Showing metabocard for D-Arabinose (MMDBc0031892)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 01:53:46 UTC
Update Date2024-10-17 18:49:11 UTC
Metabolite IDMMDBc0031892
Metabolite Identification
Common NameD-Arabinose
DescriptionArabinose is an aldopentose – a monosaccharide containing five carbon atoms, and including an aldehyde (CHO) functional group. (Wikipedia ) D-Arabinose is degraded by Escherichia coli B via some of the L-fucose pathway enzymes and a D-ribulokinase which is distinct from the L-fuculokinase of the L-fucose pathway. (PMID 3056899 )
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00005645c85085e8>


  Mrv1652303202019012D          

 10  9  0  0  1  0            999 V2000
    6.0474   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9040   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00005645c85085e8>

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3D SDF for #<Metabolite:0x00005645c85085e8>

  Mrv1652303202019012D          

 10  9  0  0  1  0            999 V2000
    6.0474   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9040   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9040   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031892

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4-,5+/m1/s1

> <INCHI_KEY>
PYMYPHUHKUWMLA-WDCZJNDASA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.417572255354672

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4R)-2,3,4,5-tetrahydroxypentanal

> <ALOGPS_LOGP>
-2.28

> <JCHEM_LOGP>
-2.9380256209999995

> <ALOGPS_LOGS>
0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.420851692159264

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.332793333319174

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9744929158468105

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
31.383099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.80e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
arabinose

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00005645c85085e8>
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PDB for #<Metabolite:0x00005645c85085e8>
HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  O   UNK     0      11.288  -3.437   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       9.955  -2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.621  -3.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.621  -4.977   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.287  -2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       7.287  -1.127   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.954  -4.977   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.286  -3.437   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for #<Metabolite:0x00005645c85085e8>
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SMILES for #<Metabolite:0x00005645c85085e8>
OC[C@@H](O)[C@@H](O)[C@H](O)C=O
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INCHI for #<Metabolite:0x00005645c85085e8>
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4-,5+/m1/s1
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Synonyms
ValueSource
(2S,3R,4R)-2,3,4,5-TetrahydroxypentanalChEBI
(+/-)-arabinoseHMDB
Aloe sugarHMDB
AloinoseHMDB
DL-ArabinoseHMDB
PectinoseHMDB
D-ArabinoseChEBI
Molecular FormulaC5H10O5
Average Mass150.1299
Monoisotopic Mass150.05282343
IUPAC Name(2S,3R,4R)-2,3,4,5-tetrahydroxypentanal
Traditional Namearabinose
CAS Registry NumberNot Available
SMILES
OC[C@@H](O)[C@@H](O)[C@H](O)C=O
InChI Identifier
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4-,5+/m1/s1
InChI KeyPYMYPHUHKUWMLA-WDCZJNDASA-N