MiMeDB: Showing metabocard for alpha-ribazole (MMDBc0054343)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:07:54 UTC

Update Date

2022-09-01 02:28:35 UTC

Metabolite ID

MMDBc0054343

Metabolite Identification

Common Name

alpha-ribazole

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv0541 07191210032D          
 
 20 22  0  0  1  0            999 V2000
   11.7073   -8.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9735   -9.0828    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.7984   -9.0710    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.0420   -8.2828    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.3677   -7.8075    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.3637  -10.2300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3637  -11.0550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0782  -11.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7927  -11.0550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7927  -10.2300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0782   -9.8175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5773  -11.3099    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.0623  -10.6425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5773   -9.9751    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.2908   -9.7287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8140   -8.0196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.3556   -6.9715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6501   -6.5775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6493   -9.8175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6493  -11.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 10 14  1  0  0  0  0
  2 14  1  1  0  0  0
  3 15  1  1  0  0  0
  4 16  1  1  0  0  0
  5 17  1  6  0  0  0
 17 18  1  0  0  0  0
  6 19  1  0  0  0  0
  7 20  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054343

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=C(C)C=C2N(C=NC2=C1)[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H18N2O4/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-13(19)12(18)11(5-17)20-14/h3-4,6,11-14,17-19H,5H2,1-2H3/t11-,12-,13-,14+/m1/s1

> <INCHI_KEY>
HLRUKOJSWOKCPP-SYQHCUMBSA-N

> <FORMULA>
C14H18N2O4

> <MOLECULAR_WEIGHT>
278.3037

> <EXACT_MASS>
278.126657074

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
29.461618500887944

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R,4S,5R)-2-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol

> <ALOGPS_LOGP>
0.35

> <JCHEM_LOGP>
0.7263956360000006

> <ALOGPS_LOGS>
-1.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.891804080288225

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.455603310049778

> <JCHEM_PKA_STRONGEST_BASIC>
5.99802750713596

> <JCHEM_POLAR_SURFACE_AREA>
87.74000000000001

> <JCHEM_REFRACTIVITY>
71.6472

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.03e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-ribazole

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-JUL-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUL-12         0                                  
HETATM    1  O   UNK     0      21.854 -15.497   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      22.350 -16.955   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      23.890 -16.933   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      24.345 -15.461   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      23.086 -14.574   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.479 -19.096   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      17.479 -20.636   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.813 -21.406   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      20.146 -20.636   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      20.146 -19.096   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      18.813 -18.326   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      21.611 -21.112   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      22.516 -19.866   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      21.611 -18.620   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0      24.810 -18.160   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      25.786 -14.970   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      23.064 -13.013   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      21.747 -12.278   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      16.145 -18.326   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      16.145 -21.406   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3   14                                                  
CONECT    3    2    4   15                                                  
CONECT    4    3    5   16                                                  
CONECT    5    4    1   17                                                  
CONECT    6    7   11   19                                                  
CONECT    7    6    8   20                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   12                                                  
CONECT   10    9   11   14                                                  
CONECT   11   10    6                                                       
CONECT   12    9   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   10    2                                                  
CONECT   15    3                                                            
CONECT   16    4                                                            
CONECT   17    5   18                                                       
CONECT   18   17                                                            
CONECT   19    6                                                            
CONECT   20    7                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

Synonyms

Value	Source
N1-(alpha-D-Ribosyl)-5,6-dimethylbenzimidazole	ChEBI
N1-(a-D-Ribosyl)-5,6-dimethylbenzimidazole	Generator
N1-(Α-D-ribosyl)-5,6-dimethylbenzimidazole	Generator
a-Ribazole	Generator
Α-ribazole	Generator
1-alpha-D-ribofuransido-5,6-Dimethylbenzimidazole	MeSH
alpha-Ribazole, (beta)-isomer	MeSH

