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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-24 07:23:22 UTC

Update Date

2021-09-24 07:23:22 UTC

HMDB ID

HMDB0304125

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-deoxy-D-manno-octulosonate

Description

3-deoxy-d-manno-octulosonate, also known as kdo or 2-dehydro-3-deoxy-D-octonate, belongs to sugar acids and derivatives class of compounds. Those are compounds containing a saccharide unit which bears a carboxylic acid group. 3-deoxy-d-manno-octulosonate is soluble (in water) and a moderately acidic compound (based on its pKa). 3-deoxy-d-manno-octulosonate can be found in a number of food items such as peppermint, okra, horseradish tree, and hazelnut, which makes 3-deoxy-d-manno-octulosonate a potential biomarker for the consumption of these food products. 3-deoxy-d-manno-octulosonate may be a unique E.coli metabolite.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0304125
     RDKit          3D
3-deoxy-D-manno-octulosonate
 30 29  0  0  0  0  0  0  0  0999 V2000
    4.8467    0.9965   -0.2453 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5781   -0.2158   -0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5926   -1.1328   -0.4062 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2211   -0.6665   -0.1088 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9655   -1.9001   -0.1205 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1630    0.3604    0.0518 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7852   -0.2679    0.1942 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7918   -1.0871    1.3160 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1898    0.8694    0.3231 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1379    1.6311   -0.8218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5994    0.4157    0.5652 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7645   -0.3538    1.6860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0991   -0.2648   -0.6924 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9071    0.5599   -1.7983 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5777   -0.5500   -0.5692 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2376    0.6635   -0.4018 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7871   -1.7544    0.3909 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1370    0.9400   -0.9015 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3524    0.9838    0.9272 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -0.9101   -0.6823 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4652   -1.9981    1.1083 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1311    1.4622    1.2258 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4508    2.4131   -0.7112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2186    1.3341    0.6922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6043   -0.1082    2.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5307   -1.2023   -0.9049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3528    1.4306   -1.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8887   -1.0270   -1.5287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8101   -1.2337    0.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8976    0.6123    0.3429 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  3 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  6
  8 21  1  0
  9 22  1  1
 10 23  1  0
 11 24  1  1
 12 25  1  0
 13 26  1  6
 14 27  1  0
 15 28  1  0
 15 29  1  0
 16 30  1  0
M  END


  Mrv0541 10231212542D          

 20 19  0  0  0  0            999 V2000
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    1.7309    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.9684    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.9684    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    1.7309    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  1  0  0  0  0
  9  2  1  0  0  0  0
  3 10  1  1  0  0  0
 11  4  2  0  0  0  0
  5 12  1  1  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
 15  8  1  0  0  0  0
 16  8  2  0  0  0  0
  3 17  1  1  0  0  0
  5 18  1  1  0  0  0
  6 19  1  6  0  0  0
  7 20  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0304125

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H14O8/c9-2-5(12)7(14)6(13)3(10)1-4(11)8(15)16/h3,5-7,9-10,12-14H,1-2H2,(H,15,16)/t3-,5-,6-,7-/m1/s1

> <INCHI_KEY>
KYQCXUMVJGMDNG-SHUUEZRQSA-N

> <FORMULA>
C8H14O8

> <MOLECULAR_WEIGHT>
238.192

> <EXACT_MASS>
238.068867424

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
20.910612612472292

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5R,6R,7R)-4,5,6,7,8-pentahydroxy-2-oxooctanoic acid

> <ALOGPS_LOGP>
-2.54

> <JCHEM_LOGP>
-3.0357011243333334

> <ALOGPS_LOGS>
-0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.630062785724625

