MiMeDB: Showing metabocard for Purine deoxyribonucleoside (MMDBc0031923)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:55:09 UTC

Update Date

2022-08-31 18:26:27 UTC

Metabolite ID

MMDBc0031923

Metabolite Identification

Common Name

Purine deoxyribonucleoside

Description

A deoxyribonucleoside containing a purine base

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041518162D          
 
 17 19  0  0  1  0            999 V2000
   11.5058   -9.4397    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.6363   -9.7296    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2925   -9.1913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0089   -8.7772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9324   -9.2327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.3879  -10.5163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2925   -8.3632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9964   -9.6054    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.5058   -8.0734    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.3113   -9.7296    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.5597  -10.5163    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.9964   -7.9491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7003   -9.1913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5246   -9.4811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1043  -11.1788    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.7003   -8.3632    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.3590   -8.6944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  2  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
  8 13  2  0  0  0  0
 10 14  1  1  0  0  0
 11 15  1  6  0  0  0
 12 16  2  0  0  0  0
 14 17  1  0  0  0  0
  7  9  1  0  0  0  0
 10 11  1  0  0  0  0
 13 16  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031923

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN=C2

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N4O3/c15-3-8-7(16)1-9(17-8)14-5-13-6-2-11-4-12-10(6)14/h2,4-5,7-9,15-16H,1,3H2/t7-,8+,9+/m0/s1

> <INCHI_KEY>
WJBNIBFTNGZFBW-DJLDLDEBSA-N

> <FORMULA>
C10H12N4O3

> <MOLECULAR_WEIGHT>
236.231

> <EXACT_MASS>
236.090940262

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
22.782785177704685

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,5R)-2-(hydroxymethyl)-5-(9H-purin-9-yl)oxolan-3-ol

> <ALOGPS_LOGP>
-0.90

> <JCHEM_LOGP>
-0.9558573846666666

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.785104071594844

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.88674346645201

> <JCHEM_PKA_STRONGEST_BASIC>
3.787379356434848

> <JCHEM_POLAR_SURFACE_AREA>
93.29

> <JCHEM_REFRACTIVITY>
56.671

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,5R)-2-(hydroxymethyl)-5-(purin-9-yl)oxolan-3-ol

> <JCHEM_VEBER_RULE>
0

$$$$

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  N   UNK     0      21.478 -17.621   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      19.854 -18.162   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      22.946 -17.157   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.550 -16.384   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      18.540 -17.234   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      19.391 -19.630   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.946 -15.611   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      24.260 -17.930   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0      21.478 -15.070   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      17.381 -18.162   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.845 -19.630   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.260 -14.838   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      25.574 -17.157   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      15.913 -17.698   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      16.995 -20.867   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0      25.574 -15.611   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      15.603 -16.230   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10                                                       
CONECT    6    2   11                                                       
CONECT    7    3   12    9                                                  
CONECT    8    3   13                                                       
CONECT    9    4    7                                                       
CONECT   10    5   14   11                                                  
CONECT   11    6   15   10                                                  
CONECT   12    7   16                                                       
CONECT   13    8   16                                                       
CONECT   14   10   17                                                       
CONECT   15   11                                                            
CONECT   16   12   13                                                       
CONECT   17   14                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

Synonyms

Value	Source
2'-Deoxy-N-beta-D-ribosylpurine	ChEBI
6-Deamino-2'-deoxyadenosine	ChEBI
9-(2-Deoxy-beta-D-ribofuranosyl)-9H-purine	ChEBI
9-(beta-D-2'-Deoxyribofuranosyl)purine	ChEBI
N-(beta-D-2'-Deoxyribosyl)purine	ChEBI
Purine 2'-deoxyribonucleoside	Kegg
2'-Deoxy-N-b-D-ribosylpurine	Generator
2'-Deoxy-N-β-D-ribosylpurine	Generator
9-(2-Deoxy-b-D-ribofuranosyl)-9H-purine	Generator
9-(2-Deoxy-β-D-ribofuranosyl)-9H-purine	Generator
9-(b-D-2'-Deoxyribofuranosyl)purine	Generator
9-(Β-D-2'-deoxyribofuranosyl)purine	Generator
N-(b-D-2'-Deoxyribosyl)purine	Generator
N-(Β-D-2'-deoxyribosyl)purine	Generator
2-Deoxy-N-D-ribosylpurine	ChEBI
2'-Deoxynebularine	MeSH

Molecular Formula

C₁₀H₁₂N₄O₃

Average Mass

236.231

Monoisotopic Mass

236.090940262

IUPAC Name

(2R,3S,5R)-2-(hydroxymethyl)-5-(9H-purin-9-yl)oxolan-3-ol

Traditional Name

(2R,3S,5R)-2-(hydroxymethyl)-5-(purin-9-yl)oxolan-3-ol

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN=C2

InChI Identifier

InChI=1S/C10H12N4O3/c15-3-8-7(16)1-9(17-8)14-5-13-6-2-11-4-12-10(6)14/h2,4-5,7-9,15-16H,1,3H2/t7-,8+,9+/m0/s1

InChI Key

WJBNIBFTNGZFBW-DJLDLDEBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Purine 2'-deoxyribonucleosides

Direct Parent

Purine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Purine 2'-deoxyribonucleoside
Imidazopyrimidine
Purine
N-substituted imidazole
Pyrimidine
Tetrahydrofuran
Heteroaromatic compound
Azole
Imidazole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine 2'-deoxyribonucleoside (CHEBI:72810 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	12 g/L	ALOGPS
logP	-0.9	ALOGPS
logP	-0.96	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	13.89	ChemAxon
pKa (Strongest Basic)	3.79	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.29 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	56.67 m³·mol⁻¹	ChemAxon
Polarizability	22.78 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown

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

Not Available

KEGG Compound ID

C20463

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

65148

PDB ID

Not Available

ChEBI ID

72810

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS: ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. [PubMed:26481353 ]

Showing metabocard for Purine deoxyribonucleoside (MMDBc0031923)

MOL for #<Metabolite:0x00007f1240658278>

3D MOL for #<Metabolite:0x00007f1240658278>

3D SDF for #<Metabolite:0x00007f1240658278>

3D-SDF for #<Metabolite:0x00007f1240658278>

PDB for #<Metabolite:0x00007f1240658278>

3D PDB for #<Metabolite:0x00007f1240658278>

SMILES for #<Metabolite:0x00007f1240658278>

INCHI for #<Metabolite:0x00007f1240658278>

Structure for #<Metabolite:0x00007f1240658278>

3D Structure for #<Metabolite:0x00007f1240658278>