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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 21:19:16 UTC

Update Date

2021-09-26 22:51:40 UTC

HMDB ID

HMDB0244134

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin

Description

1,2,3,6,7,8-hexachlorooxanthrene, also known as 1,2,3,6,7,8-hexachlorodibenzo-p-dioxin or 1,2,3,6,7,8-HXCDD, belongs to the class of organic compounds known as chlorinated dibenzo-p-dioxins. These are organic compounds containing a chlorine atom attached to a dibenzo-p-dioxin moiety. 1,2,3,6,7,8-hexachlorooxanthrene is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on 1,2,3,6,7,8-hexachlorooxanthrene. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1,2,3,6,7,8-hexachlorodibenzo-p-dioxin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 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 02241204422D          

 20 22  0  0  0  0            999 V2000
   -2.1434   -2.8875    0.0000 Cl  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
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   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
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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
   -0.7145   -0.4125    0.0000 Cl  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
   -2.1434   -1.2375    0.0000 Cl  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
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 Cl  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
    3.5724   -2.8875    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 Cl  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
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  4  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
  6 19  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244134

> <DATABASE_NAME>
hmdb

> <SMILES>
ClC1=CC2=C(OC3=C(O2)C(Cl)=C(Cl)C(Cl)=C3)C(Cl)=C1Cl

> <INCHI_IDENTIFIER>
InChI=1S/C12H2Cl6O2/c13-3-1-5-11(9(17)7(3)15)20-6-2-4(14)8(16)10(18)12(6)19-5/h1-2H

> <INCHI_KEY>
YCLUIPQDHHPDJJ-UHFFFAOYSA-N

> <FORMULA>
C12H2Cl6O2

> <MOLECULAR_WEIGHT>
390.861

> <EXACT_MASS>
387.81859555

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
32.896740116658826

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,2,3,6,7,8-hexachlorooxanthrene

> <ALOGPS_LOGP>
7.41

> <JCHEM_LOGP>
6.624842424000001

> <ALOGPS_LOGS>
-6.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-9.334308980127451

> <JCHEM_POLAR_SURFACE_AREA>
18.46

> <JCHEM_REFRACTIVITY>
81.31039999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.63e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,2,3,6,7,8-hexachlorooxanthrene

> <JCHEM_VEBER_RULE>
1

$$$$

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 Cl   UNK     0      -4.001  -5.390   0.000  0.00  0.00          Cl+0
HETATM    2  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11 Cl   UNK     0      -1.334  -0.770   0.000  0.00  0.00          Cl+0
HETATM   12  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13 Cl   UNK     0      -4.001  -2.310   0.000  0.00  0.00          Cl+0
HETATM   14  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   16 Cl   UNK     0       6.668  -2.310   0.000  0.00  0.00          Cl+0
HETATM   17  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   18 Cl   UNK     0       6.668  -5.390   0.000  0.00  0.00          Cl+0
HETATM   19  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   20 Cl   UNK     0       4.001  -6.930   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   19                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    2   13                                                  
CONECT   13   12                                                            
CONECT   14    7   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    6   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1,2,3,6,7,8-Hexachlorodibenzo-p-dioxin	Kegg
1,2,3,6,7,8-HXCDD	Kegg
PCDD 67	Kegg
1,2,3,6,7,8-Hexachlorodibenzodioxin	MeSH
HXCDD	MeSH

Chemical Formula

C₁₂H₂Cl₆O₂

Average Molecular Weight

390.861

Monoisotopic Molecular Weight

387.81859555

IUPAC Name

1,2,3,6,7,8-hexachlorooxanthrene

Traditional Name

1,2,3,6,7,8-hexachlorooxanthrene

CAS Registry Number

Not Available

SMILES

ClC1=CC2=C(OC3=C(O2)C(Cl)=C(Cl)C(Cl)=C3)C(Cl)=C1Cl

InChI Identifier

InChI=1S/C12H2Cl6O2/c13-3-1-5-11(9(17)7(3)15)20-6-2-4(14)8(16)10(18)12(6)19-5/h1-2H