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9038228877924785

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9742108660118767

> <JCHEM_POLAR_SURFACE_AREA>
155.52

> <JCHEM_REFRACTIVITY>
48.241299999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.49e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-deoxy-D-manno-octulosonate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0304125
     RDKit          3D
3-deoxy-D-manno-octulosonate
 30 29  0  0  0  0  0  0  0  0999 V2000
    4.8467    0.9965   -0.2453 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5781   -0.2158   -0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5926   -1.1328   -0.4062 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2211   -0.6665   -0.1088 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9655   -1.9001   -0.1205 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1630    0.3604    0.0518 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7852   -0.2679    0.1942 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7918   -1.0871    1.3160 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1898    0.8694    0.3231 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1379    1.6311   -0.8218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5994    0.4157    0.5652 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7645   -0.3538    1.6860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0991   -0.2648   -0.6924 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9071    0.5599   -1.7983 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5777   -0.5500   -0.5692 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2376    0.6635   -0.4018 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7871   -1.7544    0.3909 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1370    0.9400   -0.9015 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3524    0.9838    0.9272 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -0.9101   -0.6823 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4652   -1.9981    1.1083 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1311    1.4622    1.2258 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4508    2.4131   -0.7112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2186    1.3341    0.6922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6043   -0.1082    2.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5307   -1.2023   -0.9049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3528    1.4306   -1.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8887   -1.0270   -1.5287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8101   -1.2337    0.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8976    0.6123    0.3429 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  3 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  6
  8 21  1  0
  9 22  1  1
 10 23  1  0
 11 24  1  1
 12 25  1  0
 13 26  1  6
 14 27  1  0
 15 28  1  0
 15 29  1  0
 16 30  1  0
M  END

HEADER    PROTEIN                                 23-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    5    9                                                       
CONECT    3    1    6   10   17                                             
CONECT    4    1    8   11                                                  
CONECT    5    2    7   12   18                                             
CONECT    6    3    7   13   19                                             
CONECT    7    5    6   14   20                                             
CONECT    8    4   15   16                                                  
CONECT    9    2                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
CONECT   12    5                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    8                                                            
CONECT   16    8                                                            
CONECT   17    3                                                            
CONECT   18    5                                                            
CONECT   19    6                                                            
CONECT   20    7                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

COMPND    HMDB0304125
HETATM    1  O1  UNL     1       4.847   0.997  -0.245  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.578  -0.216  -0.255  1.00  0.00           C  
HETATM    3  O2  UNL     1       5.593  -1.133  -0.406  1.00  0.00           O  
HETATM    4  C2  UNL     1       3.221  -0.667  -0.109  1.00  0.00           C  
HETATM    5  O3  UNL     1       2.965  -1.900  -0.120  1.00  0.00           O  
HETATM    6  C3  UNL     1       2.163   0.360   0.052  1.00  0.00           C  
HETATM    7  C4  UNL     1       0.785  -0.268   0.194  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.792  -1.087   1.316  1.00  0.00           O  
HETATM    9  C5  UNL     1      -0.190   0.869   0.323  1.00  0.00           C  
HETATM   10  O5  UNL     1      -0.138   1.631  -0.822  1.00  0.00           O  
HETATM   11  C6  UNL     1      -1.599   0.416   0.565  1.00  0.00           C  
HETATM   12  O6  UNL     1      -1.765  -0.354   1.686  1.00  0.00           O  
HETATM   13  C7  UNL     1      -2.099  -0.265  -0.692  1.00  0.00           C  
HETATM   14  O7  UNL     1      -1.907   0.560  -1.798  1.00  0.00           O  
HETATM   15  C8  UNL     1      -3.578  -0.550  -0.569  1.00  0.00           C  
HETATM   16  O8  UNL     1      -4.238   0.663  -0.402  1.00  0.00           O  
HETATM   17  H1  UNL     1       5.787  -1.754   0.391  1.00  0.00           H  
HETATM   18  H2  UNL     1       2.137   0.940  -0.901  1.00  0.00           H  
HETATM   19  H3  UNL     1       2.352   0.984   0.927  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.548  -0.910  -0.682  1.00  0.00           H  
HETATM   21  H5  UNL     1       0.465  -1.998   1.108  1.00  0.00           H  
HETATM   22  H6  UNL     1       0.131   1.462   1.226  1.00  0.00           H  
HETATM   23  H7  UNL     1       0.451   2.413  -0.711  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.219   1.334   0.692  1.00  0.00           H  
HETATM   25  H9  UNL     1      -2.604  -0.108   2.168  1.00  0.00           H  
HETATM   26  H10 UNL     1      -1.531  -1.202  -0.905  1.00  0.00           H  
HETATM   27  H11 UNL     1      -2.353   1.431  -1.572  1.00  0.00           H  
HETATM   28  H12 UNL     1      -3.889  -1.027  -1.529  1.00  0.00           H  
HETATM   29  H13 UNL     1      -3.810  -1.234   0.259  1.00  0.00           H  
HETATM   30  H14 UNL     1      -4.898   0.612   0.343  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   17
CONECT    4    5    5    6
CONECT    6    7   18   19
CONECT    7    8    9   20
CONECT    8   21
CONECT    9   10   11   22
CONECT   10   23
CONECT   11   12   13   24
CONECT   12   25
CONECT   13   14   15   26
CONECT   14   27
CONECT   15   16   28   29
CONECT   16   30
END

