Showing metabocard for D-Xylofuranose (MMDBc0057103)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-10-17 17:52:17 UTC
Update Date2025-10-07 16:09:49 UTC
Metabolite IDMMDBc0057103
Metabolite Identification
Common NameD-Xylofuranose
DescriptionD-Xylofuranose is a monosaccharide belonging to the class of carbohydrates. This five-membered sugar is characterized by its furanose ring structure, which is essential in various biochemical pathways. D-Xylofuranose is involved in the synthesis of poly(1,2-O-isopropylidene-α-D-xylofuranose monothiocarbonate)s through ring-opening copolymerizations, demonstrating its utility in polymer chemistry (PMID:37578470 ). Additionally, it serves as a key intermediate in the preparation of benzimidazole nucleosides from D-glucose, highlighting its role in nucleoside synthesis (PMID:33045644 ). D-Xylofuranose is also a significant component of bio-crude derived from sugarcane bagasse, showcasing its potential in biofuel applications (PMID:34490211 ). Furthermore, it is recognized in immunoassays targeting specific epitopes related to Mycobacterium tuberculosis, indicating its relevance in diagnostic applications (PMID:30257899 ). The structural modifications of D-xylofuranose, such as the introduction of thioheptose and amino acid moieties, further illustrate its versatility in chemical synthesis and biological interactions (PMID:30673214 ). Overall, D-Xylofuranose plays a multifaceted role in both synthetic and biological chemistry.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fd42b6b69d8>


  Mrv1652310172219522D          

 10 10  0  0  1  0            999 V2000
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  1  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fd42b6b69d8>

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3D SDF for #<Metabolite:0x00007fd42b6b69d8>

  Mrv1652310172219522D          

 10 10  0  0  1  0            999 V2000
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057103

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1OC(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-IOVATXLUSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.13

> <EXACT_MASS>
150.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.571302172625767

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007fd42b6b69d8>
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PDB for #<Metabolite:0x00007fd42b6b69d8>
HEADER    PROTEIN                                 17-OCT-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-OCT-22         0                                  
HETATM    1  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.306   1.175   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    3   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for #<Metabolite:0x00007fd42b6b69d8>
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SMILES for #<Metabolite:0x00007fd42b6b69d8>
OC[C@H]1OC(O)[C@H](O)[C@H]1O
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INCHI for #<Metabolite:0x00007fd42b6b69d8>
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3+,4-,5?/m1/s1
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Synonyms
ValueSource
D-XylfChEBI
D-Xylo-pentofuranoseChEBI
WURCS=2.0/1,1,0/[a212h-1x_1-4]/1/ChEBI
Molecular FormulaC5H10O5
Average Mass150.13
Monoisotopic Mass150.052823422
IUPAC Name(3R,4R,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Name(3R,4R,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
CAS Registry NumberNot Available
SMILES
OC[C@H]1OC(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-IOVATXLUSA-N