MiMeDB: Showing metabocard for cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene (MMDBc0055804)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:07:06 UTC

Update Date

2025-10-07 16:09:22 UTC

Metabolite ID

MMDBc0055804

Metabolite Identification

Common Name

cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene

Description

cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene is a polycyclic aromatic compound belonging to the class of thiophenes. It is a metabolite produced during the microbial degradation of dibenzothiophene, specifically noted in the culture of Beijerinckia B8/36 when grown with succinate in the presence of dibenzothiophene, which led to the accumulation of this compound along with dibenzothiophene-5-oxide (PMID:596875 ). The compound can be oxidized by cis-Naphthalene dihydrodiol dehydrogenase, an enzyme isolated from Pseudomonas putida, resulting in the formation of a compound tentatively identified as 1,2-dihydroxydibenzothiophene (PMID:596875 ). Additionally, it was observed that crude cell extracts from the parent strain of Beijerinckia can oxidize cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene under anaerobic conditions, further illustrating its role in microbial metabolic pathways (PMID:596875 ). This compound exemplifies the complex biochemical interactions involved in the biodegradation of sulfur-containing polycyclic aromatic hydrocarbons.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222072D          

 17 19  0  0  1  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  1  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  1  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
    0.4174    1.8102    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7764    1.3686    0.0000 H   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  1  0  0  0  0
 12 11  1  0  0  0  0
  8 13  1  6  0  0  0
 12 14  1  6  0  0  0
 15  9  1  0  0  0  0
 15 10  1  0  0  0  0
  8 16  1  1  0  0  0
 12 17  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0055804

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)C=CC2=C(C3=CC=CC=C3S2)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C12H10O2S/c13-8-5-6-10-11(12(8)14)7-3-1-2-4-9(7)15-10/h1-6,8,12-14H/t8-,12-/m0/s1

> <INCHI_KEY>
OOOXLVUNFHBSNL-UFBFGSQYSA-N

> <FORMULA>
C12H10O2S

> <MOLECULAR_WEIGHT>
218.27

> <EXACT_MASS>
218.040150736

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
22.372945855948146

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
2.0049353676666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.641819829988933

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.104662815360843

> <JCHEM_PKA_STRONGEST_BASIC>
-3.39893068463338

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
60.504000000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4S)-8-thiatricyclo[7.4.0.0^{2,7}]trideca-1(13),2(7),5,9,11-pentaene-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
HETATM   16  H   UNK     0       0.779   3.379   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       3.316   2.555   0.000  0.00  0.00           H+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   16                                             
CONECT    9    4    7   15                                                  
CONECT   10    6   11   15                                                  
CONECT   11    7   10   12                                                  
CONECT   12    8   11   14   17                                             
CONECT   13    8                                                            
CONECT   14   12                                                            
CONECT   15    9   10                                                       
CONECT   16    8                                                            
CONECT   17   12                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

Synonyms

Not Available

Molecular Formula

C₁₂H₁₀O₂S

Average Mass

218.27

Monoisotopic Mass

218.040150736

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)C=CC2=C(C3=CC=CC=C3S2)[C@@]1([H])O

InChI Identifier

InChI=1S/C12H10O2S/c13-8-5-6-10-11(12(8)14)7-3-1-2-4-9(7)15-10/h1-6,8,12-14H/t8-,12-/m0/s1

InChI Key

OOOXLVUNFHBSNL-UFBFGSQYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1-benzothiophenes. These are aromatic heterocyclic compound containing the Benzo[b]thiophene ring system.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzothiophenes

Sub Class

1-benzothiophenes

Direct Parent

1-benzothiophenes

Alternative Parents

Substituents

1-benzothiophene
Benzenoid
Heteroaromatic compound
Thiophene
Secondary alcohol
1,2-diol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dibenzothiophenes (CHEBI:16941 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	2	ChemAxon
pKa (Strongest Acidic)	13.1	ChemAxon
pKa (Strongest Basic)	-3.4	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	60.5 m³·mol⁻¹	ChemAxon
Polarizability	22.37 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_2_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	482.4
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-24	32.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	378.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	439.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	351.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	331.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1831.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	95.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	400.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	332.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-24	248.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	193.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	133.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (void)	2025-10-24	8.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	344.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	125.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	334.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1197.9
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	904.0

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene_TMS_1	C[Si](C)(C)O[C@H]1C=CC2=C(C3=CC=CC=C3S2)[C@H]1O	standard non polar	2025-10-24	2163.95
Gas Chromatography	cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene_TMS_2	C[Si](C)(C)O[C@@H]1C2=C(C=C[C@@H]1O)SC1=CC=CC=C21	standard non polar	2025-10-24	2041.66
Gas Chromatography	cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene_TMS_3	C[Si](C)(C)O[C@H]1C=CC2=C(C3=CC=CC=C3S2)[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1874.85
Gas Chromatography	cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene_TMS_1	C[Si](C)(C)O[C@H]1C=CC2=C(C3=CC=CC=C3S2)[C@H]1O	standard polar	2025-10-24	3073.13
Gas Chromatography	cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene_TMS_2	C[Si](C)(C)O[C@@H]1C2=C(C=C[C@@H]1O)SC1=CC=CC=C21	standard polar	2025-10-24	2417.55
Gas Chromatography	cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene_TMS_3	C[Si](C)(C)O[C@H]1C=CC2=C(C3=CC=CC=C3S2)[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2375.56

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

4573765

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5460102

PDB ID

Not Available

ChEBI ID

16941

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 cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene (MMDBc0055804)

MOL for #<Metabolite:0x00007fae00bea8b0>

3D MOL for #<Metabolite:0x00007fae00bea8b0>

3D SDF for #<Metabolite:0x00007fae00bea8b0>

3D-SDF for #<Metabolite:0x00007fae00bea8b0>

PDB for #<Metabolite:0x00007fae00bea8b0>

3D PDB for #<Metabolite:0x00007fae00bea8b0>

SMILES for #<Metabolite:0x00007fae00bea8b0>

INCHI for #<Metabolite:0x00007fae00bea8b0>

Structure for #<Metabolite:0x00007fae00bea8b0>

3D Structure for #<Metabolite:0x00007fae00bea8b0>