Hmdb loader

Showing metabocard for Oxidized dithiothreitol (HMDB0059664)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Show more...Show more...Show more...
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-10-30 10:32:48 UTC
Update Date2023-02-21 17:29:11 UTC
HMDB IDHMDB0059664
Secondary Accession Numbers
  • HMDB59664
Metabolite Identification
Common NameOxidized dithiothreitol
DescriptionOxidized dithiothreitol, also known as dithiane diol, belongs to the class of organic compounds known as dithianes. Dithianes are compounds containing a dithiane moiety, which is composed of a cyclohexane core structure wherein two methylene units are replaced by sulfur centres. Oxidized dithiothreitol is an extremely weak basic (essentially neutral) compound (based on its pKa). Oxidized dithiothreitol exists in all living organisms, ranging from bacteria to humans. oxidized dithiothreitol can be biosynthesized from 1,4-dithiothreitol; which is mediated by the enzyme vitamin K epoxide reductase complex subunit 1. In humans, oxidized dithiothreitol is involved in vitamin k metabolism. Oxidized dithiothreitol is part of the Ubiquinone and other terpenoid-quinone biosynthesis pathway.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0059664 (Oxidized dithiothreitol)

  Mrv0541 02231215452D          

  8  8  0  0  1  0            999 V2000
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  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  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  6  0  0  0
M  END
Download

3D MOL for HMDB0059664 (Oxidized dithiothreitol)

HMDB0059664
     RDKit          3D
Oxidized dithiothreitol
 16 16  0  0  0  0  0  0  0  0999 V2000
   -1.4280   -1.4470   -0.0150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6914   -0.3030   -0.2539 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4394    0.9623    0.1549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4527    2.3864   -0.4050 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.5243    1.8089   -0.9193 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7398    0.0248   -0.5639 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6445   -0.3154    0.4530 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8984   -1.4869    1.1219 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8473   -1.8184   -0.8265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5341   -0.2041   -1.3592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4957    0.9266    1.2773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4525    0.9697   -0.2931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7252   -0.1196   -0.1068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5990   -0.5158   -1.5133 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6956    0.5235    1.2067 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5143   -1.3921    2.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  2 10  1  6
  3 11  1  0
  3 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  1
  8 16  1  0
M  END
Download

3D SDF for HMDB0059664 (Oxidized dithiothreitol)

  Mrv0541 02231215452D          

  8  8  0  0  1  0            999 V2000
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  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  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0059664

> <DATABASE_NAME>
hmdb

> <SMILES>
O[C@H]1CSSC[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O2S2/c5-3-1-7-8-2-4(3)6/h3-6H,1-2H2/t3-,4-/m0/s1

> <INCHI_KEY>
YPGMOWHXEQDBBV-IMJSIDKUSA-N

> <FORMULA>
C4H8O2S2

> <MOLECULAR_WEIGHT>
152.235

> <EXACT_MASS>
151.99657088

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
14.196997221031605

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5R)-1,2-dithiane-4,5-diol

> <ALOGPS_LOGP>
-0.44

> <JCHEM_LOGP>
-0.5909905626666665

> <ALOGPS_LOGS>
-0.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.903570118541026

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.476841094082925

> <JCHEM_PKA_STRONGEST_BASIC>
-3.333359185344703

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
37.2684

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dithiane diol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0059664 (Oxidized dithiothreitol)

HMDB0059664
     RDKit          3D
Oxidized dithiothreitol
 16 16  0  0  0  0  0  0  0  0999 V2000
   -1.4280   -1.4470   -0.0150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6914   -0.3030   -0.2539 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4394    0.9623    0.1549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4527    2.3864   -0.4050 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.5243    1.8089   -0.9193 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7398    0.0248   -0.5639 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6445   -0.3154    0.4530 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8984   -1.4869    1.1219 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8473   -1.8184   -0.8265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5341   -0.2041   -1.3592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4957    0.9266    1.2773 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4525    0.9697   -0.2931 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7252   -0.1196   -0.1068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5990   -0.5158   -1.5133 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6956    0.5235    1.2067 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5143   -1.3921    2.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  2 10  1  6
  3 11  1  0
  3 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  1
  8 16  1  0
M  END
Download

