MiMeDB: Showing metabocard for S-methyl-5'-thioinosine (MMDBc0056304)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:22:21 UTC

Update Date

2022-08-12 20:09:40 UTC

Metabolite ID

MMDBc0056304

Metabolite Identification

Common Name

S-methyl-5'-thioinosine

Description

5'-S-methyl-5'-thioinosine belongs to the class of organic compounds known as 5'-deoxy-5'-thionucleosides. These are 5'-deoxyribonucleosides in which the ribose is thio-substituted at the 5'position by a S-alkyl group. 5'-S-methyl-5'-thioinosine 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 5'-S-methyl-5'-thioinosine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222222D          

 24 26  0  0  1  0            999 V2000
    1.4827    5.3818    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    3.9841    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249    3.1994    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403    2.9445    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7403    2.1195    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249    1.8646    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0728    3.4294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0728    1.6346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0098    2.5320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2278    4.5972    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9415    3.7828    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0052    2.5700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8693    1.3047    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3397    1.7355    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  2  1  1  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 12  3  2  0  0  0  0
 12  9  1  0  0  0  0
 13  3  1  0  0  0  0
 13 10  2  0  0  0  0
 14  4  2  0  0  0  0
 14  6  1  0  0  0  0
 15  4  1  0  0  0  0
 15  9  1  0  0  0  0
 11 15  1  1  0  0  0
  7 16  1  6  0  0  0
  8 17  1  6  0  0  0
 18 10  1  0  0  0  0
 19  5  1  0  0  0  0
 19 11  1  0  0  0  0
 20  1  1  0  0  0  0
 20  2  1  0  0  0  0
  5 21  1  6  0  0  0
  7 22  1  1  0  0  0
  8 23  1  1  0  0  0
 11 24  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0056304

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CSC)O[C@@]([H])(N2C=NC3=C2N=CN=C3O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N4O4S/c1-20-2-5-7(16)8(17)11(19-5)15-4-14-6-9(15)12-3-13-10(6)18/h3-5,7-8,11,16-17H,2H2,1H3,(H,12,13,18)/t5-,7-,8-,11-/m1/s1

> <INCHI_KEY>
GXYLOXCSJFJFKA-IOSLPCCCSA-N

> <FORMULA>
C11H14N4O4S

> <MOLECULAR_WEIGHT>
298.32

> <EXACT_MASS>
298.073576121

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
28.817093834514623

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3R,4S,5S)-2-(6-hydroxy-9H-purin-9-yl)-5-[(methylsulfanyl)methyl]oxolane-3,4-diol

> <JCHEM_LOGP>
-0.08313209333333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.534124377444694

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.610374765868213

> <JCHEM_PKA_STRONGEST_BASIC>
-0.12311800215109592

> <JCHEM_POLAR_SURFACE_AREA>
113.52000000000001

> <JCHEM_REFRACTIVITY>
71.30969999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
5'-deoxy-5'-methylthioinosine

> <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       2.768  10.046   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.322   7.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.846   5.972   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.382   5.496   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.382   3.956   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.846   3.481   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       6.121   2.310   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       7.454   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       0.136   6.402   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.136   3.051   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       3.752   4.726   0.000  0.00  0.00           O+0
HETATM   20  S   UNK     0       2.292   8.581   0.000  0.00  0.00           S+0
HETATM   21  H   UNK     0       1.758   7.061   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.010   4.797   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       1.623   2.435   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       4.368   3.240   0.000  0.00  0.00           H+0
CONECT    1   20                                                            
CONECT    2    5   20                                                       
CONECT    3   12   13                                                       
CONECT    4   14   15                                                       
CONECT    5    2    7   19   21                                             
CONECT    6    9   10   14                                                  
CONECT    7    5    8   16   22                                             
CONECT    8    7   11   17   23                                             
CONECT    9    6   12   15                                                  
CONECT   10    6   13   18                                                  
CONECT   11    8   15   19   24                                             
CONECT   12    3    9                                                       
CONECT   13    3   10                                                       
CONECT   14    4    6                                                       
CONECT   15    4    9   11                                                  
CONECT   16    7                                                            
CONECT   17    8                                                            
CONECT   18   10                                                            
CONECT   19    5   11                                                       
CONECT   20    1    2                                                       
CONECT   21    5                                                            
CONECT   22    7                                                            
CONECT   23    8                                                            
CONECT   24   11                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