Molecular Formula

C₁₄H₁₈N₂O₄

Average Mass

278.3037

Monoisotopic Mass

278.126657074

IUPAC Name

(2S,3R,4S,5R)-2-(5,6-dimethyl-1H-1,3-benzodiazol-1-yl)-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

α-ribazole

CAS Registry Number

Not Available

SMILES

CC1=C(C)C=C2N(C=NC2=C1)[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C14H18N2O4/c1-7-3-9-10(4-8(7)2)16(6-15-9)14-13(19)12(18)11(5-17)20-14/h3-4,6,11-14,17-19H,5H2,1-2H3/t11-,12-,13-,14+/m1/s1

InChI Key

HLRUKOJSWOKCPP-SYQHCUMBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzimidazole ribonucleosides and ribonucleotides. These are nucleosides with a structure that consists of an imidazole moiety of benzimidazole is N-linked to a ribose (or deoxyribose). Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Benzimidazole ribonucleosides and ribonucleotides

Sub Class

Not Available

Direct Parent

Benzimidazole ribonucleosides and ribonucleotides

Alternative Parents

Substituents

1-ribofuranosylbenzimidazole
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Benzimidazole
Monosaccharide
N-substituted imidazole
Benzenoid
Azole
Heteroaromatic compound
Imidazole
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

1-ribosylbenzimidazole (CHEBI:10329 )
dimethylbenzimidazole (CHEBI:10329 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	4.03 g/L	ALOGPS
logP	0.35	ALOGPS
logP	0.73	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	12.46	ChemAxon
pKa (Strongest Basic)	6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	87.74 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	71.65 m³·mol⁻¹	ChemAxon
Polarizability	29.46 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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	splash10-002b-0960000000-22e7dd5ba006f4e08c09	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-0900000000-adc99902c99126194d59	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-0900000000-d1c0db69325e918b882f	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004j-0690000000-22e156e67c572e84f30a	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-0900000000-e8640a54f5e3dbda0922	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0002-0900000000-a402497355b75409824f	2019-02-23	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013489	adenosylcob(III)inamide-GDP	coenzyme B12	Adenosylcobinamide-GDP ribazoletransferase	Transfer of ribazole	RHEA	34755880
MMDBr0014457	N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole	alpha-ribazole	Adenosylcobalamin/alpha-ribazole phosphatase	Dephosphorylation	RHEA	34755880

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
Bacteria	Firmicutes	40	Human feces; Human ; Catfish
Bacteria	Proteobacteria	120	Human ; Human feces; Sheep ; Pig
Bacteria	Chlorobi	7
Bacteria	Actinobacteria	22	Human ; Cattle
Bacteria	Deinococcus-thermus	1
Bacteria	Thermotogae	4
Bacteria	Fusobacteria	1	Human ; Human feces
Archaea/Archaea	Euryarchaeota	21
Bacteria	Chloroflexi	2
Bacteria	Spirochaetes	5	Human
Bacteria	Cyanobacteria	8
Archaea/Archaea	Crenarchaeota	11
Archaea	Crenarchaeota	1
Bacteria	nah	1
Bacteria	Nitrospirae	1
Bacteria/NULL	Proteobacteria	1	Human ; Human feces; Sheep ; Pig

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

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C05775

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

10329

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 alpha-ribazole (MMDBc0054343)

MOL for #<Metabolite:0x00007fa4a6237678>

3D MOL for #<Metabolite:0x00007fa4a6237678>

3D SDF for #<Metabolite:0x00007fa4a6237678>

3D-SDF for #<Metabolite:0x00007fa4a6237678>

PDB for #<Metabolite:0x00007fa4a6237678>

3D PDB for #<Metabolite:0x00007fa4a6237678>

SMILES for #<Metabolite:0x00007fa4a6237678>

INCHI for #<Metabolite:0x00007fa4a6237678>

Structure for #<Metabolite:0x00007fa4a6237678>

3D Structure for #<Metabolite:0x00007fa4a6237678>