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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-24 20:27:58 UTC

Update Date

2021-09-24 20:27:58 UTC

HMDB ID

HMDB0304872

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Cedazuridine

Description

(4R)-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,4,5,6-tetrahydropyrimidine-2,4-diol belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Based on a literature review very few articles have been published on (4R)-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,4,5,6-tetrahydropyrimidine-2,4-diol.

Structure

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

HMDB0304872
     RDKit          3D
Cedazuridine
 32 33  0  0  0  0  0  0  0  0999 V2000
    1.3187    2.8119    0.3738 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6398    1.5891    0.5180 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9657    1.2552    0.9171 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5353    0.0223    0.4772 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2819    0.1827   -0.7072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5591   -1.0871    0.2692 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1753   -0.7598    0.7891 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7286    0.5188    0.2979 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4973    0.7908   -0.3606 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5578    0.6035    0.5305 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6014    0.0524   -0.1971 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5559   -0.7070    0.7026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0460    0.2288    1.6278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8801   -0.8913   -1.1571 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7164   -1.2588   -2.2054 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7808    0.0387   -1.5917 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2686   -0.5714   -2.1934 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3570    0.9001   -2.5288 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.5280    1.9058    1.5303 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2755   -0.3210    1.2424 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9131    0.9572   -0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8721   -2.0241    0.7770 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4522   -1.3619   -0.8125 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5329   -1.6069    0.6037 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2806   -0.6437    1.9074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5248    1.8934   -0.6065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1298    0.7870   -0.8393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0222   -1.5341    1.1730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4368   -1.0340    0.1133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3682    0.2538    2.3725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5504   -1.7448   -0.5533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3022   -1.9885   -1.8398 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
  8  2  1  0
 16  9  1  0
  3 19  1  0
  4 20  1  1
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  9 26  1  6
 11 27  1  6
 12 28  1  0
 12 29  1  0
 13 30  1  0
 14 31  1  1
 15 32  1  0
M  END


  Mrv1652309242122282D          

 18 19  0  0  1  0            999 V2000
    2.4324   -3.0882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3507   -2.0195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1353   -1.7646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3068   -0.9576    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0915   -0.7027    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6937   -0.4056    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9091   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2960   -0.1085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624   -0.6244    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.6244    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
  6 12  1  0  0  0  0
 12 13  2  0  0  0  0
  5 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 14 17  1  0  0  0  0
  3 17  1  0  0  0  0
 17 18  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0304872

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H]1O[C@@H](N2CC[C@@H](O)NC2=O)C(F)(F)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14F2N2O5/c10-9(11)6(16)4(3-14)18-7(9)13-2-1-5(15)12-8(13)17/h4-7,14-16H,1-3H2,(H,12,17)/t4-,5-,6-,7-/m1/s1

> <INCHI_KEY>
VUDZSIYXZUYWSC-DBRKOABJSA-N

> <FORMULA>
C9H14F2N2O5

> <MOLECULAR_WEIGHT>
268.217

> <EXACT_MASS>
268.087077885

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
22.706456310779394

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R)-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,3-diazinan-2-one

> <ALOGPS_LOGP>
-0.64

> <JCHEM_LOGP>
-1.4109009796666667

> <ALOGPS_LOGS>
-0.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.69037280910183

