MiMeDB: Showing metabocard for Purine nucleoside (MMDBc0031800)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:49:48 UTC

Update Date

2022-08-31 18:24:51 UTC

Metabolite ID

MMDBc0031800

Metabolite Identification

Common Name

Purine nucleoside

Description

A purine ribonucleoside that is 9H-purine attached to a Œ≤-D-ribofuranosyl residue at position 9 via a glycosidic (N-glycosyl) linkage

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10101211232D          

 22 24  0  0  0  0            999 V2000
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3687   -2.8174    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -4.2695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4991   -3.9515    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5351   -4.2326    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7432   -3.5525    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6986   -2.0209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  2  0  0  0  0
  6  2  1  1  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  1  1  0  0  0  0
 11  3  2  0  0  0  0
 12  3  1  0  0  0  0
 12  9  2  0  0  0  0
 13  4  2  0  0  0  0
 13  5  1  0  0  0  0
 14  4  1  0  0  0  0
 14  9  1  0  0  0  0
 10 14  1  1  0  0  0
 15  2  1  0  0  0  0
  7 16  1  6  0  0  0
  8 17  1  6  0  0  0
 18  6  1  0  0  0  0
 18 10  1  0  0  0  0
  6 19  1  6  0  0  0
  7 20  1  1  0  0  0
  8 21  1  1  0  0  0
 10 22  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031800

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=NC3=CN=CN=C23)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N4O4/c15-2-6-7(16)8(17)10(18-6)14-4-13-5-1-11-3-12-9(5)14/h1,3-4,6-8,10,15-17H,2H2/t6-,7-,8-,10-/m1/s1

> <INCHI_KEY>
MRWXACSTFXYYMV-FDDDBJFASA-N

> <FORMULA>
C10H12N4O4

> <MOLECULAR_WEIGHT>
252.2267

> <EXACT_MASS>
252.085854892

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
23.514367899578446

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-(9H-purin-9-yl)oxolane-3,4-diol

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-1.8564954476666669

> <ALOGPS_LOGS>
-1.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.891226311459594

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.45400449058085

> <JCHEM_PKA_STRONGEST_BASIC>
3.774993845986062

> <JCHEM_POLAR_SURFACE_AREA>
113.52000000000001

> <JCHEM_REFRACTIVITY>
58.1817

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.68e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
purine nucleoside

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5   11                                                       
CONECT    2    6   15                                                       
CONECT    3   11   12                                                       
CONECT    4   13   14                                                       
CONECT    5    1    9   13                                                  
CONECT    6    2    7   18   19                                             
CONECT    7    6    8   16   20                                             
CONECT    8    7   10   17   21                                             
CONECT    9    5   12   14                                                  
CONECT   10    8   14   18   22                                             
CONECT   11    1    3                                                       
CONECT   12    3    9                                                       
CONECT   13    4    5                                                       
CONECT   14    4    9   10                                                  
CONECT   15    2                                                            
CONECT   16    7                                                            
CONECT   17    8                                                            
CONECT   18    6   10                                                       
CONECT   19    6                                                            
CONECT   20    7                                                            
CONECT   21    8                                                            
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Value	Source
N-D-Ribosylpurine	ChEBI
Purine nucleoside	ChEBI
Purine riboside	ChEBI
Purine ribonucleoside	Kegg
9-(beta-D-Ribofuranosyl)purine	MeSH
Purine-1-D-ribofuranoside	MeSH

Molecular Formula

C₁₀H₁₂N₄O₄

Average Mass

252.2267

Monoisotopic Mass

252.085854892

IUPAC Name

(2R,3S,4R,5R)-2-(hydroxymethyl)-5-(9H-purin-9-yl)oxolane-3,4-diol

Traditional Name

purine nucleoside

CAS Registry Number

550-33-4

SMILES

[H][C@]1(CO)O[C@@]([H])(N2C=NC3=CN=CN=C23)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C10H12N4O4/c15-2-6-7(16)8(17)10(18-6)14-4-13-5-1-11-3-12-9(5)14/h1,3-4,6-8,10,15-17H,2H2/t6-,7-,8-,10-/m1/s1

InChI Key

MRWXACSTFXYYMV-FDDDBJFASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Not Available

Direct Parent

Purine nucleosides

Alternative Parents

Substituents

Purine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Imidazopyrimidine
Purine
Monosaccharide
N-substituted imidazole
Pyrimidine
Heteroaromatic compound
Azole
Imidazole
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Primary alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine ribonucleoside (CHEBI:18255 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	16.8 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-1.9	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	12.45	ChemAxon
pKa (Strongest Basic)	3.77	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	2	ChemAxon
Refractivity	58.18 m³·mol⁻¹	ChemAxon
Polarizability	23.51 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
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0gba-0960000000-02588b36be524da1fbdb	2017-09-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0uk9-0690000000-3132e9cf975c9d333807	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-0900000000-30611d46c742b20458a6	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-0900000000-bf687a37f1a8fdee4b9f	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-0900000000-1ca445719eb772d826e5	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-00di-2900000000-d4186191baed33ece266	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT , positive	splash10-00di-0900000000-fe942a1442dc2ba58705	2017-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-0940000000-558c13580fe37e7be7cc	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-1900000000-c0a60904cd95924d259f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00dl-8900000000-dece14475c7e39a2463e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0uxr-0790000000-52cdec17cf806f6a8d60	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-0900000000-825da67e9ee8ead415d1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-014l-9800000000-eeb587fff62d67752a0c	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	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

Not Available

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; Human stool	Unknown

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

DB04440

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00018685

Chemspider ID

Not Available

KEGG Compound ID

C15586

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

68368

PDB ID

Not Available

ChEBI ID

18255

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 nucleoside (MMDBc0031800)

MOL for #<Metabolite:0x00007f46e047b3b8>

3D MOL for #<Metabolite:0x00007f46e047b3b8>

3D SDF for #<Metabolite:0x00007f46e047b3b8>

3D-SDF for #<Metabolite:0x00007f46e047b3b8>

PDB for #<Metabolite:0x00007f46e047b3b8>

3D PDB for #<Metabolite:0x00007f46e047b3b8>

SMILES for #<Metabolite:0x00007f46e047b3b8>

INCHI for #<Metabolite:0x00007f46e047b3b8>

Structure for #<Metabolite:0x00007f46e047b3b8>

3D Structure for #<Metabolite:0x00007f46e047b3b8>