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Showing metabocard for 2-keto-3-deoxy-L-rhamnonate (HMDB0304074)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:56:22 UTC
Update Date2021-09-24 06:56:22 UTC
HMDB IDHMDB0304074
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-keto-3-deoxy-L-rhamnonate
Description2-keto-3-deoxy-l-rhamnonate, also known as kdr or 2-dehydro-3,6-dideoxy-L-mannonate, belongs to medium-chain keto acids and derivatives class of compounds. Those are keto acids with a 6 to 12 carbon atoms long side chain. 2-keto-3-deoxy-l-rhamnonate is soluble (in water) and a weakly acidic compound (based on its pKa). 2-keto-3-deoxy-l-rhamnonate can be found in a number of food items such as red beetroot, evergreen huckleberry, winter squash, and pepper (c. pubescens), which makes 2-keto-3-deoxy-l-rhamnonate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304074 (2-keto-3-deoxy-L-rhamnonate)

  Mrv1533007131514082D          

 13 12  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  1  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
    4.6184    1.8414    0.0000 C   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
    2.4750    0.6039    0.0000 O   0  0  0  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
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  6  5  1  0  0  0  0
  3  7  1  6  0  0  0
  4  8  1  1  0  0  0
  9  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  6  2  0  0  0  0
  3 12  1  6  0  0  0
  4 13  1  1  0  0  0
M  CHG  1  10  -1
M  END
Download

3D MOL for HMDB0304074 (2-keto-3-deoxy-L-rhamnonate)

HMDB0304074
     RDKit          3D
2-keto-3-deoxy-L-rhamnonate
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.1146    0.6865   -0.3645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3012   -0.5120   -0.8022 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0985   -1.6560   -0.7581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1121   -0.7372    0.1080 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4648   -0.9695    1.4173 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8710    0.4164   -0.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0109    0.1432    0.9081 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0594   -0.8920    1.6049 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1123    1.1160    0.9914 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0887    2.1574    0.3066 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1912    0.9046    1.8217 O   0  0  0  0  0  1  0  0  0  0  0  0
   -3.1796    0.5413   -0.6286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7759    1.6183   -0.8539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0488    0.8656    0.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9177   -0.3465   -1.8193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7123   -1.5625    0.0129 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4169   -1.6407   -0.3063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6264   -1.9236    1.5756 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2596    0.4364   -1.0606 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3417    1.3542    0.2414 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
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
  9 11  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  6
  5 18  1  0
  6 19  1  0
  6 20  1  0
M  CHG  1  11  -1
M  END
Download

3D SDF for HMDB0304074 (2-keto-3-deoxy-L-rhamnonate)

  Mrv1533007131514082D          

 13 12  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  1  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
    4.6184    1.8414    0.0000 C   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
    2.4750    0.6039    0.0000 O   0  0  0  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
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  6  5  1  0  0  0  0
  3  7  1  6  0  0  0
  4  8  1  1  0  0  0
  9  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  6  2  0  0  0  0
  3 12  1  6  0  0  0
  4 13  1  1  0  0  0
M  CHG  1  10  -1
M  END
> <DATABASE_ID>
HMDB0304074

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O5/c1-3(7)4(8)2-5(9)6(10)11/h3-4,7-8H,2H2,1H3,(H,10,11)/p-1/t3-,4+/m0/s1

> <INCHI_KEY>
FRIWJYNKZPJVRL-IUYQGCFVSA-M

> <FORMULA>
C6H9O5

> <MOLECULAR_WEIGHT>
161.134

> <EXACT_MASS>
161.04554697

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.181948737963035

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5S)-4,5-dihydroxy-2-oxohexanoate

> <ALOGPS_LOGP>
-1.22

> <JCHEM_LOGP>
-0.7281212736666668

> <ALOGPS_LOGS>
0.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.893889380196693

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.0645523555521614

> <JCHEM_PKA_STRONGEST_BASIC>
-3.017945905375046

> <JCHEM_POLAR_SURFACE_AREA>
97.66

> <JCHEM_REFRACTIVITY>
45.6097

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-dehydro-3-deoxy-L-rhamnonate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304074 (2-keto-3-deoxy-L-rhamnonate)

HMDB0304074
     RDKit          3D
2-keto-3-deoxy-L-rhamnonate
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.1146    0.6865   -0.3645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3012   -0.5120   -0.8022 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0985   -1.6560   -0.7581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1121   -0.7372    0.1080 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4648   -0.9695    1.4173 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8710    0.4164   -0.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0109    0.1432    0.9081 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0594   -0.8920    1.6049 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1123    1.1160    0.9914 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0887    2.1574    0.3066 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1912    0.9046    1.8217 O   0  0  0  0  0  1  0  0  0  0  0  0
   -3.1796    0.5413   -0.6286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7759    1.6183   -0.8539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0488    0.8656    0.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9177   -0.3465   -1.8193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7123   -1.5625    0.0129 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4169   -1.6407   -0.3063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6264   -1.9236    1.5756 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2596    0.4364   -1.0606 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3417    1.3542    0.2414 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
  4  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
  9 11  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  6
  5 18  1  0
  6 19  1  0
  6 20  1  0
M  CHG  1  11  -1
M  END
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PDB for HMDB0304074 (2-keto-3-deoxy-L-rhamnonate)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       4.620   4.207   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       5.954   1.897   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    4    5                                                       
CONECT    3    1    4    7   12                                             
CONECT    4    2    3    8   13                                             
CONECT    5    2    6    9                                                  
CONECT    6    5   10   11                                                  
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    3                                                            
CONECT   13    4                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for HMDB0304074 (2-keto-3-deoxy-L-rhamnonate)

COMPND    HMDB0304074
HETATM    1  C1  UNL     1      -2.115   0.687  -0.364  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.301  -0.512  -0.802  1.00  0.00           C  
HETATM    3  O1  UNL     1      -2.099  -1.656  -0.758  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.112  -0.737   0.108  1.00  0.00           C  
HETATM    5  O2  UNL     1      -0.465  -0.970   1.417  1.00  0.00           O  
HETATM    6  C4  UNL     1       0.871   0.416  -0.001  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.011   0.143   0.908  1.00  0.00           C  
HETATM    8  O3  UNL     1       2.059  -0.892   1.605  1.00  0.00           O  
HETATM    9  C6  UNL     1       3.112   1.116   0.991  1.00  0.00           C  
HETATM   10  O4  UNL     1       3.089   2.157   0.307  1.00  0.00           O  
HETATM   11  O5  UNL     1       4.191   0.905   1.822  1.00  0.00           O1-
HETATM   12  H1  UNL     1      -3.180   0.541  -0.629  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.776   1.618  -0.854  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.049   0.866   0.734  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.918  -0.346  -1.819  1.00  0.00           H  
HETATM   16  H5  UNL     1      -2.712  -1.562   0.013  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.417  -1.641  -0.306  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.626  -1.924   1.576  1.00  0.00           H  
HETATM   19  H8  UNL     1       1.260   0.436  -1.061  1.00  0.00           H  
HETATM   20  H9  UNL     1       0.342   1.354   0.241  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4   15
CONECT    3   16
CONECT    4    5    6   17
CONECT    5   18
CONECT    6    7   19   20
CONECT    7    8    8    9
CONECT    9   10   10   11
END
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SMILES for HMDB0304074 (2-keto-3-deoxy-L-rhamnonate)

[H][C@@](C)(O)[C@]([H])(O)CC(=O)C([O-])=O
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INCHI for HMDB0304074 (2-keto-3-deoxy-L-rhamnonate)

InChI=1S/C6H10O5/c1-3(7)4(8)2-5(9)6(10)11/h3-4,7-8H,2H2,1H3,(H,10,11)/p-1/t3-,4+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Dehydro-3-deoxy-L-rhamnonate anionChEBI
2-Dehydro-3-deoxy-L-rhamnonate(1-)ChEBI
2-Dehydro-3-deoxy-L-rhamnonic acid anionGenerator
2-Dehydro-3-deoxy-L-rhamnonic acid(1-)Generator
2-Dehydro-3-deoxy-L-rhamnonic acidGenerator
2-Keto-3-deoxy-L-rhamnonic acidGenerator
Chemical FormulaC6H9O5
Average Molecular Weight161.134
Monoisotopic Molecular Weight161.04554697
IUPAC Name(4R,5S)-4,5-dihydroxy-2-oxohexanoate
Traditional Name2-dehydro-3-deoxy-L-rhamnonate
CAS Registry NumberNot Available
SMILES
[H][C@@](C)(O)[C@]([H])(O)CC(=O)C([O-])=O
InChI Identifier
InChI=1S/C6H10O5/c1-3(7)4(8)2-5(9)6(10)11/h3-4,7-8H,2H2,1H3,(H,10,11)/p-1/t3-,4+/m0/s1
InChI KeyFRIWJYNKZPJVRL-IUYQGCFVSA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassMedium-chain keto acids and derivatives
Direct ParentMedium-chain keto acids and derivatives
Alternative Parents
Substituents
  • Medium-chain keto acid
  • Alpha-keto acid
  • Beta-hydroxy ketone
  • 1,2-diol
  • Ketone
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Alcohol
  • Carbonyl group
  • Organic oxide
  • Organic oxygen compound
  • Organooxygen compound
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-keto-3-deoxy-L-rhamnonate 10V, Negative-QTOFsplash10-0006-4900000000-f5de63a8818661bad9e02019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-keto-3-deoxy-L-rhamnonate 20V, Negative-QTOFsplash10-00y0-9200000000-4bdcb6f3f08609462c2d2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-keto-3-deoxy-L-rhamnonate 40V, Negative-QTOFsplash10-00dl-9000000000-7efc926d60d895e310572019-02-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030341
KNApSAcK IDNot Available
Chemspider ID26331139
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID58371
Food Biomarker OntologyNot Available
VMH IDNot Available
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References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available