HMDB0304125
     RDKit          3D
3-deoxy-D-manno-octulosonate
 30 29  0  0  0  0  0  0  0  0999 V2000
    4.8467    0.9965   -0.2453 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5781   -0.2158   -0.2546 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5926   -1.1328   -0.4062 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2211   -0.6665   -0.1088 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9655   -1.9001   -0.1205 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1630    0.3604    0.0518 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7852   -0.2679    0.1942 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7918   -1.0871    1.3160 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1898    0.8694    0.3231 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1379    1.6311   -0.8218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5994    0.4157    0.5652 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7645   -0.3538    1.6860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0991   -0.2648   -0.6924 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9071    0.5599   -1.7983 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5777   -0.5500   -0.5692 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2376    0.6635   -0.4018 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7871   -1.7544    0.3909 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1370    0.9400   -0.9015 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3524    0.9838    0.9272 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -0.9101   -0.6823 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4652   -1.9981    1.1083 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1311    1.4622    1.2258 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4508    2.4131   -0.7112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2186    1.3341    0.6922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6043   -0.1082    2.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5307   -1.2023   -0.9049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3528    1.4306   -1.5717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8887   -1.0270   -1.5287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8101   -1.2337    0.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8976    0.6123    0.3429 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
  3 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  6
  8 21  1  0
  9 22  1  1
 10 23  1  0
 11 24  1  1
 12 25  1  0
 13 26  1  6
 14 27  1  0
 15 28  1  0
 15 29  1  0
 16 30  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-Dehydro-3-deoxy-D-octonate	ChEBI
3-Deoxy-D-manno-2-octulosonate	ChEBI
3-Deoxy-D-manno-2-octulosonic acid	ChEBI
3-Deoxy-D-manno-octulosonate	ChEBI
3-Deoxyoctulosonic acid	ChEBI
KDO	ChEBI
Ketodeoxyoctonate	Kegg
2-Dehydro-3-deoxy-D-octonic acid	Generator
3-Deoxy-D-manno-octulosonic acid	Generator
3-Deoxyoctulosonate	Generator
Ketodeoxyoctonic acid	Generator
Keto-3-deoxy-D-manno-octulosonate	Generator
3-Deoxy-D-manno-oct-2-ulopyranosonic acid	MeSH
3-Deoxy-manno-oct-2-ulopyranosonic acid	MeSH
oligo-alpha(2,8)-3-Deoxy-D-manno-2-octulosonic acid	MeSH
kdo Sugar acid	MeSH

