Showing metabocard for L-Rhamnulose (MMDBc0029806)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:42:29 UTC
Update Date2022-08-31 17:18:32 UTC
Metabolite IDMMDBc0029806
Metabolite Identification
Common NameL-Rhamnulose
DescriptionL-Rhamnulose is a breakdown product of L-rhamnose, which is ubiquitous and particularly abundant in some plants, such as buckthorn. Rhamnose is also one of the sugars regularly used to conduct the dual sugar permeability test. Rhamnose is fermented by some colonic bacteria into L-rhamnulose. Three bacterial (gut micrflora) enzymes are involved in Rhamnose degradation including rhaB (rhamulose kinase), rhaA (rhamnose isomerase), and rhaD (rhamnulose-1-phosphate aldolase). L-rhamnulose kinase catalyzes the transfer of the gamma-phosphate group from ATP to the 1-hydroxyl group of L-rhamnulose. E.coli are growing depending on L-rhamnose as a source of carbon and energy. (PMID: 40956 )
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007f91fde0a768>


  Mrv0541 02241200322D          

 11 10  0  0  1  0            999 V2000
   17.3743   -6.4078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.6598   -8.4704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8033   -7.2329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9454   -6.4078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5164   -7.2329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3743   -7.2329    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.6598   -7.6454    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.0889   -7.6454    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.0889   -8.4704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9454   -7.2329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2309   -7.6454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  6  0  0  0
  7  2  1  6  0  0  0
  8  3  1  1  0  0  0
  4 10  2  0  0  0  0
  5 11  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7 10  1  0  0  0  0
  8  9  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f91fde0a768>

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3D SDF for #<Metabolite:0x00007f91fde0a768>

  Mrv0541 02241200322D          

 11 10  0  0  1  0            999 V2000
   17.3743   -6.4078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.6598   -8.4704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8033   -7.2329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9454   -6.4078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5164   -7.2329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3743   -7.2329    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.6598   -7.6454    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.0889   -7.6454    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.0889   -8.4704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9454   -7.2329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2309   -7.6454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  6  0  0  0
  7  2  1  6  0  0  0
  8  3  1  1  0  0  0
  4 10  2  0  0  0  0
  5 11  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7 10  1  0  0  0  0
  8  9  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029806

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h3,5-8,10-11H,2H2,1H3/t3-,5+,6+/m0/s1

> <INCHI_KEY>
QZNPNKJXABGCRC-OTWZMJIISA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.1565

> <EXACT_MASS>
164.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
15.423736237215246

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4R,5S)-1,3,4,5-tetrahydroxyhexan-2-one

> <ALOGPS_LOGP>
-1.79

> <JCHEM_LOGP>
-2.2201219253333333

> <ALOGPS_LOGS>
0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.868998423237063

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.471629095473586

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0542936306726167

> <JCHEM_POLAR_SURFACE_AREA>
97.99

> <JCHEM_REFRACTIVITY>
36.0181

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.88e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-rhamnulose

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007f91fde0a768>
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PDB for #<Metabolite:0x00007f91fde0a768>
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      32.432 -11.961   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      31.098 -15.811   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      35.099 -13.501   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      29.765 -11.961   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      27.097 -13.501   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      32.432 -13.501   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      31.098 -14.271   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      33.766 -14.271   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      33.766 -15.811   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      29.765 -13.501   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      28.431 -14.271   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    7                                                            
CONECT    3    8                                                            
CONECT    4   10                                                            
CONECT    5   11                                                            
CONECT    6    1    7    8                                                  
CONECT    7    2    6   10                                                  
CONECT    8    3    6    9                                                  
CONECT    9    8                                                            
CONECT   10    4    7   11                                                  
CONECT   11    5   10                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for #<Metabolite:0x00007f91fde0a768>
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SMILES for #<Metabolite:0x00007f91fde0a768>
C[C@H](O)[C@@H](O)[C@H](O)C(=O)CO
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INCHI for #<Metabolite:0x00007f91fde0a768>
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h3,5-8,10-11H,2H2,1H3/t3-,5+,6+/m0/s1
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Synonyms
ValueSource
6-Deoxy-L-mannoseHMDB
6-Deoxy-L-sorboseHMDB
6-Deoxy-L-xylo-hex-2-uloseHMDB
L-MannomethyloseHMDB
L-RhamnoseHMDB
RhamnuloseHMDB
Molecular FormulaC6H12O5
Average Mass164.1565
Monoisotopic Mass164.068473494
IUPAC Name(3S,4R,5S)-1,3,4,5-tetrahydroxyhexan-2-one
Traditional NameL-rhamnulose
CAS Registry Number14807-05-7
SMILES
C[C@H](O)[C@@H](O)[C@H](O)C(=O)CO
InChI Identifier
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h3,5-8,10-11H,2H2,1H3/t3-,5+,6+/m0/s1
InChI KeyQZNPNKJXABGCRC-OTWZMJIISA-N