Synonyms

Value	Source
5'-Deoxy-5'-methylthioinosine	ChEBI
9-(5-S-Methyl-5-thio-beta-D-ribofuranosyl)-9H-purin-6-ol	ChEBI
S-Methyl-5'-thioinosine	ChEBI
9-(5-S-Methyl-5-thio-b-D-ribofuranosyl)-9H-purin-6-ol	Generator
9-(5-S-Methyl-5-thio-β-D-ribofuranosyl)-9H-purin-6-ol	Generator

Molecular Formula

C₁₁H₁₄N₄O₄S

Average Mass

298.32

Monoisotopic Mass

298.073576121

IUPAC Name

(2R,3R,4S,5S)-2-(6-hydroxy-9H-purin-9-yl)-5-[(methylsulfanyl)methyl]oxolane-3,4-diol

Traditional Name

5'-deoxy-5'-methylthioinosine

CAS Registry Number

Not Available

SMILES

[H][C@]1(CSC)O[C@@]([H])(N2C=NC3=C2N=CN=C3O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C11H14N4O4S/c1-20-2-5-7(16)8(17)11(19-5)15-4-14-6-9(15)12-3-13-10(6)18/h3-5,7-8,11,16-17H,2H2,1H3,(H,12,13,18)/t5-,7-,8-,11-/m1/s1

InChI Key

GXYLOXCSJFJFKA-IOSLPCCCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxy-5'-thionucleosides. These are 5'-deoxyribonucleosides in which the ribose is thio-substituted at the 5'position by a S-alkyl group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

5'-deoxy-5'-thionucleosides

Direct Parent

5'-deoxy-5'-thionucleosides

Alternative Parents

Substituents

5'-deoxy-5'-thionucleoside
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Pentose monosaccharide
Purinone
Imidazopyrimidine
Purine
Pyrimidone
Monosaccharide
N-substituted imidazole
Pyrimidine
Tetrahydrofuran
Vinylogous amide
Heteroaromatic compound
Azole
Imidazole
Secondary alcohol
1,2-diol
Thioether
Organoheterocyclic compound
Azacycle
Oxacycle
Dialkylthioether
Sulfenyl compound
Alcohol
Hydrocarbon derivative
Organic nitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organosulfur compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

inosines (CHEBI:48595 )
5'-deoxyribonucleoside (CHEBI:48595 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-0.083	ChemAxon
pKa (Strongest Acidic)	11.61	ChemAxon
pKa (Strongest Basic)	-0.12	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.52 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	71.31 m³·mol⁻¹	ChemAxon
Polarizability	28.82 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_3_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

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

Metabolic Reactions

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
Archaea/Archaea	Euryarchaeota	27
Archaea	Euryarchaeota	2
Bacteria	Firmicutes	32	Human feces; Human
Bacteria	Aquificae	1
Bacteria	Proteobacteria	14	Sheep ; Pig ; Human
Bacteria	Dictyoglomi	2
Bacteria	Thermotogae	1
Bacteria	Nitrospirae	1

Exposure Sources

Source Type	Source Sub-type	Species	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

141619

KEGG Compound ID

C19787

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

161214

PDB ID

Not Available

ChEBI ID

48595

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 S-methyl-5'-thioinosine (MMDBc0056304)

MOL for #<Metabolite:0x00007fecb36846b8>

3D MOL for #<Metabolite:0x00007fecb36846b8>

3D SDF for #<Metabolite:0x00007fecb36846b8>

3D-SDF for #<Metabolite:0x00007fecb36846b8>

PDB for #<Metabolite:0x00007fecb36846b8>

3D PDB for #<Metabolite:0x00007fecb36846b8>

SMILES for #<Metabolite:0x00007fecb36846b8>

INCHI for #<Metabolite:0x00007fecb36846b8>

Structure for #<Metabolite:0x00007fecb36846b8>

3D Structure for #<Metabolite:0x00007fecb36846b8>