Chemical Formula

C₈H₁₄O₈

Average Molecular Weight

238.192

Monoisotopic Molecular Weight

238.068867424

IUPAC Name

(4R,5R,6R,7R)-4,5,6,7,8-pentahydroxy-2-oxooctanoic acid

Traditional Name

3-deoxy-D-manno-octulosonate

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)[C@@]([H])(O)[C@]([H])(O)[C@]([H])(O)CC(=O)C(O)=O

InChI Identifier

InChI=1S/C8H14O8/c9-2-5(12)7(14)6(13)3(10)1-4(11)8(15)16/h3,5-7,9-10,12-14H,1-2H2,(H,15,16)/t3-,5-,6-,7-/m1/s1

InChI Key

KYQCXUMVJGMDNG-SHUUEZRQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Octose monosaccharide
Medium-chain keto acid
Sugar acid
Alpha-keto acid
Beta-hydroxy ketone
Monosaccharide
Keto acid
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Alcohol
Carbonyl group
Primary alcohol
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

3-deoxy-D-manno-octulosonic acid (CHEBI:32817 )

Ontology

Not Available

Herbs and Spices (FooDB: FOOD00866)

Nut

Almond (FooDB: FOOD00148)
Brazil nut (FooDB: FOOD00024)
Cashew nut (FooDB: FOOD00011)
Chestnut (FooDB: FOOD00045)
Hazelnut (FooDB: FOOD00376)
Peanut (FooDB: FOOD00016)
Pecan nut (FooDB: FOOD00044)
Pine nut (FooDB: FOOD00138)
Pistachio (FooDB: FOOD00140)
Walnut (FooDB: FOOD00608)
Acorn (FooDB: FOOD00282)
Beech nut (FooDB: FOOD00299)
Butternut (FooDB: FOOD00316)
Chinese chestnut (FooDB: FOOD00331)
European chestnut (FooDB: FOOD00363)
Hickory nut (FooDB: FOOD00377)
Macadamia nut (FooDB: FOOD00525)
Mixed nuts (FooDB: FOOD00771)
Pili nut (FooDB: FOOD00432)
Colorado pinyon (FooDB: FOOD00433)
Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)
Japanese chestnut (FooDB: FOOD00385)
Common hazelnut (FooDB: FOOD00062)
Macadamia nut (M. tetraphylla) (FooDB: FOOD00225)
Japanese walnut (FooDB: FOOD00240)
Nuts (FooDB: FOOD00869)

Fruit

Pome

Drupe

Apricot (FooDB: FOOD00144)
Prunus (Cherry, Plum) (FooDB: FOOD00143)
Nectarine (FooDB: FOOD00229)
Peach (FooDB: FOOD00149)
European plum (FooDB: FOOD00147)
Sour cherry (FooDB: FOOD00146)
Sweet cherry (FooDB: FOOD00145)
Common chokecherry (FooDB: FOOD00562)
Peach (var.) (FooDB: FOOD00230)

