MiMeDB: Showing metabocard for scyllo-inosine (MMDBc0054725)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-06 16:41:34 UTC

Update Date

2022-08-12 20:09:03 UTC

Metabolite ID

MMDBc0054725

Metabolite Identification

Common Name

scyllo-inosine

Description

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  C   UNK     0      11.935 -14.014   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.935 -15.554   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.269 -16.324   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.602 -15.554   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.602 -14.014   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.269 -13.244   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      13.269 -11.704   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      10.601 -13.244   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      13.269 -17.864   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      15.957 -13.232   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      10.601 -16.324   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      15.957 -16.336   0.000  0.00  0.00           O+0
CONECT    1    2    6    8                                                  
CONECT    2    1    3   11                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5   12                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    1                                                            
CONECT    9    3                                                            
CONECT   10    5                                                            
CONECT   11    2                                                            
CONECT   12    4                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
Scyllo-inosine	ChEBI

Molecular Formula

C₆H₁₀O₆

Average Mass

178.14

Monoisotopic Mass

178.047738042

IUPAC Name

(2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexan-1-one

Traditional Name

(2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexan-1-one

CAS Registry Number

Not Available

SMILES

O[C@H]1[C@H](O)[C@@H](O)C(=O)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C6H10O6/c7-1-2(8)4(10)6(12)5(11)3(1)9/h1-5,7-11H/t1-,2-,3+,4-,5-/m1/s1

InChI Key

VYEGBDHSGHXOGT-QFYCRYKCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclitols and derivatives. Cyclitols and derivatives are compounds containing a cycloalkane moiety with one hydroxyl group on each of three or more ring atoms. These of also include derivatives where the hydrogen atom of one or more of the hydroxyl groups is replaced with another atom.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Cyclitols and derivatives

Alternative Parents

Substituents

Cyclitol or derivatives
Cyclic ketone
Secondary alcohol
Ketone
Polyol
Organic oxide
Hydrocarbon derivative
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

pentahydroxycyclohexanone (CHEBI:50920 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	393 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-3.2	ChemAxon
logS	0.34	ALOGPS
pKa (Strongest Acidic)	8.78	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	118.22 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	35.01 m³·mol⁻¹	ChemAxon
Polarizability	15.22 Å³	ChemAxon
Number of Rings	1	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_2_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-b9df6511e13f2a7b4a3f	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-0900000000-75ff32f81a12dfe8a536	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06tf-9600000000-d5fa5936b4d41736c0ff	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-0900000000-db199818f07d7e15f3c7	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-1900000000-fcda293d240253904cd7	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a70-9200000000-f2ad9de21fc34a4c3998	2019-02-23	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	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	Microbial Links
Bacteria	Firmicutes	7	Human feces; Human ; Human supragingival plaque

Exposure Sources

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

Not Available

KEGG Compound ID

C20251

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

50920

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 scyllo-inosine (MMDBc0054725)

MOL for #<Metabolite:0x00007fdb54617498>

3D MOL for #<Metabolite:0x00007fdb54617498>

3D SDF for #<Metabolite:0x00007fdb54617498>

3D-SDF for #<Metabolite:0x00007fdb54617498>

PDB for #<Metabolite:0x00007fdb54617498>

3D PDB for #<Metabolite:0x00007fdb54617498>

SMILES for #<Metabolite:0x00007fdb54617498>

INCHI for #<Metabolite:0x00007fdb54617498>

Structure for #<Metabolite:0x00007fdb54617498>

3D Structure for #<Metabolite:0x00007fdb54617498>