MiMeDB: Showing metabocard for CMP-3-Deoxy-D-manno-octulosonate (MMDBc0030052)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:52:07 UTC

Update Date

2022-08-31 17:39:16 UTC

Metabolite ID

MMDBc0030052

Metabolite Identification

Common Name

CMP-3-Deoxy-D-manno-octulosonate

Description

CMP-3-deoxy-D-manno-octulosonate is a member of the chemical class known as Pyrimidine Nucleotide Sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. CMP KDO is involved in the biosynthesis of lipopolysaccharides. CKS is a pharmaceutical target because CMP-KDO is used in the biosynthesis of lipopolysaccharides that are vital for Gram-negative bacteria. (PMID 11545592 ) E. coli KdtA (EcKdtA) is a bifunctional enzyme that transfers two KDO units from two CMP-KDO molecules to lipid IV(A). (PMID 20394418 )

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303102018232D          

 37 39  0  0  1  0            999 V2000
   11.4826   -2.0592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4826   -1.2342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1971   -2.4716    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.9116   -2.0592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9116   -1.2342    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.1971   -0.8217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1971   -3.2967    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.5297   -3.7817    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7847   -4.5662    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.6097   -4.5662    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.6263   -2.4716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0947   -5.2337    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7883   -6.2577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7883   -4.6077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7883   -5.4326    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.5029   -5.0202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2998   -5.2337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8646   -3.7817    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.6616   -3.5681    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1971    0.0033    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.5260   -6.1807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8116   -6.5933    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.8116   -7.4183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0970   -6.1807    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3824   -6.5933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8116   -4.9433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3824   -4.9433    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.3824   -4.1184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6680   -5.3559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9537   -4.9433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0970   -5.3559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.0970   -4.5308    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5260   -5.3559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.0739   -5.0202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5260   -4.5308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8116   -4.1184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2404   -4.1184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  1  1  0  0  0  0
  7  3  1  1  0  0  0
  3  4  1  0  0  0  0
  4 11  2  0  0  0  0
  4  5  1  0  0  0  0
  2  6  1  0  0  0  0
  5  6  2  0  0  0  0
  6 20  1  0  0  0  0
  7  8  1  0  0  0  0
  7 18  1  0  0  0  0
  8  9  1  0  0  0  0
 18 10  1  0  0  0  0
  9 17  1  1  0  0  0
  9 10  1  0  0  0  0
 10 12  1  6  0  0  0
 34 15  1  0  0  0  0
 15 13  2  0  0  0  0
 15 14  1  0  0  0  0
 15 16  1  0  0  0  0
 17 16  1  0  0  0  0
 18 19  1  6  0  0  0
 33 21  1  0  0  0  0
 33 26  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  1  0  0  0
 24 31  1  0  0  0  0
 31 26  1  0  0  0  0
 31 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 31 32  1  6  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
M  END


  Mrv1652303102018232D          

 37 39  0  0  1  0            999 V2000
   11.4826   -2.0592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4826   -1.2342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1971   -2.4716    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.9116   -2.0592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9116   -1.2342    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.1971   -0.8217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1971   -3.2967    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.5297   -3.7817    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7847   -4.5662    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.6097   -4.5662    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.6263   -2.4716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0947   -5.2337    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7883   -6.2577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7883   -4.6077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7883   -5.4326    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.5029   -5.0202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2998   -5.2337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8646   -3.7817    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.6616   -3.5681    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1971    0.0033    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.5260   -6.1807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8116   -6.5933    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.8116   -7.4183    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0970   -6.1807    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3824   -6.5933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8116   -4.9433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3824   -4.9433    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.3824   -4.1184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6680   -5.3559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9537   -4.9433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0970   -5.3559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.0970   -4.5308    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5260   -5.3559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.0739   -5.0202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5260   -4.5308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8116   -4.1184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2404   -4.1184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  3  1  1  0  0  0  0
  7  3  1  1  0  0  0
  3  4  1  0  0  0  0
  4 11  2  0  0  0  0
  4  5  1  0  0  0  0
  2  6  1  0  0  0  0
  5  6  2  0  0  0  0
  6 20  1  0  0  0  0
  7  8  1  0  0  0  0
  7 18  1  0  0  0  0
  8  9  1  0  0  0  0
 18 10  1  0  0  0  0
  9 17  1  1  0  0  0
  9 10  1  0  0  0  0
 10 12  1  6  0  0  0
 34 15  1  0  0  0  0
 15 13  2  0  0  0  0
 15 14  1  0  0  0  0
 15 16  1  0  0  0  0
 17 16  1  0  0  0  0
 18 19  1  6  0  0  0
 33 21  1  0  0  0  0
 33 26  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  1  0  0  0
 24 31  1  0  0  0  0
 31 26  1  0  0  0  0
 31 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 31 32  1  6  0  0  0
 33 34  1  6  0  0  0
 33 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030052