Tropical fruit

Berry

Bilberry (FooDB: FOOD00193)
Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Elderberry (FooDB: FOOD00358)
Gooseberry (FooDB: FOOD00157)
Grape (FooDB: FOOD00369)
Lingonberry (FooDB: FOOD00194)
Loganberry (FooDB: FOOD00400)
Strawberry (FooDB: FOOD00083)
Boysenberry (FooDB: FOOD00542)
American cranberry (FooDB: FOOD00192)
Common grape (FooDB: FOOD00204)
Strawberry guava (FooDB: FOOD00482)
Black mulberry (FooDB: FOOD00117)
Red raspberry (FooDB: FOOD00162)
Muscadine grape (FooDB: FOOD00203)
Salmonberry (FooDB: FOOD00456)
Alaska blueberry (FooDB: FOOD00380)
Sea-buckthornberry (FooDB: FOOD00087)
Black elderberry (FooDB: FOOD00166)
Black crowberry (FooDB: FOOD00075)
Black huckleberry (FooDB: FOOD00084)
Mulberry (FooDB: FOOD00116)
Black chokeberry (FooDB: FOOD00136)
Cloudberry (FooDB: FOOD00161)
Black raspberry (FooDB: FOOD00163)
Rowanberry (FooDB: FOOD00176)
Lowbush blueberry (FooDB: FOOD00189)
Sparkleberry (FooDB: FOOD00190)
Highbush blueberry (FooDB: FOOD00191)
Arctic blackberry (FooDB: FOOD00207)
Bayberry (FooDB: FOOD00209)
Elliott's blueberry (FooDB: FOOD00210)
Canada blueberry (FooDB: FOOD00211)
Bog bilberry (FooDB: FOOD00212)
Buffalo currant (FooDB: FOOD00213)
European cranberry (FooDB: FOOD00217)
Deerberry (FooDB: FOOD00218)
Cascade huckleberry (FooDB: FOOD00220)
Oval-leaf huckleberry (FooDB: FOOD00221)
Evergreen huckleberry (FooDB: FOOD00222)
Red huckleberry (FooDB: FOOD00223)
Summer grape (FooDB: FOOD00227)
Fox grape (FooDB: FOOD00228)
Half-highbush blueberry (FooDB: FOOD00248)
Jostaberry (FooDB: FOOD00257)
Sweet rowanberry (FooDB: FOOD00265)
Skunk currant (FooDB: FOOD00267)
Squashberry (FooDB: FOOD00344)
Ohelo berry (FooDB: FOOD00419)
Chinese bayberry (FooDB: FOOD00852)
Saskatoon berry (FooDB: FOOD00884)
Nanking cherry (FooDB: FOOD00885)

Other fruit

Date (FooDB: FOOD00135)
Fig (FooDB: FOOD00081)
Jujube (FooDB: FOOD00388)

Citrus

Grapefruit (FooDB: FOOD00256)
Lemon (FooDB: FOOD00054)
Lime (FooDB: FOOD00053)
Sweet orange (FooDB: FOOD00057)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Persian lime (FooDB: FOOD00543)
Pummelo (FooDB: FOOD00055)
Grapefruit/Pummelo hybrid (FooDB: FOOD00255)
Citrus (FooDB: FOOD00859)

Fruits (FooDB: FOOD00871)

Vegetable

Shoot vegetable

Fruit vegetable

Eggplant (FooDB: FOOD00174)
Avocado (FooDB: FOOD00130)
Groundcherry (FooDB: FOOD00371)
Olive (FooDB: FOOD00121)
Pepper (FooDB: FOOD00040)
Garden tomato (FooDB: FOOD00171)
Mexican groundcherry (FooDB: FOOD00491)
Green bell pepper (FooDB: FOOD00877)
Yellow bell pepper (FooDB: FOOD00878)
Red bell pepper (FooDB: FOOD00880)
Italian sweet red pepper (FooDB: FOOD00881)
Garden tomato (var.) (FooDB: FOOD00173)
Cherry tomato (FooDB: FOOD00172)
Pepper (C. baccatum) (FooDB: FOOD00231)
Pepper (C. chinense) (FooDB: FOOD00232)
Pepper (Capsicum) (FooDB: FOOD00233)
Pepper (C. frutescens) (FooDB: FOOD00428)
Pepper (C. pubescens) (FooDB: FOOD00849)
Orange bell pepper (FooDB: FOOD00879)

