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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 07:05:02 UTC

Update Date

2021-09-26 23:01:22 UTC

HMDB ID

HMDB0250110

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-Chloro-2'-deoxyuridine

Description

5-Chloro-2'-deoxyuridine, also known as 2'-deoxy-5-chlorouridine, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Based on a literature review very few articles have been published on 5-Chloro-2'-deoxyuridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-chloro-2'-deoxyuridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Chloro-2'-deoxyuridine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0250110
     RDKit          3D
5-Chloro-2'-deoxyuridine
 28 29  0  0  0  0  0  0  0  0999 V2000
   -5.2102    0.3111    0.7808 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9857    0.1541    0.4628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4538   -1.0767    0.3391 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1658   -1.2374    0.0045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7374   -2.4282   -0.0926 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3399   -0.2151   -0.2241 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0236   -0.5025   -0.5768 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7330   -1.1766    0.5747 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0408   -0.3881    0.6414 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1216   -1.2391    0.8587 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0810    0.1929   -0.7577 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0616    1.3322   -0.8678 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8709    2.2979    0.0866 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7585    0.6266   -0.8969 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8377    1.0256   -0.1094 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1499    1.2221    0.2310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8389    2.8260    0.3911 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.0997   -1.8884    0.5180 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0251   -1.1540   -1.4845 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9980   -2.2058    0.2868 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1738   -1.1074    1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9859    0.4360    1.3532 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8689   -2.0027    1.4293 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2844   -0.6043   -1.4784 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9626    1.7720   -1.8808 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0807    0.9127   -0.8082 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9414    2.2518    0.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1928    1.8654   -0.2884 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
  6 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 14  7  1  0
  3 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 15 28  1  0
M  END


  Mrv1652309112109052D          

 17 18  0  0  0  0            999 V2000
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    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
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   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
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526   -3.9282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  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
  8 14  1  0  0  0  0
  3 15  1  0  0  0  0
 15 16  1  0  0  0  0
  2 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250110

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC1OC(CC1O)N1C=C(Cl)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H11ClN2O5/c10-4-2-12(9(16)11-8(4)15)7-1-5(14)6(3-13)17-7/h2,5-7,13-14H,1,3H2,(H,11,15,16)

> <INCHI_KEY>
NJCXGFKPQSFZIB-UHFFFAOYSA-N

> <FORMULA>
C9H11ClN2O5

> <MOLECULAR_WEIGHT>
262.65

> <EXACT_MASS>
262.0356492

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
23.323887683184285

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-chloro-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-0.90

> <JCHEM_LOGP>
-0.8538184286666664

> <ALOGPS_LOGS>
-0.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.907879189670556

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.372003373098185

> <JCHEM_PKA_STRONGEST_BASIC>
-2.978083593382732

> <JCHEM_POLAR_SURFACE_AREA>
99.10000000000001

> <JCHEM_REFRACTIVITY>
55.846199999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.42e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-chloro-2'-deoxyuridine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0250110
     RDKit          3D
5-Chloro-2'-deoxyuridine
 28 29  0  0  0  0  0  0  0  0999 V2000
   -5.2102    0.3111    0.7808 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9857    0.1541    0.4628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4538   -1.0767    0.3391 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1658   -1.2374    0.0045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7374   -2.4282   -0.0926 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3399   -0.2151   -0.2241 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0236   -0.5025   -0.5768 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7330   -1.1766    0.5747 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0408   -0.3881    0.6414 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1216   -1.2391    0.8587 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0810    0.1929   -0.7577 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0616    1.3322   -0.8678 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8709    2.2979    0.0866 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7585    0.6266   -0.8969 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8377    1.0256   -0.1094 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1499    1.2221    0.2310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8389    2.8260    0.3911 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.0997   -1.8884    0.5180 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0251   -1.1540   -1.4845 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9980   -2.2058    0.2868 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1738   -1.1074    1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9859    0.4360    1.3532 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8689   -2.0027    1.4293 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2844   -0.6043   -1.4784 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9626    1.7720   -1.8808 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0807    0.9127   -0.8082 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9414    2.2518    0.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1928    1.8654   -0.2884 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
  6 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 14  7  1  0
  3 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 15 28  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.088  -3.215   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+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   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   14 Cl   UNK     0      -1.334   2.310   0.000  0.00  0.00          Cl+0
HETATM   15  C   UNK     0      -0.342  -5.926   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.285  -7.333   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.009  -5.926   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3   17                                                  
CONECT    3    2    4   15                                                  
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11    6   13                                                  
CONECT   13   12                                                            
CONECT   14    8                                                            
CONECT   15    3   16                                                       
CONECT   16   15                                                            
CONECT   17    2                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0250110
HETATM    1  O1  UNL     1      -5.210   0.311   0.781  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.986   0.154   0.463  1.00  0.00           C  
HETATM    3  N1  UNL     1      -3.454  -1.077   0.339  1.00  0.00           N  
HETATM    4  C2  UNL     1      -2.166  -1.237   0.005  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.737  -2.428  -0.093  1.00  0.00           O  
HETATM    6  N2  UNL     1      -1.340  -0.215  -0.224  1.00  0.00           N  
HETATM    7  C3  UNL     1       0.024  -0.503  -0.577  1.00  0.00           C  
HETATM    8  C4  UNL     1       0.733  -1.177   0.575  1.00  0.00           C  
HETATM    9  C5  UNL     1       2.041  -0.388   0.641  1.00  0.00           C  
HETATM   10  O3  UNL     1       3.122  -1.239   0.859  1.00  0.00           O  
HETATM   11  C6  UNL     1       2.081   0.193  -0.758  1.00  0.00           C  
HETATM   12  C7  UNL     1       3.062   1.332  -0.868  1.00  0.00           C  
HETATM   13  O4  UNL     1       2.871   2.298   0.087  1.00  0.00           O  
HETATM   14  O5  UNL     1       0.759   0.627  -0.897  1.00  0.00           O  
HETATM   15  C8  UNL     1      -1.838   1.026  -0.109  1.00  0.00           C  
HETATM   16  C9  UNL     1      -3.150   1.222   0.231  1.00  0.00           C  
HETATM   17 CL1  UNL     1      -3.839   2.826   0.391  1.00  0.00          CL  
HETATM   18  H1  UNL     1      -4.100  -1.888   0.518  1.00  0.00           H  
HETATM   19  H2  UNL     1       0.025  -1.154  -1.485  1.00  0.00           H  
HETATM   20  H3  UNL     1       0.998  -2.206   0.287  1.00  0.00           H  
HETATM   21  H4  UNL     1       0.174  -1.107   1.523  1.00  0.00           H  
HETATM   22  H5  UNL     1       1.986   0.436   1.353  1.00  0.00           H  
HETATM   23  H6  UNL     1       2.869  -2.003   1.429  1.00  0.00           H  
HETATM   24  H7  UNL     1       2.284  -0.604  -1.478  1.00  0.00           H  
HETATM   25  H8  UNL     1       2.963   1.772  -1.881  1.00  0.00           H  
HETATM   26  H9  UNL     1       4.081   0.913  -0.808  1.00  0.00           H  
HETATM   27  H10 UNL     1       1.941   2.252   0.419  1.00  0.00           H  
HETATM   28  H11 UNL     1      -1.193   1.865  -0.288  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   16
CONECT    3    4   18
CONECT    4    5    5    6
CONECT    6    7   15
CONECT    7    8   14   19
CONECT    8    9   20   21
CONECT    9   10   11   22
CONECT   10   23
CONECT   11   12   14   24
CONECT   12   13   25   26
CONECT   13   27
CONECT   15   16   16   28
CONECT   16   17
END

HMDB0250110
     RDKit          3D
5-Chloro-2'-deoxyuridine
 28 29  0  0  0  0  0  0  0  0999 V2000
   -5.2102    0.3111    0.7808 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9857    0.1541    0.4628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4538   -1.0767    0.3391 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1658   -1.2374    0.0045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7374   -2.4282   -0.0926 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3399   -0.2151   -0.2241 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0236   -0.5025   -0.5768 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7330   -1.1766    0.5747 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0408   -0.3881    0.6414 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1216   -1.2391    0.8587 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0810    0.1929   -0.7577 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0616    1.3322   -0.8678 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8709    2.2979    0.0866 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7585    0.6266   -0.8969 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8377    1.0256   -0.1094 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1499    1.2221    0.2310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8389    2.8260    0.3911 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -4.0997   -1.8884    0.5180 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0251   -1.1540   -1.4845 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9980   -2.2058    0.2868 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1738   -1.1074    1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9859    0.4360    1.3532 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8689   -2.0027    1.4293 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2844   -0.6043   -1.4784 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9626    1.7720   -1.8808 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0807    0.9127   -0.8082 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9414    2.2518    0.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1928    1.8654   -0.2884 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
  6 15  1  0
 15 16  2  0
 16 17  1  0
 16  2  1  0
 14  7  1  0
  3 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  9 22  1  0
 10 23  1  0
 11 24  1  0
 12 25  1  0
 12 26  1  0
 13 27  1  0
 15 28  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
5-Chlorodeoxyuridine	MeSH
2'-Deoxy-5-chlorouridine	MeSH

Chemical Formula

C₉H₁₁ClN₂O₅

Average Molecular Weight

262.65

Monoisotopic Molecular Weight

262.0356492

IUPAC Name

5-chloro-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional Name

5-chloro-2'-deoxyuridine

CAS Registry Number

Not Available

SMILES

OCC1OC(CC1O)N1C=C(Cl)C(=O)NC1=O

InChI Identifier

InChI=1S/C9H11ClN2O5/c10-4-2-12(9(16)11-8(4)15)7-1-5(14)6(3-13)17-7/h2,5-7,13-14H,1,3H2,(H,11,15,16)

InChI Key

NJCXGFKPQSFZIB-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Halopyrimidine
Pyrimidone
Aryl chloride
Aryl halide
Hydropyrimidine
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Lactam
Urea
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

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	-0.9	ALOGPS
logP	-0.85	ChemAxon
logS	-0.69	ALOGPS
pKa (Strongest Acidic)	8.37	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	99.1 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.85 m³·mol⁻¹	ChemAxon
Polarizability	23.32 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
DeepCCS	[M+H]+	148.421	30932474
DeepCCS	[M-H]-	146.063	30932474
DeepCCS	[M-2H]-	180.929	30932474
DeepCCS	[M+Na]+	155.975	30932474
AllCCS	[M+H]+	155.9	32859911
AllCCS	[M+H-H2O]+	152.3	32859911
AllCCS	[M+NH4]+	159.4	32859911
AllCCS	[M+Na]+	160.3	32859911
AllCCS	[M-H]-	153.7	32859911
AllCCS	[M+Na-2H]-	153.8	32859911
AllCCS	[M+HCOO]-	154.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-Chloro-2'-deoxyuridine	OCC1OC(CC1O)N1C=C(Cl)C(=O)NC1=O	3430.3	Standard polar	33892256
5-Chloro-2'-deoxyuridine	OCC1OC(CC1O)N1C=C(Cl)C(=O)NC1=O	2304.6	Standard non polar	33892256
5-Chloro-2'-deoxyuridine	OCC1OC(CC1O)N1C=C(Cl)C(=O)NC1=O	2420.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-Chloro-2'-deoxyuridine,3TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C)C2=O)CC1O[Si](C)(C)C	2414.6	Semi standard non polar	33892256
5-Chloro-2'-deoxyuridine,3TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C)C2=O)CC1O[Si](C)(C)C	2470.9	Standard non polar	33892256
5-Chloro-2'-deoxyuridine,3TMS,isomer #1	C[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C)C2=O)CC1O[Si](C)(C)C	2686.8	Standard polar	33892256
5-Chloro-2'-deoxyuridine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1O[Si](C)(C)C(C)(C)C	3130.8	Semi standard non polar	33892256
5-Chloro-2'-deoxyuridine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1O[Si](C)(C)C(C)(C)C	3091.1	Standard non polar	33892256
5-Chloro-2'-deoxyuridine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1OC(N2C=C(Cl)C(=O)N([Si](C)(C)C(C)(C)C)C2=O)CC1O[Si](C)(C)C(C)(C)C	2965.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9140000000-4db1a75877e9cbb1811e	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-Chloro-2'-deoxyuridine GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-2'-deoxyuridine 10V, Positive-QTOF	splash10-03dj-0590000000-4bb8503cc96cfb733d42	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-2'-deoxyuridine 20V, Positive-QTOF	splash10-0002-2900000000-e1f2621b946f7e3df754	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-2'-deoxyuridine 40V, Positive-QTOF	splash10-0002-2900000000-0bf19767062d663ef39a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-2'-deoxyuridine 10V, Negative-QTOF	splash10-03dl-0290000000-110761e89e9a23341fbc	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-2'-deoxyuridine 20V, Negative-QTOF	splash10-0006-5920000000-fda5f39db03b6f3b85b5	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-Chloro-2'-deoxyuridine 40V, Negative-QTOF	splash10-0006-9200000000-9cc286929730daa884e4	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

311995

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

351382

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 5-Chloro-2'-deoxyuridine (HMDB0250110)

MOL for HMDB0250110 (5-Chloro-2'-deoxyuridine)

3D MOL for HMDB0250110 (5-Chloro-2'-deoxyuridine)

3D SDF for HMDB0250110 (5-Chloro-2'-deoxyuridine)

3D-SDF for HMDB0250110 (5-Chloro-2'-deoxyuridine)

PDB for HMDB0250110 (5-Chloro-2'-deoxyuridine)

3D PDB for HMDB0250110 (5-Chloro-2'-deoxyuridine)

SMILES for HMDB0250110 (5-Chloro-2'-deoxyuridine)

INCHI for HMDB0250110 (5-Chloro-2'-deoxyuridine)

Structure for HMDB0250110 (5-Chloro-2'-deoxyuridine)

3D Structure for HMDB0250110 (5-Chloro-2'-deoxyuridine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra