MiMeDB: Showing metabocard for 1,2-dihydroxydibenzothiophene (MMDBc0055129)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:44:11 UTC

Update Date

2025-10-07 16:08:57 UTC

Metabolite ID

MMDBc0055129

Metabolite Identification

Common Name

1,2-dihydroxydibenzothiophene

Description

1,2-dihydroxydibenzothiophene is a polycyclic aromatic compound belonging to the class of dibenzothiophenes. This metabolite is primarily formed during the microbial degradation of dibenzothiophene (DBT), a sulfur-containing polycyclic aromatic hydrocarbon. In the degradation pathway, strain JB cometabolically degrades DBT to 1,2-dihydroxydibenzothiophene, which is subsequently converted to a ring cleavage product (PMID:28821932 ). The compound can be oxidized by cis-Naphthalene dihydrodiol dehydrogenase, an enzyme isolated from Pseudomonas putida, resulting in a product tentatively identified as 1,2-dihydroxydibenzothiophene (PMID:596875 ). Further metabolism of this compound by heat-treated cell extracts leads to the formation of 4[2-(3-hydroxy)-thionaphthenyl]-2-oxo-3-butenoic acid, indicating its involvement in complex metabolic pathways (PMID:596875 ). The chemical structure of 1,2-dihydroxydibenzothiophene features hydroxyl groups at the 1 and 2 positions of the dibenzothiophene framework, contributing to its reactivity and interactions with various biological systems.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221442D          

 15 17  0  0  0  0            999 V2000
    3.7054    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3896    1.6387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2243    1.9817    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.6855    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  5  2  0  0  0  0
  7  3  2  0  0  0  0
  8  5  1  0  0  0  0
  9  4  2  0  0  0  0
  9  7  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 11 10  2  0  0  0  0
 12  8  2  0  0  0  0
 12 11  1  0  0  0  0
 13  8  1  0  0  0  0
 14 12  1  0  0  0  0
 15  9  1  0  0  0  0
 15 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0055129

> <DATABASE_NAME>
MIME

> <SMILES>
OC1=C(O)C2=C(SC3=CC=CC=C23)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C12H8O2S/c13-8-5-6-10-11(12(8)14)7-3-1-2-4-9(7)15-10/h1-6,13-14H

> <INCHI_KEY>
VKHFOUIAKVUCEF-UHFFFAOYSA-N

> <FORMULA>
C12H8O2S

> <MOLECULAR_WEIGHT>
216.25

> <EXACT_MASS>
216.024500672

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
21.92871589177358

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-thiatricyclo[7.4.0.0^{2,7}]trideca-1(13),2(7),3,5,9,11-hexaene-3,4-diol

> <JCHEM_LOGP>
3.3377228123333325

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.016877169213585

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.060729684131285

> <JCHEM_PKA_STRONGEST_BASIC>
-6.379160363165451

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
59.594200000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
8-thiatricyclo[7.4.0.0^{2,7}]trideca-1(13),2(7),3,5,9,11-hexaene-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       6.917   1.914   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.393   0.450   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.410   2.235   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.362  -0.695   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.173   0.450   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.810   2.235   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.727   3.059   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.285   3.699   0.000  0.00  0.00           O+0
HETATM   15  S   UNK     0       3.610  -1.280   0.000  0.00  0.00           S+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    7                                                       
CONECT    4    2    9                                                       
CONECT    5    6    8                                                       
CONECT    6    5   10                                                       
CONECT    7    3    9   11                                                  
CONECT    8    5   12   13                                                  
CONECT    9    4    7   15                                                  
CONECT   10    6   11   15                                                  
CONECT   11    7   10   12                                                  
CONECT   12    8   11   14                                                  
CONECT   13    8                                                            
CONECT   14   12                                                            
CONECT   15    9   10                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   34    0
END