Root vegetable

Cabbage

Leaf vegetable

Lettuce (FooDB: FOOD00095)
Swiss chard (FooDB: FOOD00237)
Garden cress (FooDB: FOOD00099)
Endive (FooDB: FOOD00048)
Spinach (FooDB: FOOD00178)
Common beet (FooDB: FOOD00025)
Garland chrysanthemum (FooDB: FOOD00333)
Jute (FooDB: FOOD00389)
Lambsquarters (FooDB: FOOD00394)
New Zealand spinach (FooDB: FOOD00415)
Swamp cabbage (FooDB: FOOD00091)
Rocket salad (ssp.) (FooDB: FOOD00077)
Yautia (FooDB: FOOD00510)
Romaine lettuce (FooDB: FOOD00888)
Rocket salad (FooDB: FOOD00244)
Chicory leaves (FooDB: FOOD00250)
Corn salad (FooDB: FOOD00340)
Malabar spinach (FooDB: FOOD00404)
Ostrich fern (FooDB: FOOD00556)
Green vegetables (FooDB: FOOD00872)

Mushroom

Tuber

Onion-family vegetable

Leek (FooDB: FOOD00007)
Allium (FooDB: FOOD00005)
Wild leek (FooDB: FOOD00396)
Shallot (FooDB: FOOD00243)
Garden onion (FooDB: FOOD00006)
Garden onion (var.) (FooDB: FOOD00226)
Onion-family vegetables (FooDB: FOOD00855)
Green onion (FooDB: FOOD00963)
Red onion (FooDB: FOOD00962)

Other vegetable

Okra (FooDB: FOOD00420)
Horseradish tree (FooDB: FOOD00379)
Sacred lotus (FooDB: FOOD00402)
Tree fern (FooDB: FOOD00797)
Chinese water chestnut (FooDB: FOOD00332)
Nopal (FooDB: FOOD00416)
Carob (FooDB: FOOD00321)
Agave (FooDB: FOOD00563)
Narrowleaf cattail (FooDB: FOOD00564)
Giant butterbur (FooDB: FOOD00314)
Sesbania flower (FooDB: FOOD00469)

Stalk vegetable

Brassica

Brassicas (FooDB: FOOD00857)

Cereal and cereal product

Other bread

Other bread (FooDB: FOOD00269)

Cereal

Cereal product

Dough

Sourdough (FooDB: FOOD00275)

Cereals and cereal products (FooDB: FOOD00858)

Soy

Soy bean (FooDB: FOOD00085)

Soy product

Other soy product (FooDB: FOOD00271)

Pulse

Bean

Lentil

Lentils (FooDB: FOOD00098)

Pea

Other pulse

White lupine (FooDB: FOOD00403)
Lupine (FooDB: FOOD00104)

Pulses (FooDB: FOOD00867)

Abalone (FooDB: FOOD00279)
Conch (FooDB: FOOD00611)

Gourd

Chayote (FooDB: FOOD00325)
Cucumber (FooDB: FOOD00065)
Muskmelon (FooDB: FOOD00064)
Cucurbita (FooDB: FOOD00066)
Watermelon (FooDB: FOOD00052)
Bitter gourd (FooDB: FOOD00115)
Calabash (FooDB: FOOD00318)
Towel gourd (FooDB: FOOD00492)
Winter squash (FooDB: FOOD00283)
Butternut squash (FooDB: FOOD00317)
Wax gourd (FooDB: FOOD00499)
Green zucchini (FooDB: FOOD00875)
Yellow zucchini (FooDB: FOOD00876)
Japanese pumpkin (FooDB: FOOD00886)
Sunburst squash (pattypan squash) (FooDB: FOOD00874)
Tinda (FooDB: FOOD00559)
Horned melon (FooDB: FOOD00761)

Tea

Herbal tea

Greenthread tea (FooDB: FOOD00820)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Lipopolysaccharide Biosynthesis (PathBank: SMP0000851)
Lipopolysaccharide Biosynthesis II (PathBank: SMP0001919)
Lipopolysaccharide Biosynthesis III (PathBank: SMP0002071)