PDB for HMDB0059664 (Oxidized dithiothreitol)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0       1.334  -0.770   0.000  0.00  0.00           S+0
HETATM    5  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
Download

3D PDB for HMDB0059664 (Oxidized dithiothreitol)

COMPND    HMDB0059664
HETATM    1  O1  UNL     1      -1.428  -1.447  -0.015  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.691  -0.303  -0.254  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.439   0.962   0.155  1.00  0.00           C  
HETATM    4  S1  UNL     1      -0.453   2.386  -0.405  1.00  0.00           S  
HETATM    5  S2  UNL     1       1.524   1.809  -0.919  1.00  0.00           S  
HETATM    6  C3  UNL     1       1.740   0.025  -0.564  1.00  0.00           C  
HETATM    7  C4  UNL     1       0.645  -0.315   0.453  1.00  0.00           C  
HETATM    8  O2  UNL     1       0.898  -1.487   1.122  1.00  0.00           O  
HETATM    9  H1  UNL     1      -1.847  -1.818  -0.827  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.534  -0.204  -1.359  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.496   0.927   1.277  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.453   0.970  -0.293  1.00  0.00           H  
HETATM   13  H5  UNL     1       2.725  -0.120  -0.107  1.00  0.00           H  
HETATM   14  H6  UNL     1       1.599  -0.516  -1.513  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.696   0.524   1.207  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.514  -1.392   2.042  1.00  0.00           H  
CONECT    1    2    9
CONECT    2    3    7   10
CONECT    3    4   11   12
CONECT    4    5
CONECT    5    6
CONECT    6    7   13   14
CONECT    7    8   15
CONECT    8   16
END
Download

SMILES for HMDB0059664 (Oxidized dithiothreitol)

O[C@H]1CSSC[C@@H]1O
Download

INCHI for HMDB0059664 (Oxidized dithiothreitol)

InChI=1S/C4H8O2S2/c5-3-1-7-8-2-4(3)6/h3-6H,1-2H2/t3-,4-/m0/s1
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
DITHIANE diolChEBI
Chemical FormulaC4H8O2S2
Average Molecular Weight152.235
Monoisotopic Molecular Weight151.99657088
IUPAC Name(4R,5R)-1,2-dithiane-4,5-diol
Traditional Namedithiane diol
CAS Registry NumberNot Available
SMILES
O[C@H]1CSSC[C@@H]1O
InChI Identifier
InChI=1S/C4H8O2S2/c5-3-1-7-8-2-4(3)6/h3-6H,1-2H2/t3-,4-/m0/s1
InChI KeyYPGMOWHXEQDBBV-IMJSIDKUSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dithianes. Dithianes are compounds containing a dithiane moiety, which is composed of a cyclohexane core structure wherein two methylene units are replaced by sulfur centres.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDithianes
Sub ClassNot Available
Direct ParentDithianes
Alternative Parents
Substituents
  • 1,2-dithiane
  • Secondary alcohol
  • Organic disulfide
  • 1,2-diol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
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 LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01822
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID388524
KEGG Compound IDC01119
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439407
PDB IDDTD
ChEBI ID42147
Food Biomarker OntologyNot Available
VMH IDDTTOX
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Vitamin K epoxide reductase complex subunit 1
General function:
Involved in vitamin-K-epoxide reductase (warfarin-sensi
Specific function:
Involved in vitamin K metabolism. Catalytic subunit of the vitamin K epoxide reductase (VKOR) complex which reduces inactive vitamin K 2,3-epoxide to active vitamin K.
Gene Name:
VKORC1
Uniprot ID:
Q9BQB6
Molecular weight:
18234.3
Reactions
Phylloquinol + Oxidized dithiothreitol → Vitamin K1 2,3-epoxide + 1,4-Dithiothreitoldetails
Vitamin K1 + Oxidized dithiothreitol + Water → Vitamin K1 2,3-epoxide + 1,4-Dithiothreitoldetails
Vitamin K + Oxidized dithiothreitol + Water → Vitamin K epoxide + 1,4-Dithiothreitoldetails
2,3-Epoxymenaquinone + 1,4-Dithiothreitol → Menatetrenone + Oxidized dithiothreitol + Waterdetails