Showing metabocard for beta-D-ribofuranose (MMDBc0030146)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:55:41 UTC
Update Date2022-08-31 17:40:07 UTC
Metabolite IDMMDBc0030146
Metabolite Identification
Common Namebeta-D-ribofuranose
DescriptionBeta-D-ribofuranose is the cyclic form of D-ribose. Ribose, primarily occurring as D-ribose, is an organic compound that occurs widely in nature. It is an aldopentose, a monosaccharide containing five carbon atoms that in its acyclic form has an aldehyde functional group at one end. Typically, ribose exists in the cyclic form. It comprises the backbone of RNA, a biopolymer that is the basis of genetic transcription. It is related to deoxyribose, as found in DNA, by the removal of one hydroxy group. Once phosphorylated, ribose can become a subunit of ATP, NADH, and several other compounds that are critical to metabolism.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007f923054cd00>

            
  Mrv1652305161817372D          

 10 10  0  0  1  0            999 V2000
   12.9393   -2.8516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0419   -4.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8368   -4.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3915   -3.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3158   -2.2746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5269   -4.1210    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2721   -3.3364    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.3518   -4.1210    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.6070   -3.3364    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.4874   -3.0815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1  9  1  0  0  0  0
  6  2  1  6  0  0  0
  8  3  1  6  0  0  0
  5 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7 10  1  1  0  0  0
  8  9  1  0  0  0  0
  9  4  1  1  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f923054cd00>

Download
3D SDF for #<Metabolite:0x00007f923054cd00>
            
  Mrv1652305161817372D          

 10 10  0  0  1  0            999 V2000
   12.9393   -2.8516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0419   -4.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8368   -4.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3915   -3.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3158   -2.2746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5269   -4.1210    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2721   -3.3364    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.3518   -4.1210    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.6070   -3.3364    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.4874   -3.0815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1  9  1  0  0  0  0
  6  2  1  6  0  0  0
  8  3  1  6  0  0  0
  5 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7 10  1  1  0  0  0
  8  9  1  0  0  0  0
  9  4  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030146

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
HMFHBZSHGGEWLO-TXICZTDVSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.621018245765843

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.65

> <JCHEM_LOGP>
-2.302204276

> <ALOGPS_LOGS>
0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.899514700313038

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.30569577774193

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811390578102284

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
29.96089999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.07e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-D-ribofuranoside

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for #<Metabolite:0x00007f923054cd00>
Download
PDB for #<Metabolite:0x00007f923054cd00>
HEADER    PROTEIN                                 16-MAY-18   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-18         0                                  
HETATM    1  O   UNK     0      24.153  -5.323   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      22.478  -8.938   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      25.829  -8.938   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      26.864  -5.752   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      21.123  -4.246   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      23.384  -7.693   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.908  -6.228   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      24.923  -7.693   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      25.400  -6.228   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.443  -5.752   0.000  0.00  0.00           C+0
CONECT    1    7    9                                                       
CONECT    2    6                                                            
CONECT    3    8                                                            
CONECT    4    9                                                            
CONECT    5   10                                                            
CONECT    6    2    7    8                                                  
CONECT    7    1    6   10                                                  
CONECT    8    3    6    9                                                  
CONECT    9    1    8    4                                                  
CONECT   10    5    7                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

Download
3D PDB for #<Metabolite:0x00007f923054cd00>
Download
SMILES for #<Metabolite:0x00007f923054cd00>
OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O
Download
INCHI for #<Metabolite:0x00007f923054cd00>
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5-/m1/s1
Download
Synonyms
ValueSource
beta-D-RibChEBI
BETA-D-RIBOFURANOSYLChEBI
b-D-RibGenerator
Β-D-ribGenerator
b-D-RIBOFURANOSYLGenerator
Β-D-ribofuranosylGenerator
b-D-RibofuranoseGenerator
Β-D-ribofuranoseGenerator
Molecular FormulaC5H10O5
Average Mass150.1299
Monoisotopic Mass150.05282343
IUPAC Name(2R,3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Nameβ-D-ribofuranoside
CAS Registry Number50-69-1
SMILES
OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5-/m1/s1
InChI KeyHMFHBZSHGGEWLO-TXICZTDVSA-N