MiMeDB: Showing metabocard for D-Biotin D-sulfoxide (MMDBc0030134)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:55:13 UTC

Update Date

2022-08-31 17:39:59 UTC

Metabolite ID

MMDBc0030134

Metabolite Identification

Common Name

D-Biotin D-sulfoxide

Description

D-biotin d-sulfoxide is a member of the chemical class known as Biotin and Derivatives. These are organic compounds containing a ureido (tetrahydroimidizalone) ring fused with a tetrahydrothiophene ring. Biotin sulfoxide is the substance that is formed when biotin is exposed to ultraviolet light in the presence of oxygen. (WikiPedia)

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08131209382D          

 20 21  0  0  0  0            999 V2000
    4.7579   -3.7632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0434   -4.1757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4724   -4.1757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3289   -3.7632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0800   -2.7712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4925   -3.4856    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1868   -3.7632    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6145   -4.1757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9405   -4.0987    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.1600   -4.6417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2462   -3.8212    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.3530   -4.8132    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9000   -3.7632    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6145   -5.0007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7731   -5.1937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6600   -2.3907    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2731   -2.9427    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.0446   -2.8725    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5092   -4.5226    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6314   -4.8637    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  6  0  0  0
  8  4  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  1  0  0  0  0
 11  6  1  0  0  0  0
 11 10  2  0  0  0  0
 12  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  8  2  0  0  0  0
 14  8  1  0  0  0  0
 15 10  1  0  0  0  0
 17  5  1  0  0  0  0
 17  7  1  0  0  0  0
 17 16  2  0  0  0  0
  6 18  1  1  0  0  0
  7 19  1  1  0  0  0
  9 20  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030134

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12CS(=O)[C@@]([H])(CCCCC(O)=O)[C@@]1([H])NC(O)=N2

> <INCHI_IDENTIFIER>
InChI=1S/C10H16N2O4S/c13-8(14)4-2-1-3-7-9-6(5-17(7)16)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-,17?/m0/s1

> <INCHI_KEY>
KCSKCIQYNAOBNQ-YBSFLMRUSA-N

> <FORMULA>
C10H16N2O4S

> <MOLECULAR_WEIGHT>
260.31

> <EXACT_MASS>
260.0830777

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
25.406391678847616

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(3aR,6S,6aS)-2-hydroxy-5-oxo-1H,3aH,4H,6H,6aH-5λ⁴-thieno[3,4-d]imidazol-6-yl]pentanoic acid

> <ALOGPS_LOGP>
-0.94

> <JCHEM_LOGP>
-2.015660034810551

> <ALOGPS_LOGS>
-1.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.730582913845565

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.581544965786889

> <JCHEM_PKA_STRONGEST_BASIC>
6.066921968708759

> <JCHEM_POLAR_SURFACE_AREA>
98.99000000000001

> <JCHEM_REFRACTIVITY>
62.109899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.41e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(3aS,4S,6aR)-2-hydroxy-5-oxo-3H,3aH,4H,6H,6aH-5λ⁴-thieno[3,4-d]imidazol-4-yl]pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   18  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    6   17                                                       
CONECT    6    5    9   11   18                                             
CONECT    7    3    9   17   19                                             
CONECT    8    4   13   14                                                  
CONECT    9    6    7   12   20                                             
CONECT   10   11   12   15                                                  
CONECT   11    6   10                                                       
CONECT   12    9   10                                                       
CONECT   13    8                                                            
CONECT   14    8                                                            
CONECT   15   10                                                            
CONECT   16   17                                                            
CONECT   17    5    7   16                                                  
CONECT   18    6                                                            
CONECT   19    7                                                            
CONECT   20    9                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

Synonyms

Value	Source
Biotin S-oxide	ChEBI
D-Biotin D-sulphoxide	Generator
D-Biotin-D-sulfoxide	MeSH

Molecular Formula

C₁₀H₁₆N₂O₄S

Average Mass

260.31

Monoisotopic Mass

260.0830777

IUPAC Name

5-[(3aR,6S,6aS)-2-hydroxy-5-oxo-1H,3aH,4H,6H,6aH-5λ⁴-thieno[3,4-d]imidazol-6-yl]pentanoic acid

Traditional Name

5-[(3aS,4S,6aR)-2-hydroxy-5-oxo-3H,3aH,4H,6H,6aH-5λ⁴-thieno[3,4-d]imidazol-4-yl]pentanoic acid

CAS Registry Number

10406-89-0

SMILES

[H][C@]12CS(=O)[C@@]([H])(CCCCC(O)=O)[C@@]1([H])NC(O)=N2

InChI Identifier

InChI=1S/C10H16N2O4S/c13-8(14)4-2-1-3-7-9-6(5-17(7)16)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-,17?/m0/s1

InChI Key

KCSKCIQYNAOBNQ-YBSFLMRUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as biotin and derivatives. These are organic compounds containing a ureido (tetrahydroimidizalone) ring fused with a tetrahydrothiophene ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Biotin and derivatives

Sub Class

Not Available

Direct Parent

Biotin and derivatives

Alternative Parents

Substituents

Biotin_derivative
Biotin
Thienoimidazolidine
Medium-chain fatty acid
Heterocyclic fatty acid
Imidazolidinone
Fatty acid
Fatty acyl
Imidazolidine
Thiolane
Thiophene
Carbonic acid derivative
Sulfoxide
Urea
Azacycle
Monocarboxylic acid or derivatives
Sulfinyl compound
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

sulfoxide (CHEBI:62193 )
biotins (CHEBI:62193 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.41 g/L	ALOGPS
logP	-0.94	ALOGPS
logP	-2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	3.58	ChemAxon
pKa (Strongest Basic)	6.07	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	98.99 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	62.11 m³·mol⁻¹	ChemAxon
Polarizability	25.41 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-0090000000-f3a4d502612e8c7a7ab9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0296-3290000000-daa46a46142b7d70b3c7	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0089-7920000000-0641cab1071cddbf264f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4j-2490000000-db7d011b23b1ad94511d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00kf-8390000000-8c08de9fdd8bd6719dc2	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-000f22c3d652c0a7bcd6	2015-09-15	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0007179	D-Biotin D-sulfoxide	Biotin	Not Available		VMH	30371894
MMDBr0007180	D-Biotin D-sulfoxide	Biotin	Not Available		VMH	30371894

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	Proteobacteria	56	Human feces; Human sputum; Human ; Human feces; pleural fluid plaque; bal; Human stool	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	5	Human feces; Human	Metabolic reconstruction

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

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

Not Available

KEGG Compound ID

C20386

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

83833

PDB ID

Not Available

ChEBI ID

62193

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for D-Biotin D-sulfoxide (MMDBc0030134)

MOL for #<Metabolite:0x00007fdb134deb08>

3D MOL for #<Metabolite:0x00007fdb134deb08>

3D SDF for #<Metabolite:0x00007fdb134deb08>

3D-SDF for #<Metabolite:0x00007fdb134deb08>

PDB for #<Metabolite:0x00007fdb134deb08>

3D PDB for #<Metabolite:0x00007fdb134deb08>

SMILES for #<Metabolite:0x00007fdb134deb08>

INCHI for #<Metabolite:0x00007fdb134deb08>

Structure for #<Metabolite:0x00007fdb134deb08>

3D Structure for #<Metabolite:0x00007fdb134deb08>