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O[C@@](C[C@@H](O)[C@H]1O)(OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)C(O)=O)[C@H](O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C17H26N3O15P/c18-9-1-2-20(16(29)19-9)14-12(26)11(25)8(33-14)5-32-36(30,31)35-17(15(27)28)3-6(22)10(24)13(34-17)7(23)4-21/h1-2,6-8,10-14,21-26H,3-5H2,(H,27,28)(H,30,31)(H2,18,19,29)/t6-,7-,8-,10-,11-,12-,13-,14-,17+/m1/s1

> <INCHI_KEY>
YWWJKULNWGRYAS-XKKDATLGSA-N

> <FORMULA>
C17H26N3O15P

> <MOLECULAR_WEIGHT>
543.3732

> <EXACT_MASS>
543.110153689

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
47.01526778802524

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R,5R,6R)-2-[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
-2.75

> <JCHEM_LOGP>
-4.823154998266714

> <ALOGPS_LOGS>
-1.04

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.897103776854346

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4815300715179833

> <JCHEM_PKA_STRONGEST_BASIC>
-0.21967637344987512

> <JCHEM_POLAR_SURFACE_AREA>
291.59

> <JCHEM_REFRACTIVITY>
108.35629999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.96e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4R,5R,6R)-2-({[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy)-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0      21.434  -3.844   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      21.434  -2.304   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      22.768  -4.614   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      24.102  -3.844   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      24.102  -2.304   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      22.768  -1.534   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.768  -6.154   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      21.522  -7.059   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      21.998  -8.524   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      23.538  -8.524   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      25.436  -4.614   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      24.443  -9.770   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      18.271 -11.681   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      18.271  -8.601   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0      18.271 -10.141   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0      19.605  -9.371   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      21.093  -9.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      24.014  -7.059   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      25.502  -6.660   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      22.768   0.006   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      15.915 -11.537   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.582 -12.307   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      14.582 -13.847   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      13.248 -11.537   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      11.914 -12.307   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      14.582  -9.227   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      11.914  -9.227   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      11.914  -7.688   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      10.580  -9.998   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       9.247  -9.227   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      13.248  -9.998   0.000  0.00  0.00           C+0
HETATM   32  H   UNK     0      13.248  -8.457   0.000  0.00  0.00           H+0
HETATM   33  C   UNK     0      15.915  -9.998   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      16.938  -9.371   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      15.915  -8.457   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      14.582  -7.688   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      17.249  -7.688   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1    7    4                                                  
CONECT    4    3   11    5                                                  
CONECT    5    4    6                                                       
CONECT    6    2    5   20                                                  
CONECT    7    3    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   17   10                                                  
CONECT   10   18    9   12                                                  
CONECT   11    4                                                            
CONECT   12   10                                                            
CONECT   13   15                                                            
CONECT   14   15                                                            
CONECT   15   34   13   14   16                                             
CONECT   16   15   17                                                       
CONECT   17    9   16                                                       
CONECT   18    7   10   19                                                  
CONECT   19   18                                                            
CONECT   20    6                                                            
CONECT   21   33   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   31                                                  
CONECT   25   24                                                            
CONECT   26   33   31                                                       
CONECT   27   31   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29                                                            
CONECT   31   24   26   27   32                                             
CONECT   32   31                                                            
CONECT   33   21   26   34   35                                             
CONECT   34   15   33                                                       
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   78    0
END

Synonyms

Value	Source
CMP-KDO	ChEBI
CMP-3-Deoxy-α-D-manno-octulosonic acid ⇥	Generator
CMP-3-Deoxy-D-manno-octulosonic acid	Generator

Molecular Formula

C₁₇H₂₆N₃O₁₅P

Average Mass

543.3732

Monoisotopic Mass

543.110153689

IUPAC Name

(2S,4R,5R,6R)-2-[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylic acid

Traditional Name

(2S,4R,5R,6R)-2-({[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy)-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O[C@@](C[C@@H](O)[C@H]1O)(OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)C(O)=O)[C@H](O)CO

InChI Identifier

InChI=1S/C17H26N3O15P/c18-9-1-2-20(16(29)19-9)14-12(26)11(25)8(33-14)5-32-36(30,31)35-17(15(27)28)3-6(22)10(24)13(34-17)7(23)4-21/h1-2,6-8,10-14,21-26H,3-5H2,(H,27,28)(H,30,31)(H2,18,19,29)/t6-,7-,8-,10-,11-,12-,13-,14-,17+/m1/s1

InChI Key

YWWJKULNWGRYAS-XKKDATLGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

1,2-diols

Alternative Parents

Substituents

Secondary alcohol
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

3-[(5S,6R)-5,6-dihydroxycyclohexa-1,3-dienyl]acrylic acid (CHEBI:61462 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	49.6 g/L	ALOGPS
logP	-2.8	ALOGPS
logP	-4.8	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-0.22	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	291.59 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	108.36 m³·mol⁻¹	ChemAxon
Polarizability	47.02 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0912010000-c95ca105a90c9bee40f6	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-2901000000-f1f2e070390b27d5be4c	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-6910000000-1ee99630fbd08166a369	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-022c-3623890000-d177a6c58bcdec474c6e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0i6r-8903000000-995189481426d066ebff	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0201-9300000000-312ab44de18da7b89d88	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0006954	CMP-3-Deoxy-D-manno-octulosonate	Cytidine monophosphate	Not Available	3-deoxy-D-manno-octulosonic acid transferase III (LPS core biosynthesis)	VMH	30371894
MMDBr0007284	CMP-3-Deoxy-D-manno-octulosonate	Cytidine monophosphate	Not Available	3-deoxy-D-manno-octulosonic acid transferase	VMH	30371894
MMDBr0018383	Cytidine triphosphate	Pyrophosphate	3-deoxy-manno-octulosonate cytidylyltransferase	Transfer of a cytidylyl group	PathBank	31602464
MMDBr0018384	CMP-3-Deoxy-D-manno-octulosonate	Hydrogen Ion	3-deoxy-D-manno-octulosonic acid transferase	Transfer of 3-deoxy-D-manno-octulosonic acid	PathBank	31602464
MMDBr0018385	CMP-3-Deoxy-D-manno-octulosonate	Hydrogen Ion	3-deoxy-D-manno-octulosonic acid transferase	Transfer of 3-deoxy-D-manno-octulosonic acid	PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	172	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	22	Pig ; Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	88	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	116	Human feces; Human appendix biopsy; Human ; Human gastric fluid; Human saliva; Human subgingival plaque; Human supragingival plaque; Human stool; Human urine	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

CMP-KDO

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46873830

PDB ID

Not Available

ChEBI ID

18014

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for CMP-3-Deoxy-D-manno-octulosonate (MMDBc0030052)

MOL for #<Metabolite:0x00007f5a9c483430>

3D MOL for #<Metabolite:0x00007f5a9c483430>

3D SDF for #<Metabolite:0x00007f5a9c483430>

3D-SDF for #<Metabolite:0x00007f5a9c483430>

PDB for #<Metabolite:0x00007f5a9c483430>

3D PDB for #<Metabolite:0x00007f5a9c483430>

SMILES for #<Metabolite:0x00007f5a9c483430>

INCHI for #<Metabolite:0x00007f5a9c483430>

Structure for #<Metabolite:0x00007f5a9c483430>

3D Structure for #<Metabolite:0x00007f5a9c483430>