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.000571990556669

> <JCHEM_PKA_STRONGEST_BASIC>
-2.983177788597496

> <JCHEM_POLAR_SURFACE_AREA>
102.26

> <JCHEM_REFRACTIVITY>
51.7505

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.82e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R)-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,3-diazinan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0304872
     RDKit          3D
Cedazuridine
 32 33  0  0  0  0  0  0  0  0999 V2000
    1.3187    2.8119    0.3738 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6398    1.5891    0.5180 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9657    1.2552    0.9171 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5353    0.0223    0.4772 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2819    0.1827   -0.7072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5591   -1.0871    0.2692 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1753   -0.7598    0.7891 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7286    0.5188    0.2979 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4973    0.7908   -0.3606 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5578    0.6035    0.5305 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6014    0.0524   -0.1971 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5559   -0.7070    0.7026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0460    0.2288    1.6278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8801   -0.8913   -1.1571 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7164   -1.2588   -2.2054 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7808    0.0387   -1.5917 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2686   -0.5714   -2.1934 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3570    0.9001   -2.5288 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.5280    1.9058    1.5303 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2755   -0.3210    1.2424 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9131    0.9572   -0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8721   -2.0241    0.7770 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4522   -1.3619   -0.8125 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5329   -1.6069    0.6037 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2806   -0.6437    1.9074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5248    1.8934   -0.6065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1298    0.7870   -0.8393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0222   -1.5341    1.1730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4368   -1.0340    0.1133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3682    0.2538    2.3725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5504   -1.7448   -0.5533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3022   -1.9885   -1.8398 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
  8  2  1  0
 16  9  1  0
  3 19  1  0
  4 20  1  1
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  9 26  1  6
 11 27  1  6
 12 28  1  0
 12 29  1  0
 13 30  1  0
 14 31  1  1
 15 32  1  0
M  END

HEADER    PROTEIN                                 24-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-SEP-21         0                                  
HETATM    1  O   UNK     0       4.540  -5.765   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.009  -5.926   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.564  -4.680   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -1.377  -2.739   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -2.521  -3.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.986  -3.294   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.306  -1.788   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -5.771  -1.312   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0      -3.162  -0.757   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -1.697  -1.233   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.553  -0.202   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  F   UNK     0       0.303  -1.166   0.000  0.00  0.00           F+0
HETATM   16  F   UNK     0       2.364  -1.166   0.000  0.00  0.00           F+0
HETATM   17  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.044  -2.739   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   14                                                  
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11    6   13                                                  
CONECT   13   12                                                            
CONECT   14    5   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14    3   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0304872
HETATM    1  O1  UNL     1       1.319   2.812   0.374  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.640   1.589   0.518  1.00  0.00           C  
HETATM    3  N1  UNL     1       2.966   1.255   0.917  1.00  0.00           N  
HETATM    4  C2  UNL     1       3.535   0.022   0.477  1.00  0.00           C  
HETATM    5  O2  UNL     1       4.282   0.183  -0.707  1.00  0.00           O  
HETATM    6  C3  UNL     1       2.559  -1.087   0.269  1.00  0.00           C  
HETATM    7  C4  UNL     1       1.175  -0.760   0.789  1.00  0.00           C  
HETATM    8  N2  UNL     1       0.729   0.519   0.298  1.00  0.00           N  
HETATM    9  C5  UNL     1      -0.497   0.791  -0.361  1.00  0.00           C  
HETATM   10  O3  UNL     1      -1.558   0.604   0.531  1.00  0.00           O  
HETATM   11  C6  UNL     1      -2.601   0.052  -0.197  1.00  0.00           C  
HETATM   12  C7  UNL     1      -3.556  -0.707   0.703  1.00  0.00           C  
HETATM   13  O4  UNL     1      -4.046   0.229   1.628  1.00  0.00           O  
HETATM   14  C8  UNL     1      -1.880  -0.891  -1.157  1.00  0.00           C  
HETATM   15  O5  UNL     1      -2.716  -1.259  -2.205  1.00  0.00           O  
HETATM   16  C9  UNL     1      -0.781   0.039  -1.592  1.00  0.00           C  
HETATM   17  F1  UNL     1       0.269  -0.571  -2.193  1.00  0.00           F  
HETATM   18  F2  UNL     1      -1.357   0.900  -2.529  1.00  0.00           F  
HETATM   19  H1  UNL     1       3.528   1.906   1.530  1.00  0.00           H  
HETATM   20  H2  UNL     1       4.276  -0.321   1.242  1.00  0.00           H  
HETATM   21  H3  UNL     1       4.913   0.957  -0.630  1.00  0.00           H  
HETATM   22  H4  UNL     1       2.872  -2.024   0.777  1.00  0.00           H  
HETATM   23  H5  UNL     1       2.452  -1.362  -0.812  1.00  0.00           H  
HETATM   24  H6  UNL     1       0.533  -1.607   0.604  1.00  0.00           H  
HETATM   25  H7  UNL     1       1.281  -0.644   1.907  1.00  0.00           H  
HETATM   26  H8  UNL     1      -0.525   1.893  -0.606  1.00  0.00           H  
HETATM   27  H9  UNL     1      -3.130   0.787  -0.839  1.00  0.00           H  
HETATM   28  H10 UNL     1      -3.022  -1.534   1.173  1.00  0.00           H  
HETATM   29  H11 UNL     1      -4.437  -1.034   0.113  1.00  0.00           H  
HETATM   30  H12 UNL     1      -3.368   0.254   2.373  1.00  0.00           H  
HETATM   31  H13 UNL     1      -1.550  -1.745  -0.553  1.00  0.00           H  
HETATM   32  H14 UNL     1      -3.302  -1.988  -1.840  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4   19
CONECT    4    5    6   20
CONECT    5   21
CONECT    6    7   22   23
CONECT    7    8   24   25
CONECT    8    9
CONECT    9   10   16   26
CONECT   10   11
CONECT   11   12   14   27
CONECT   12   13   28   29
CONECT   13   30
CONECT   14   15   16   31
CONECT   15   32
CONECT   16   17   18
END

HMDB0304872
     RDKit          3D
Cedazuridine
 32 33  0  0  0  0  0  0  0  0999 V2000
    1.3187    2.8119    0.3738 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6398    1.5891    0.5180 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9657    1.2552    0.9171 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5353    0.0223    0.4772 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2819    0.1827   -0.7072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5591   -1.0871    0.2692 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1753   -0.7598    0.7891 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7286    0.5188    0.2979 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4973    0.7908   -0.3606 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5578    0.6035    0.5305 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6014    0.0524   -0.1971 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5559   -0.7070    0.7026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0460    0.2288    1.6278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8801   -0.8913   -1.1571 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7164   -1.2588   -2.2054 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7808    0.0387   -1.5917 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2686   -0.5714   -2.1934 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3570    0.9001   -2.5288 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.5280    1.9058    1.5303 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2755   -0.3210    1.2424 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9131    0.9572   -0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8721   -2.0241    0.7770 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4522   -1.3619   -0.8125 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5329   -1.6069    0.6037 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2806   -0.6437    1.9074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5248    1.8934   -0.6065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1298    0.7870   -0.8393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0222   -1.5341    1.1730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4368   -1.0340    0.1133 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3682    0.2538    2.3725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5504   -1.7448   -0.5533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3022   -1.9885   -1.8398 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
  8  2  1  0
 16  9  1  0
  3 19  1  0
  4 20  1  1
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  9 26  1  6
 11 27  1  6
 12 28  1  0
 12 29  1  0
 13 30  1  0
 14 31  1  1
 15 32  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(4R)-2'-Deoxy-2',2'-difluoro-3,4,5,6-tetrahydrouridine	MeSH

Chemical Formula

C₉H₁₄F₂N₂O₅

Average Molecular Weight

268.217

Monoisotopic Molecular Weight

268.087077885

IUPAC Name

(4R)-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,3-diazinan-2-one

Traditional Name

(4R)-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,3-diazinan-2-one

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](N2CC[C@@H](O)NC2=O)C(F)(F)[C@@H]1O

InChI Identifier

InChI=1S/C9H14F2N2O5/c10-9(11)6(16)4(3-14)18-7(9)13-2-1-5(15)12-8(13)17/h4-7,14-16H,1-3H2,(H,12,17)/t4-,5-,6-,7-/m1/s1

InChI Key

VUDZSIYXZUYWSC-DBRKOABJSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Pyrimidone
1,3-diazinane
Pyrimidine
Tetrahydrofuran
Urea
Secondary alcohol
Fluorohydrin
Halohydrin
Carbonic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Alkanolamine
Organic oxide
Organonitrogen compound
Organofluoride
Organohalogen compound
Organic nitrogen compound
Primary alcohol
Alcohol
Carbonyl group
Alkyl halide
Alkyl fluoride
Organopnictogen compound
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Not Available

Not Available

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	-0.64	ALOGPS
logP	-1.4	ChemAxon
logS	-0.17	ALOGPS
pKa (Strongest Acidic)	11	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	102.26 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	51.75 m³·mol⁻¹	ChemAxon
Polarizability	22.71 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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]+	159.196	32859911
AllCCS	[M+H-H2O]+	155.617	32859911
AllCCS	[M+Na]+	163.472	32859911
AllCCS	[M+NH4]+	162.517	32859911
AllCCS	[M-H]-	155.578	32859911
AllCCS	[M+Na-2H]-	155.48	32859911
AllCCS	[M+HCOO]-	155.477	32859911
DeepCCS	[M+H]+	155.148	30932474
DeepCCS	[M-H]-	152.752	30932474
DeepCCS	[M-2H]-	187.338	30932474
DeepCCS	[M+Na]+	161.876	30932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cedazuridine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2CC[C@@H](O[Si](C)(C)C)N([Si](C)(C)C)C2=O)C(F)(F)[C@@H]1O[Si](C)(C)C	2076.0	Semi standard non polar	33892256
Cedazuridine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2CC[C@@H](O[Si](C)(C)C)N([Si](C)(C)C)C2=O)C(F)(F)[C@@H]1O[Si](C)(C)C	2225.4	Standard non polar	33892256
Cedazuridine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2CC[C@@H](O[Si](C)(C)C)N([Si](C)(C)C)C2=O)C(F)(F)[C@@H]1O[Si](C)(C)C	2278.3	Standard polar	33892256
Cedazuridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CC[C@@H](O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C2=O)C(F)(F)[C@@H]1O[Si](C)(C)C(C)(C)C	2918.0	Semi standard non polar	33892256
Cedazuridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CC[C@@H](O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C2=O)C(F)(F)[C@@H]1O[Si](C)(C)C(C)(C)C	3061.3	Standard non polar	33892256
Cedazuridine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2CC[C@@H](O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C2=O)C(F)(F)[C@@H]1O[Si](C)(C)C(C)(C)C	2655.8	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 - Cedazuridine 10V, Positive-QTOF	splash10-014i-2090000000-5319df91b86ab9aa2531	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cedazuridine 20V, Positive-QTOF	splash10-014j-9770000000-4d3882061129d6ce934d	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cedazuridine 40V, Positive-QTOF	splash10-014j-7900000000-b9f5590366c87fc04114	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cedazuridine 10V, Negative-QTOF	splash10-014i-0190000000-49c94c908556ede4ca8a	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cedazuridine 20V, Negative-QTOF	splash10-00kf-9380000000-6cbd0600640bef26d5bf	2021-10-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cedazuridine 40V, Negative-QTOF	splash10-0006-9000000000-168797b689ed5e1307dc	2021-10-22	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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

34236147

KEGG Compound ID

Not Available

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

Not Available

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 Cedazuridine (HMDB0304872)

MOL for HMDB0304872 (Cedazuridine)

3D MOL for HMDB0304872 (Cedazuridine)

3D SDF for HMDB0304872 (Cedazuridine)

3D-SDF for HMDB0304872 (Cedazuridine)

PDB for HMDB0304872 (Cedazuridine)

3D PDB for HMDB0304872 (Cedazuridine)

SMILES for HMDB0304872 (Cedazuridine)

INCHI for HMDB0304872 (Cedazuridine)

Structure for HMDB0304872 (Cedazuridine)

3D Structure for HMDB0304872 (Cedazuridine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra