MiMeDB: Showing metabocard for 5'-deoxyinosine (MMDBc0055588)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:59:39 UTC

Update Date

2022-08-12 20:09:25 UTC

Metabolite ID

MMDBc0055588

Metabolite Identification

Common Name

5'-deoxyinosine

Description

5'-deoxyinosine belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. 5'-deoxyinosine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on 5'-deoxyinosine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221592D          

 22 24  0  0  1  0            999 V2000
    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
    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
  4  1  1  1  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
 10  7  1  0  0  0  0
 11  2  2  0  0  0  0
 11  8  1  0  0  0  0
 12  2  1  0  0  0  0
 12  9  2  0  0  0  0
 13  3  2  0  0  0  0
 13  5  1  0  0  0  0
 14  3  1  0  0  0  0
 14  8  1  0  0  0  0
 10 14  1  1  0  0  0
  6 15  1  6  0  0  0
  7 16  1  6  0  0  0
 17  9  1  0  0  0  0
 18  4  1  0  0  0  0
 18 10  1  0  0  0  0
  4 19  1  6  0  0  0
  6 20  1  1  0  0  0
  7 21  1  1  0  0  0
 10 22  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0055588

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N4O4/c1-4-6(15)7(16)10(18-4)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H3,(H,11,12,17)/t4-,6-,7-,10-/m1/s1

> <INCHI_KEY>
IPJDTNIZLKTLEU-KQYNXXCUSA-N

> <FORMULA>
C10H12N4O4

> <MOLECULAR_WEIGHT>
252.23

> <EXACT_MASS>
252.085854882

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
23.5819137942755

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-2-(6-hydroxy-9H-purin-9-yl)-5-methyloxolane-3,4-diol

> <JCHEM_LOGP>
-0.5186932726666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.543473472748584

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.611829769374378

> <JCHEM_PKA_STRONGEST_BASIC>
-0.12310910316005697

> <JCHEM_POLAR_SURFACE_AREA>
113.52000000000001

> <JCHEM_REFRACTIVITY>
58.932399999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5R)-2-(6-hydroxypurin-9-yl)-5-methyloxolane-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       3.322   7.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.846   5.972   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.382   5.496   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.382   3.956   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.846   3.481   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       6.121   2.310   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       7.454   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       0.136   6.402   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.136   3.051   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       3.752   4.726   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       1.758   7.061   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.010   4.797   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.623   2.435   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       4.368   3.240   0.000  0.00  0.00           H+0
CONECT    1    4                                                            
CONECT    2   11   12                                                       
CONECT    3   13   14                                                       
CONECT    4    1    6   18   19                                             
CONECT    5    8    9   13                                                  
CONECT    6    4    7   15   20                                             
CONECT    7    6   10   16   21                                             
CONECT    8    5   11   14                                                  
CONECT    9    5   12   17                                                  
CONECT   10    7   14   18   22                                             
CONECT   11    2    8                                                       
CONECT   12    2    9                                                       
CONECT   13    3    5                                                       
CONECT   14    3    8   10                                                  
CONECT   15    6                                                            
CONECT   16    7                                                            
CONECT   17    9                                                            
CONECT   18    4   10                                                       
CONECT   19    4                                                            
CONECT   20    6                                                            
CONECT   21    7                                                            
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₀H₁₂N₄O₄

Average Mass

252.23

Monoisotopic Mass

252.085854882

IUPAC Name

(2R,3R,4S,5R)-2-(6-hydroxy-9H-purin-9-yl)-5-methyloxolane-3,4-diol

Traditional Name

(2R,3R,4S,5R)-2-(6-hydroxypurin-9-yl)-5-methyloxolane-3,4-diol

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C10H12N4O4/c1-4-6(15)7(16)10(18-4)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H3,(H,11,12,17)/t4-,6-,7-,10-/m1/s1

InChI Key

IPJDTNIZLKTLEU-KQYNXXCUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

Not Available

Direct Parent

5'-deoxyribonucleosides

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

inosines (CHEBI:82775 )
5'-deoxyribonucleoside (CHEBI:82775 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-0.52	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	1	ChemAxon
Refractivity	58.93 m³·mol⁻¹	ChemAxon
Polarizability	23.58 Å³	ChemAxon
Number of Rings	3	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_3) - 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	Microbial Links
Archaea/Archaea	Euryarchaeota	16
Archaea	Euryarchaeota	2

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

23255678

KEGG Compound ID

Not Available

BioCyc ID

CPD-16806

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14693755

PDB ID

Not Available

ChEBI ID

82775

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 5'-deoxyinosine (MMDBc0055588)

MOL for #<Metabolite:0x00005588d5cba760>

3D MOL for #<Metabolite:0x00005588d5cba760>

3D SDF for #<Metabolite:0x00005588d5cba760>

3D-SDF for #<Metabolite:0x00005588d5cba760>

PDB for #<Metabolite:0x00005588d5cba760>

3D PDB for #<Metabolite:0x00005588d5cba760>

SMILES for #<Metabolite:0x00005588d5cba760>

INCHI for #<Metabolite:0x00005588d5cba760>

Structure for #<Metabolite:0x00005588d5cba760>

3D Structure for #<Metabolite:0x00005588d5cba760>