Showing metabocard for L-rhamnofuranose (MMDBc0054544)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:17:16 UTC
Update Date2022-08-12 20:09:01 UTC
Metabolite IDMMDBc0054544
Metabolite Identification
Common NameL-rhamnofuranose
DescriptionL-rhamnofuranose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. L-rhamnofuranose exists in all living organisms, ranging from bacteria to humans. L-rhamnofuranose is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on L-rhamnofuranose.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb48008608>

 
  Mrv1533006051508002D          
 
 12 12  0  0  1  0            999 V2000
   18.8717   -6.9151    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.1214   -7.7023    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.5302   -6.4345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.0883   -6.6578    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.9464   -7.7023    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.6333   -8.3646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.2039   -6.9151    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
   17.9218   -5.8517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4752   -7.2065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.4309   -8.3683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.9834   -6.6578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7068   -6.0904    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  6  0  0  0
  3  7  1  0  0  0  0
  4  8  1  6  0  0  0
  4  9  1  0  0  0  0
  5 10  1  6  0  0  0
  7 11  1  4  0  0  0
  5  7  1  0  0  0  0
  1 12  1  1  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007fdb48008608>

HMDB0304405
     RDKit          3D
L-rhamnofuranose
 23 23  0  0  0  0  0  0  0  0999 V2000
    2.5965   -0.3540    0.4798 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7636    0.1336   -0.7096 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7439    1.5256   -0.7219 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3680   -0.3716   -0.4926 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5151    0.0347   -1.4811 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7875   -0.0472   -0.9829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5443   -1.0510   -1.5894 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6895   -0.2595    0.5147 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6169    0.4804    1.2202 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2699    0.2154    0.7495 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2526    1.5959    0.6617 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6283   -0.5730    0.1912 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1642   -1.3293    0.8507 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4991    0.3564    1.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2108   -0.2969   -1.6034 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6508    1.8169   -0.9828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3319   -1.4741   -0.4129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089    0.9457   -1.1175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5549   -1.8632   -1.0356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7175   -1.3418    0.7373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4706   -0.0164    1.1962 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1639   -0.1759    1.6829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3934    2.0493    1.5205 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  4  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  6
  3 16  1  0
  4 17  1  1
  6 18  1  0
  7 19  1  0
  8 20  1  6
  9 21  1  0
 10 22  1  1
 11 23  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fdb48008608>

 
  Mrv1533006051508002D          
 
 12 12  0  0  1  0            999 V2000
   18.8717   -6.9151    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.1214   -7.7023    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.5302   -6.4345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.0883   -6.6578    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.9464   -7.7023    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.6333   -8.3646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.2039   -6.9151    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
   17.9218   -5.8517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4752   -7.2065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.4309   -8.3683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.9834   -6.6578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7068   -6.0904    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  6  0  0  0
  3  7  1  0  0  0  0
  4  8  1  6  0  0  0
  4  9  1  0  0  0  0
  5 10  1  6  0  0  0
  7 11  1  4  0  0  0
  5  7  1  0  0  0  0
  1 12  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054544

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c1-2(7)5-3(8)4(9)6(10)11-5/h2-10H,1H3/t2-,3-,4+,5-,6?/m0/s1

> <INCHI_KEY>
AFNUZVCFKQUDBJ-ZZWDRFIYSA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.157

> <EXACT_MASS>
164.068473486

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.494205073978522

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5S)-5-[(1S)-1-hydroxyethyl]oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.27

> <JCHEM_LOGP>
-1.885629251333333

> <ALOGPS_LOGS>
0.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.890426860522364

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.30506591436722

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0556878791359425

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
34.37969999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-rhamnofuranose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007fdb48008608>

HMDB0304405
     RDKit          3D
L-rhamnofuranose
 23 23  0  0  0  0  0  0  0  0999 V2000
    2.5965   -0.3540    0.4798 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7636    0.1336   -0.7096 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7439    1.5256   -0.7219 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3680   -0.3716   -0.4926 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5151    0.0347   -1.4811 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7875   -0.0472   -0.9829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5443   -1.0510   -1.5894 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6895   -0.2595    0.5147 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6169    0.4804    1.2202 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2699    0.2154    0.7495 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2526    1.5959    0.6617 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6283   -0.5730    0.1912 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1642   -1.3293    0.8507 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4991    0.3564    1.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2108   -0.2969   -1.6034 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6508    1.8169   -0.9828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3319   -1.4741   -0.4129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089    0.9457   -1.1175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5549   -1.8632   -1.0356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7175   -1.3418    0.7373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4706   -0.0164    1.1962 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1639   -0.1759    1.6829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3934    2.0493    1.5205 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  4  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  6
  3 16  1  0
  4 17  1  1
  6 18  1  0
  7 19  1  0
  8 20  1  6
  9 21  1  0
 10 22  1  1
 11 23  1  0
M  END
Download

PDB for #<Metabolite:0x00007fdb48008608>

HEADER    PROTEIN                                 05-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-15         0                                  
HETATM    1  C   UNK     0      35.227 -12.908   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      35.693 -14.378   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      36.456 -12.011   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      33.765 -12.428   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      37.233 -14.378   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      34.782 -15.614   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      37.714 -12.908   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      33.454 -10.923   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      32.620 -13.452   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      38.138 -15.621   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      39.169 -12.428   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0      34.919 -11.369   0.000  0.00  0.00           H+0
CONECT    1    2    3    4   12                                             
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2   10    7                                                  
CONECT    6    2                                                            
CONECT    7    3   11    5                                                  
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    7                                                            
CONECT   12    1                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for #<Metabolite:0x00007fdb48008608>

COMPND    HMDB0304405
HETATM    1  C1  UNL     1       2.596  -0.354   0.480  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.764   0.134  -0.710  1.00  0.00           C  
HETATM    3  O1  UNL     1       1.744   1.526  -0.722  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.368  -0.372  -0.493  1.00  0.00           C  
HETATM    5  O2  UNL     1      -0.515   0.035  -1.481  1.00  0.00           O  
HETATM    6  C4  UNL     1      -1.788  -0.047  -0.983  1.00  0.00           C  
HETATM    7  O3  UNL     1      -2.544  -1.051  -1.589  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.689  -0.260   0.515  1.00  0.00           C  
HETATM    9  O4  UNL     1      -2.617   0.480   1.220  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.270   0.215   0.750  1.00  0.00           C  
HETATM   11  O5  UNL     1      -0.253   1.596   0.662  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.628  -0.573   0.191  1.00  0.00           H  
HETATM   13  H2  UNL     1       2.164  -1.329   0.851  1.00  0.00           H  
HETATM   14  H3  UNL     1       2.499   0.356   1.325  1.00  0.00           H  
HETATM   15  H4  UNL     1       2.211  -0.297  -1.603  1.00  0.00           H  
HETATM   16  H5  UNL     1       2.651   1.817  -0.983  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.332  -1.474  -0.413  1.00  0.00           H  
HETATM   18  H7  UNL     1      -2.309   0.946  -1.117  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.555  -1.863  -1.036  1.00  0.00           H  
HETATM   20  H9  UNL     1      -1.717  -1.342   0.737  1.00  0.00           H  
HETATM   21  H10 UNL     1      -3.471  -0.016   1.196  1.00  0.00           H  
HETATM   22  H11 UNL     1       0.164  -0.176   1.683  1.00  0.00           H  
HETATM   23  H12 UNL     1      -0.393   2.049   1.521  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4   15
CONECT    3   16
CONECT    4    5   10   17
CONECT    5    6
CONECT    6    7    8   18
CONECT    7   19
CONECT    8    9   10   20
CONECT    9   21
CONECT   10   11   22
CONECT   11   23
END
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SMILES for #<Metabolite:0x00007fdb48008608>

[H][C@]1(OC(O)[C@H](O)[C@@H]1O)[C@H](C)O
Download

INCHI for #<Metabolite:0x00007fdb48008608>

InChI=1S/C6H12O5/c1-2(7)5-3(8)4(9)6(10)11-5/h2-10H,1H3/t2-,3-,4+,5-,6?/m0/s1
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SynonymsNot Available
Molecular FormulaC6H12O5
Average Mass164.157
Monoisotopic Mass164.068473486
IUPAC Name(3R,4S,5S)-5-[(1S)-1-hydroxyethyl]oxolane-2,3,4-triol
Traditional NameL-rhamnofuranose
CAS Registry NumberNot Available
SMILES
[H][C@]1(OC(O)[C@H](O)[C@@H]1O)[C@H](C)O
InChI Identifier
InChI=1S/C6H12O5/c1-2(7)5-3(8)4(9)6(10)11-5/h2-10H,1H3/t2-,3-,4+,5-,6?/m0/s1
InChI KeyAFNUZVCFKQUDBJ-ZZWDRFIYSA-N