Synonyms

Value	Source
Dibenzothiophene-1,2-diol	ChEBI

Molecular Formula

C₁₂H₈O₂S

Average Mass

216.25

Monoisotopic Mass

216.024500672

IUPAC Name

8-thiatricyclo[7.4.0.0^{2,7}]trideca-1(13),2(7),3,5,9,11-hexaene-3,4-diol

Traditional Name

8-thiatricyclo[7.4.0.0^{2,7}]trideca-1(13),2(7),3,5,9,11-hexaene-3,4-diol

CAS Registry Number

Not Available

SMILES

OC1=C(O)C2=C(SC3=CC=CC=C23)C=C1

InChI Identifier

InChI=1S/C12H8O2S/c13-8-5-6-10-11(12(8)14)7-3-1-2-4-9(7)15-10/h1-6,13-14H

InChI Key

VKHFOUIAKVUCEF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dibenzothiophenes. These are organic heterocyclic compounds with a structure containing a dibenzothiophene moiety, made up of two benzene rings fused to a central thiophene ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzothiophenes

Sub Class

Dibenzothiophenes

Direct Parent

Dibenzothiophenes

Alternative Parents

Substituents

Dibenzothiophene
1-benzothiophene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Heteroaromatic compound
Thiophene
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dibenzothiophenes (CHEBI:17212 )
an organosulfur compound (12-DIHYDROXYDIBENZOTHIOPHENE )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	3.34	ChemAxon
pKa (Strongest Acidic)	8.06	ChemAxon
pKa (Strongest Basic)	-6.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	59.59 m³·mol⁻¹	ChemAxon
Polarizability	21.93 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	434.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-24	50.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	645.7
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	887.3
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	852.1
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	596.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	2582.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	207.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	728.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	426.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	331.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	403.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	246.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	120.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	688.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	417.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	653.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1691.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	1466.1

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	1,2-dihydroxydibenzothiophene_TMS_1	C[Si](C)(C)OC1=CC=C2SC3=CC=CC=C3C2=C1O	standard non polar	2025-10-24	2127.04
Gas Chromatography	1,2-dihydroxydibenzothiophene_TMS_2	C[Si](C)(C)OC1=C(O)C=CC2=C1C1=CC=CC=C1S2	standard non polar	2025-10-24	1664.34
Gas Chromatography	1,2-dihydroxydibenzothiophene_TMS_3	C[Si](C)(C)OC1=CC=C2SC3=CC=CC=C3C2=C1O[Si](C)(C)C	standard non polar	2025-10-24	1573.79
Gas Chromatography	1,2-dihydroxydibenzothiophene_TMS_1	C[Si](C)(C)OC1=CC=C2SC3=CC=CC=C3C2=C1O	standard polar	2025-10-24	1556.96
Gas Chromatography	1,2-dihydroxydibenzothiophene_TMS_2	C[Si](C)(C)OC1=C(O)C=CC2=C1C1=CC=CC=C1S2	standard polar	2025-10-24	2305.49
Gas Chromatography	1,2-dihydroxydibenzothiophene_TMS_3	C[Si](C)(C)OC1=CC=C2SC3=CC=CC=C3C2=C1O[Si](C)(C)C	standard polar	2025-10-24	1943.78

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human
Bacteria	Proteobacteria	1	Human

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

389943

KEGG Compound ID

C06722

BioCyc ID

12-DIHYDROXYDIBENZOTHIOPHENE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

441151

PDB ID

Not Available

ChEBI ID

17212

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 1,2-dihydroxydibenzothiophene (MMDBc0055129)

MOL for #<Metabolite:0x00007fade02ffb08>

3D MOL for #<Metabolite:0x00007fade02ffb08>

3D SDF for #<Metabolite:0x00007fade02ffb08>

3D-SDF for #<Metabolite:0x00007fade02ffb08>

PDB for #<Metabolite:0x00007fade02ffb08>

3D PDB for #<Metabolite:0x00007fade02ffb08>

SMILES for #<Metabolite:0x00007fade02ffb08>

INCHI for #<Metabolite:0x00007fade02ffb08>

Structure for #<Metabolite:0x00007fade02ffb08>

3D Structure for #<Metabolite:0x00007fade02ffb08>