NP-MRD: Showing NP-Card for α-ribazole (NP0142713)

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Record Information

Version

1.0

Created at

2022-09-01 21:19:03 UTC

Updated at

2022-09-01 21:19:04 UTC

NP-MRD ID

NP0142713

Secondary Accession Numbers

None

Natural Product Identification

Common Name

α-ribazole

Description

Not Available

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 38 40  0  0  0  0  0  0  0  0999 V2000
    5.2488    0.2425   -0.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8265   -0.1137   -0.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3838   -1.2790   -0.9016 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0293   -1.6065   -0.9674 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3301   -2.6235   -1.4591 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0021   -2.4300   -1.2458 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1242   -1.2533   -0.6002 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3088   -0.5953   -0.1477 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7840    0.4023   -0.9841 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1247    0.5627   -0.7474 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5040    1.9369   -0.2734 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1408    2.8735   -1.2395 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5651   -0.4315    0.3043 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8238   -0.9275    0.0661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4808   -1.5127    0.1238 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8905   -2.2347   -0.9904 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1265   -0.7231   -0.4165 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5349    0.4597    0.1885 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9028    0.7498    0.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3713    1.9860    0.8620 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5161    1.1437   -0.8057 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8468   -0.6019   -0.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5896    0.3213    0.8399 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0611   -1.9755   -1.3330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8122   -3.0860   -1.5330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1239   -0.0784    0.8429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6635    0.3535   -1.7016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0235    2.1911    0.6801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6041    1.9412   -0.1079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4630    3.7759   -0.9900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4402   -0.0119    1.3097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8392   -1.8757   -0.1452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3657   -2.1175    1.0194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9772   -1.6466   -1.7597 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8165    1.1290    0.6087 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6207    2.7169    0.0398 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2610    1.8637    1.4933 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5912    2.4745    1.4808 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2 19  2  0
 19 20  1  0
 19 18  1  0
 18 17  2  0
 17  7  1  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  4  3  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  3  2  1  0
 15  8  1  0
  4 17  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
 20 36  1  0
 20 37  1  0
 20 38  1  0
 18 35  1  0
  6 25  1  0
  3 24  1  0
  8 26  1  1
 10 27  1  6
 11 28  1  0
 11 29  1  0
 12 30  1  0
 13 31  1  1
 14 32  1  0
 15 33  1  1
 16 34  1  0
M  END

 
  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>
NP0142713

> <DATABASE_NAME>
NP-MRD

> <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

View in JSmol

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

Chemical Formula

C₁₄H₁₈N₂O₄

Average Mass

278.3037 Da

Monoisotopic Mass

278.12666 Da

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

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for α-ribazole (NP0142713)

MOL for NP0142713 (α-ribazole)

3D MOL for NP0142713 (α-ribazole)

3D SDF for NP0142713 (α-ribazole)

3D-SDF for NP0142713 (α-ribazole)

PDB for NP0142713 (α-ribazole)

3D PDB for NP0142713 (α-ribazole)

SMILES for NP0142713 (α-ribazole)

INCHI for NP0142713 (α-ribazole)

Structure for NP0142713 (α-ribazole)

3D Structure for NP0142713 (α-ribazole)