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.5	ALOGPS
logP	-3	ChemAxon
logS	-0.57	ALOGPS
pKa (Strongest Acidic)	2.9	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	155.52 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	48.24 m³·mol⁻¹	ChemAxon
Polarizability	20.91 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	152.527	32859911
AllCCS	[M+H-H2O]+	149.085	32859911
AllCCS	[M+Na]+	156.64	32859911
AllCCS	[M+NH4]+	155.722	32859911
AllCCS	[M-H]-	145.892	32859911
AllCCS	[M+Na-2H]-	146.398	32859911
AllCCS	[M+HCOO]-	147.052	32859911
DeepCCS	[M+H]+	153.492	30932474
DeepCCS	[M-H]-	151.096	30932474
DeepCCS	[M-2H]-	185.576	30932474
DeepCCS	[M+Na]+	160.024	30932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-deoxy-D-manno-octulosonate,7TMS,isomer #1	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	2328.3	Semi standard non polar	33892256
3-deoxy-D-manno-octulosonate,7TMS,isomer #1	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	2323.7	Standard non polar	33892256
3-deoxy-D-manno-octulosonate,7TMS,isomer #1	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	2348.3	Standard polar	33892256
3-deoxy-D-manno-octulosonate,5TBDMS,isomer #19	CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3336.7	Semi standard non polar	33892256
3-deoxy-D-manno-octulosonate,5TBDMS,isomer #19	CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2969.6	Standard non polar	33892256
3-deoxy-D-manno-octulosonate,5TBDMS,isomer #19	CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2988.9	Standard polar	33892256
3-deoxy-D-manno-octulosonate,5TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H](CC(=O)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3277.4	Semi standard non polar	33892256
3-deoxy-D-manno-octulosonate,5TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H](CC(=O)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3094.7	Standard non polar	33892256
3-deoxy-D-manno-octulosonate,5TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H](CC(=O)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2902.0	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 10V, Positive-QTOF	splash10-00dr-2590000000-c8365537f240bd17c092	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 20V, Positive-QTOF	splash10-03k9-9420000000-7c62b05f704b94da4ed3	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 40V, Positive-QTOF	splash10-074m-9200000000-1f9f181dd8666e848b35	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 10V, Negative-QTOF	splash10-002s-7920000000-37d0c8b357cc7b9ec55b	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 20V, Negative-QTOF	splash10-000i-9400000000-35aeded87e6a52f7d9d0	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 40V, Negative-QTOF	splash10-06rf-9300000000-6953cb4ddc486610ea71	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 10V, Negative-QTOF	splash10-000i-7950000000-446f15944c20db6ad35a	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 20V, Negative-QTOF	splash10-00di-9200000000-b31695a3aea736e88e0a	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 40V, Negative-QTOF	splash10-0006-9000000000-e15cd12fb8544fac2178	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 10V, Positive-QTOF	splash10-0fl9-1960000000-51fe300eedf94aa4af65	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 20V, Positive-QTOF	splash10-0uk9-9700000000-ffaef97a55c72fe661fc	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-deoxy-D-manno-octulosonate 40V, Positive-QTOF	splash10-00fu-9100000000-08188961ad90e14c8a7e	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030420

KNApSAcK ID

Not Available

Chemspider ID

106511

KEGG Compound ID

C01187

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

32817

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 3-deoxy-D-manno-octulosonate (HMDB0304125)

MOL for HMDB0304125 (3-deoxy-D-manno-octulosonate)

3D MOL for HMDB0304125 (3-deoxy-D-manno-octulosonate)

3D SDF for HMDB0304125 (3-deoxy-D-manno-octulosonate)

3D-SDF for HMDB0304125 (3-deoxy-D-manno-octulosonate)

PDB for HMDB0304125 (3-deoxy-D-manno-octulosonate)

3D PDB for HMDB0304125 (3-deoxy-D-manno-octulosonate)

SMILES for HMDB0304125 (3-deoxy-D-manno-octulosonate)

INCHI for HMDB0304125 (3-deoxy-D-manno-octulosonate)

Structure for HMDB0304125 (3-deoxy-D-manno-octulosonate)

3D Structure for HMDB0304125 (3-deoxy-D-manno-octulosonate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra