Showing metabocard for Rhamnose (MMDBc0000158)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:37:59 UTC
Update Date2024-04-30 19:31:15 UTC
Metabolite IDMMDBc0000158
Metabolite Identification
Common NameRhamnose
DescriptionRhamnose (Rham) is a naturally occurring deoxy sugar. It can be classified as either a methyl-pentose or a 6-deoxy-hexose. Rhamnose occurs in nature in its L-form as L-rhamnose (6-deoxy-L-mannose). This is unusual, since most of the naturally occurring sugars are in D-form. Rhamnose is commonly bound to other sugars in nature. It is a common glycone component of glycosides from many plants. Rhamnose is also a component of the outer cell membrane of certain bacteria. L-rhamnose is metabolized to L-Lactaldehyde, which is a branching point in the metabolic pathway of L-fucose and L-rhamnose utilization. It exists in two anomeric forms, alpha-L-rhamnose and beta-L-rhamnose. Rhamnose has been found in Klebsiella, Pseudomonas (https://link.springer.com/article/10.1007/BF00369505) (https://onlinelibrary.wiley.com/doi/abs/10.1002/ejlt.200300816).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645c6f81f80>

Untitled Document-1
  Mrv1652304202021562D          

 11 11  0  0  0  0            999 V2000
   -0.7145    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.2375    0.0000 O   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
  5  6  1  0  0  0  0
  6  1  1  0  0  0  0
  1  7  1  6  0  0  0
  3  8  1  6  0  0  0
  4  9  1  6  0  0  0
  2 10  1  1  0  0  0
  5 11  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00005645c6f81f80>

HMDB0000849
     RDKit          3D
Rhamnose
 23 23  0  0  0  0  0  0  0  0999 V2000
   -2.0937   -0.8451    0.7146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9241   -0.8156   -0.2855 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0754   -1.5567    0.2492 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3484   -1.1192    0.0871 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7924   -1.0569   -1.2153 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3992    0.2997    0.6642 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7367    0.2433    1.8827 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6741    1.1369   -0.3538 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5649    2.4756    0.0857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6407    0.5542   -0.7175 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7933    0.7036   -2.1167 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0060   -0.6007    0.1246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9943   -0.0577    1.4743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2429   -1.8520    1.1192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3267   -1.3934   -1.1723 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0316   -1.7372    0.6908 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2730   -1.5689   -1.8564 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4204    0.6280    0.8496 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3863    0.0269    2.6045 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3479    1.1934   -1.2499 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5813    2.5262    1.0700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4307    1.2460   -0.2951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1791    1.5696   -2.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  6
  4 16  1  0
  5 17  1  0
  6 18  1  1
  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:0x00005645c6f81f80>

Untitled Document-1
  Mrv1652304202021562D          

 11 11  0  0  0  0            999 V2000
   -0.7145    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.2375    0.0000 O   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
  5  6  1  0  0  0  0
  6  1  1  0  0  0  0
  1  7  1  6  0  0  0
  3  8  1  6  0  0  0
  4  9  1  6  0  0  0
  2 10  1  1  0  0  0
  5 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000158

> <DATABASE_NAME>
MIME

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

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

> <INCHI_KEY>
SHZGCJCMOBCMKK-JFNONXLTSA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.1565

> <EXACT_MASS>
164.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.364952562022367

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R,5R,6S)-6-methyloxane-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-2.39

> <JCHEM_LOGP>
-1.885629251333333

> <ALOGPS_LOGS>
0.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.724419195509512

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.30218058050956

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6121738272477764

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
34.37969999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-(+)-rhamnose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00005645c6f81f80>

HMDB0000849
     RDKit          3D
Rhamnose
 23 23  0  0  0  0  0  0  0  0999 V2000
   -2.0937   -0.8451    0.7146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9241   -0.8156   -0.2855 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0754   -1.5567    0.2492 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3484   -1.1192    0.0871 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7924   -1.0569   -1.2153 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3992    0.2997    0.6642 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7367    0.2433    1.8827 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6741    1.1369   -0.3538 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5649    2.4756    0.0857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6407    0.5542   -0.7175 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7933    0.7036   -2.1167 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0060   -0.6007    0.1246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9943   -0.0577    1.4743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2429   -1.8520    1.1192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3267   -1.3934   -1.1723 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0316   -1.7372    0.6908 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2730   -1.5689   -1.8564 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4204    0.6280    0.8496 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3863    0.0269    2.6045 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3479    1.1934   -1.2499 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5813    2.5262    1.0700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4307    1.2460   -0.2951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1791    1.5696   -2.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  6
  4 16  1  0
  5 17  1  0
  6 18  1  1
  7 19  1  0
  8 20  1  6
  9 21  1  0
 10 22  1  1
 11 23  1  0
M  END
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PDB for #<Metabolite:0x00005645c6f81f80>

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Untitled Document-1                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0      -1.334   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   1.540   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -2.667   2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000  -2.310   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       2.667  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -2.667  -0.770   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       2.667   2.310   0.000  0.00  0.00           O+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3   10                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    1                                                       
CONECT    7    1                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    2                                                            
CONECT   11    5                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for #<Metabolite:0x00005645c6f81f80>

COMPND    HMDB0000849
HETATM    1  C1  UNL     1      -2.094  -0.845   0.715  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.924  -0.816  -0.285  1.00  0.00           C  
HETATM    3  O1  UNL     1       0.075  -1.557   0.249  1.00  0.00           O  
HETATM    4  C3  UNL     1       1.348  -1.119   0.087  1.00  0.00           C  
HETATM    5  O2  UNL     1       1.792  -1.057  -1.215  1.00  0.00           O  
HETATM    6  C4  UNL     1       1.399   0.300   0.664  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.737   0.243   1.883  1.00  0.00           O  
HETATM    8  C5  UNL     1       0.674   1.137  -0.354  1.00  0.00           C  
HETATM    9  O4  UNL     1       0.565   2.476   0.086  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.641   0.554  -0.718  1.00  0.00           C  
HETATM   11  O5  UNL     1      -0.793   0.704  -2.117  1.00  0.00           O  
HETATM   12  H1  UNL     1      -3.006  -0.601   0.125  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.994  -0.058   1.474  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.243  -1.852   1.119  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.327  -1.393  -1.172  1.00  0.00           H  
HETATM   16  H5  UNL     1       2.032  -1.737   0.691  1.00  0.00           H  
HETATM   17  H6  UNL     1       1.273  -1.569  -1.856  1.00  0.00           H  
HETATM   18  H7  UNL     1       2.420   0.628   0.850  1.00  0.00           H  
HETATM   19  H8  UNL     1       1.386   0.027   2.605  1.00  0.00           H  
HETATM   20  H9  UNL     1       1.348   1.193  -1.250  1.00  0.00           H  
HETATM   21  H10 UNL     1       0.581   2.526   1.070  1.00  0.00           H  
HETATM   22  H11 UNL     1      -1.431   1.246  -0.295  1.00  0.00           H  
HETATM   23  H12 UNL     1      -1.179   1.570  -2.354  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3   10   15
CONECT    3    4
CONECT    4    5    6   16
CONECT    5   17
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:0x00005645c6f81f80>

C[C@@H]1OC(O)[C@H](O)[C@H](O)[C@H]1O
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INCHI for #<Metabolite:0x00005645c6f81f80>

InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6?/m0/s1
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Synonyms
ValueSource
6-Deoxy-L-mannoseChEBI
L-(+)-RhamnoseChEBI
L-MannomethyloseChEBI
L-RhaChEBI
L-RhamnoseChEBI
L-RhamnopyranoseKegg
6-Deoxy-L(+)-mannoseHMDB
6-Deoxy-L-mannopyranoseHMDB
6-Deoxy-mannoseHMDB
6-DeoxyhexopyranoseHMDB
6-DeoxyhexoseHMDB
6-DeoxymannoseHMDB
IsodulcitHMDB
IsodulcitolHMDB
L(+)-RhamnoseHMDB
L(+)-Rhamnose monohydrateHMDB
L-(+)-Rhamnose 1-hydrateHMDB
L-(+)-Rhamnose hydrate = 6-deoxy-L-mannose monohydrateHMDB
L-(+)-Rhamnose monohydrateHMDB
L-Rhamnose for biochemistryHMDB
L-Rhamnose monohydrateHMDB
LocaoseHMDB
mono(6-Deoxy-b-L-mannopyranosyl) esterHMDB
mono(6-Deoxy-beta-L-mannopyranosyl) esterHMDB
p-(6-Deoxy-b-L-mannopyranosyl) esterHMDB
p-(6-Deoxy-beta-L-mannopyranosyl) esterHMDB
RhamnopyranoseHMDB
RhamnosemonohydrateHMDB
UDP-RhamnoseHMDB
Uridine 5-pyrophosphateHMDB
Uridine diphosphate rhamnoseHMDB
DeoxymannoseHMDB
Rhamnose, L isomerHMDB
Rhamnose, L-isomerHMDB
RhamnoseMeSH, HMDB
Molecular FormulaC6H12O5
Average Mass164.1565
Monoisotopic Mass164.068473494
IUPAC Name(3R,4R,5R,6S)-6-methyloxane-2,3,4,5-tetrol
Traditional NameL-(+)-rhamnose
CAS Registry Number3615-41-6
SMILES
C[C@@H]1OC(O)[C@H](O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6?/m0/s1
InChI KeySHZGCJCMOBCMKK-JFNONXLTSA-N