HMDB0256646 (Plumbagin)

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

INCHI for HMDB0256646 (Plumbagin)

InChI=1S/C11H8O3/c1-6-5-9(13)10-7(11(6)14)3-2-4-8(10)12/h2-5,12H,1H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Methyl-5-hydroxy-1,4-naphthoquinoneChEBI
2-MethyljugloneChEBI
5-Hydroxy-2-methyl-1,4-naphthalenedioneChEBI
5-Hydroxy-2-methyl-1,4-naphthoquinoneChEBI
PlumbaeinChEBI
PlumbagineChEBI
PlumbagoneChEBI
Chemical FormulaC11H8O3
Average Molecular Weight188.1794
Monoisotopic Molecular Weight188.047344122
IUPAC Name5-hydroxy-2-methyl-1,4-dihydronaphthalene-1,4-dione
Traditional Nameplumbagin
CAS Registry NumberNot 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 KeyVCMMXZQDRFWYSE-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).
KingdomOrganic compounds
Super ClassBenzenoids
ClassNaphthalenes
Sub ClassNaphthoquinones
Direct ParentNaphthoquinones
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 FrameworkAromatic homopolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB005844
KNApSAcK IDC00002852
Chemspider ID9790
KEGG Compound IDC10387
BioCyc IDCPD-4461
BiGG IDNot Available
Wikipedia LinkPlumbagin
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID8273
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1275251
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]