InChI Key

YCLUIPQDHHPDJJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as chlorinated dibenzo-p-dioxins. These are organic compounds containing a chlorine atom attached to a dibenzo-p-dioxin moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzodioxins

Sub Class

Benzo-p-dioxins

Direct Parent

Chlorinated dibenzo-p-dioxins

Alternative Parents

Substituents

Chlorinated-dibenzo-p-dioxin
Diaryl ether
Benzenoid
Aryl halide
Aryl chloride
Oxacycle
Ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Organochloride
Organohalogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dibenzodioxine (CHEBI:81503 )
PCDDs (C18101 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Cellular substructure

Membrane (HMDB: HMDB0244134)

Process

Not Available

Role

Biological role

calcium channel blocker (HMDB: HMDB0244134)

Modulator

Inhibitor

Enzyme inhibitor

EC 3.6.3.8 (Ca(2+)-transporting ATPase) inhibitor (HMDB: HMDB0244134)

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	7.41	ALOGPS
logP	6.62	ChemAxon
logS	-6.8	ALOGPS
pKa (Strongest Basic)	-9.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	18.46 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	81.31 m³·mol⁻¹	ChemAxon
Polarizability	32.9 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	171.466	30932474
DeepCCS	[M-H]-	169.108	30932474
DeepCCS	[M-2H]-	203.03	30932474
DeepCCS	[M+Na]+	178.257	30932474
AllCCS	[M+H]+	165.2	32859911
AllCCS	[M+H-H2O]+	162.3	32859911
AllCCS	[M+NH4]+	167.9	32859911
AllCCS	[M+Na]+	168.6	32859911
AllCCS	[M-H]-	120.2	32859911
AllCCS	[M+Na-2H]-	118.3	32859911
AllCCS	[M+HCOO]-	116.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin	ClC1=CC2=C(OC3=C(O2)C(Cl)=C(Cl)C(Cl)=C3)C(Cl)=C1Cl	3461.3	Standard polar	33892256
1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin	ClC1=CC2=C(OC3=C(O2)C(Cl)=C(Cl)C(Cl)=C3)C(Cl)=C1Cl	2792.7	Standard non polar	33892256
1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin	ClC1=CC2=C(OC3=C(O2)C(Cl)=C(Cl)C(Cl)=C3)C(Cl)=C1Cl	2790.8	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 - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin GC-MS (Non-derivatized) - 70eV, Positive	splash10-000l-0019000000-c6b0423e6eba04209100	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-0006-0219000000-f6e47eed7165be9040de	2014-09-20	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 10V, Positive-QTOF	splash10-000i-0009000000-2a23ee9dc15685f33f6c	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 20V, Positive-QTOF	splash10-000i-0009000000-2a23ee9dc15685f33f6c	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 40V, Positive-QTOF	splash10-000i-0009000000-2a23ee9dc15685f33f6c	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 10V, Negative-QTOF	splash10-000i-0009000000-3d3c43bccd9ba1a9ad9a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 20V, Negative-QTOF	splash10-000i-0009000000-cd3ee89cd1aa411de59a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 40V, Negative-QTOF	splash10-000i-0009000000-684b592f3c42b864af6c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 10V, Negative-QTOF	splash10-000i-0009000000-efb6116aebb54e51b4ed	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 20V, Negative-QTOF	splash10-000i-0009000000-efb6116aebb54e51b4ed	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 40V, Negative-QTOF	splash10-000i-0009000000-efb6116aebb54e51b4ed	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 10V, Positive-QTOF	splash10-000i-0009000000-928cd731c98959c5c274	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 20V, Positive-QTOF	splash10-000i-0009000000-928cd731c98959c5c274	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin 40V, Positive-QTOF	splash10-000i-0009000000-928cd731c98959c5c274	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

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

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

38799

KEGG Compound ID

C18101

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

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 1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin (HMDB0244134)

MOL for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

3D MOL for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

3D SDF for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

3D-SDF for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

PDB for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

3D PDB for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

SMILES for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

INCHI for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

Structure for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

3D Structure for HMDB0244134 (1,2,3,6,7,8-Hexachlorodibenzo-P-dioxin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra