MiMeDB: Showing metabocard for 5-amino-1-(beta-D-ribosyl)imidazole (MMDBc0055550)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:58:40 UTC

Update Date

2025-10-07 16:09:11 UTC

Metabolite ID

MMDBc0055550

Metabolite Identification

Common Name

5-amino-1-(beta-D-ribosyl)imidazole

Description

5-amino-1-(beta-D-ribosyl)imidazole is a purine derivative. There is limited literature available on this metabolite, indicating that further research may be needed to fully understand its biological significance and potential roles in metabolic pathways.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221582D          

 19 20  0  0  1  0            999 V2000
    1.9239    2.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7605    4.4559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8439    1.9642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2756    3.7884    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2564    3.2338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5305    3.0038    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8631    2.5189    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1956    3.0038    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2564    4.0588    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.6689    1.9642    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5890    2.7489    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5810    4.3696    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3151    2.7489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8631    1.6939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4506    3.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0904    3.6594    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6596    2.1890    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1280    2.1443    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3877    3.5872    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  1  0  0  0
  5  1  2  0  0  0  0
  6  4  1  0  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  1  1  0  0  0  0
 10  3  2  0  0  0  0
 11  3  1  0  0  0  0
 11  5  1  0  0  0  0
  8 11  1  1  0  0  0
 12  2  1  0  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
 15  4  1  0  0  0  0
 15  8  1  0  0  0  0
  4 16  1  6  0  0  0
  6 17  1  1  0  0  0
  7 18  1  1  0  0  0
  8 19  1  6  0  0  0
M  CHG  1   9   1
M  END
> <DATABASE_ID>
MMDBc0055550

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=NC=C2[NH3+])[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C8H13N3O4/c9-5-1-10-3-11(5)8-7(14)6(13)4(2-12)15-8/h1,3-4,6-8,12-14H,2,9H2/p+1/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
NKYAAYKKNSYIIW-XVFCMESISA-O

> <FORMULA>
C8H14N3O4

> <MOLECULAR_WEIGHT>
216.216

> <EXACT_MASS>
216.097882363

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
20.690885467216

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-imidazol-5-aminium

> <JCHEM_LOGP>
-2.444810294

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.891448544566309

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.454636222858003

> <JCHEM_PKA_STRONGEST_BASIC>
7.908584977736245

> <JCHEM_POLAR_SURFACE_AREA>
115.38000000000001

> <JCHEM_REFRACTIVITY>
59.7936

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazol-4-aminium

> <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       3.591   5.131   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.286   8.318   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.575   3.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.381   7.072   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.345   6.036   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.857   5.607   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.611   4.702   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.365   5.607   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.345   7.576   0.000  0.00  0.00           N+1
HETATM   10  N   UNK     0       3.115   3.667   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       1.099   5.131   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0      -4.818   8.157   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -4.322   5.131   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.611   3.162   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -0.841   7.072   0.000  0.00  0.00           O+0
HETATM   16  H   UNK     0      -3.902   6.831   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0      -3.098   4.086   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0      -0.239   4.003   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.724   6.696   0.000  0.00  0.00           H+0
CONECT    1    5   10                                                       
CONECT    2    4   12                                                       
CONECT    3   10   11                                                       
CONECT    4    2    6   15   16                                             
CONECT    5    1    9   11                                                  
CONECT    6    4    7   13   17                                             
CONECT    7    6    8   14   18                                             
CONECT    8    7   11   15   19                                             
CONECT    9    5                                                            
CONECT   10    1    3                                                       
CONECT   11    3    5    8                                                  
CONECT   12    2                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    4    8                                                       
CONECT   16    4                                                            
CONECT   17    6                                                            
CONECT   18    7                                                            
CONECT   19    8                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

Synonyms

Value	Source
5-Amino-1-(beta-D-ribofuranose)imidazol-3-ium	ChEBI
5-Amino-1-(beta-D-ribofuranosyl)imidazol-3-ium	ChEBI
5-Amino-1-(beta-D-ribosyl)imidazo-3-ium	ChEBI
5-Amino-1-(beta-D-ribosyl)imidazole	ChEBI
5-Amino-1-(D-ribosyl)imidazol-3-ium ribosyl-5-aminoimidazol-3-ium	ChEBI
5-Aminoimidazole ribonucleoside(1+)	ChEBI
5-Amino-1-(b-D-ribofuranose)imidazol-3-ium	Generator
5-Amino-1-(β-D-ribofuranose)imidazol-3-ium	Generator
5-Amino-1-(b-D-ribofuranosyl)imidazol-3-ium	Generator
5-Amino-1-(β-D-ribofuranosyl)imidazol-3-ium	Generator
5-Amino-1-(b-D-ribosyl)imidazo-3-ium	Generator
5-Amino-1-(β-D-ribosyl)imidazo-3-ium	Generator
5-Amino-1-(b-D-ribosyl)imidazole	Generator
5-Amino-1-(β-D-ribosyl)imidazole	Generator

Molecular Formula

C₈H₁₄N₃O₄

Average Mass

216.216

Monoisotopic Mass

216.097882363

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-imidazol-5-aminium

Traditional Name

3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazol-4-aminium

CAS Registry Number

Not Available

SMILES

[H][C@]1(CO)O[C@@]([H])(N2C=NC=C2[NH3+])[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C8H13N3O4/c9-5-1-10-3-11(5)8-7(14)6(13)4(2-12)15-8/h1,3-4,6-8,12-14H,2,9H2/p+1/t4-,6-,7-,8-/m1/s1

InChI Key

NKYAAYKKNSYIIW-XVFCMESISA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as imidazole ribonucleosides and ribonucleotides. These are organic compounds in which the C-1 of a ribosyl moiety is N-linked to an imidazole ring. Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety. This class does not contain benzimidazole nucleosides and nucleotides.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Imidazole ribonucleosides and ribonucleotides

Sub Class

Not Available

Direct Parent

Imidazole ribonucleosides and ribonucleotides

Alternative Parents

Substituents

Imidazole ribonucleoside
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
N-substituted imidazole
Monosaccharide
Aminoimidazole
Heteroaromatic compound
Tetrahydrofuran
Imidazole
Azole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.4	ChemAxon
pKa (Strongest Acidic)	12.45	ChemAxon
pKa (Strongest Basic)	7.91	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	59.79 m³·mol⁻¹	ChemAxon
Polarizability	20.69 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	453.3
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	309.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	49.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	237.7
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	315.6
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	271.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	493.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	765.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	782.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	154.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	571.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	167.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	39.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	315.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	734.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	74.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	236.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	798.6
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	573.9

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC=C2[NH3+])[C@H](O)[C@@H]1O	standard non polar	2025-10-24	2077.11
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_2	C[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=NC=C1[NH3+]	standard non polar	2025-10-24	1921.49
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_3	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=NC=C2[NH3+])[C@@H]1O	standard non polar	2025-10-24	1732.43
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC=C2[NH3+])[C@H](O[Si](C)(C)C)[C@@H]1O	standard non polar	2025-10-24	2102.85
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_5	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC=C2[NH3+])[C@H](O)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2128.38
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_6	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=NC=C2[NH3+])[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1926.23
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_7	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC=C2[NH3+])[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2338.11
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC=C2[NH3+])[C@H](O)[C@@H]1O	standard polar	2025-10-24	2406.15
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_2	C[Si](C)(C)O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=NC=C1[NH3+]	standard polar	2025-10-24	2716.99
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_3	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=NC=C2[NH3+])[C@@H]1O	standard polar	2025-10-24	1842.05
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_4	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC=C2[NH3+])[C@H](O[Si](C)(C)C)[C@@H]1O	standard polar	2025-10-24	1869.24
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_5	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC=C2[NH3+])[C@H](O)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-24	2594.93
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_6	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=NC=C2[NH3+])[C@@H]1O[Si](C)(C)C	standard polar	2025-10-24	1426.11
Gas Chromatography	5-amino-1-(beta-D-ribosyl)imidazole_TMS_7	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC=C2[NH3+])[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C	standard polar	2025-10-24	2016.84

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/Eubacteria	Proteobacteria	1	Human

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

76963363

KEGG Compound ID

Not Available

BioCyc ID

CPD-21378

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

134820109

PDB ID

Not Available

ChEBI ID

142407

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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-amino-1-(beta-D-ribosyl)imidazole (MMDBc0055550)

MOL for #<Metabolite:0x00007f9acf1cba58>

3D MOL for #<Metabolite:0x00007f9acf1cba58>

3D SDF for #<Metabolite:0x00007f9acf1cba58>

3D-SDF for #<Metabolite:0x00007f9acf1cba58>

PDB for #<Metabolite:0x00007f9acf1cba58>

3D PDB for #<Metabolite:0x00007f9acf1cba58>

SMILES for #<Metabolite:0x00007f9acf1cba58>

INCHI for #<Metabolite:0x00007f9acf1cba58>

Structure for #<Metabolite:0x00007f9acf1cba58>

3D Structure for #<Metabolite:0x00007f9acf1cba58>