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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 11:08:57 UTC

Update Date

2021-09-26 23:05:56 UTC

HMDB ID

HMDB0252984

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate

Description

Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate belongs to the class of organic compounds known as benzoic acid esters. These are ester derivatives of benzoic acid. Based on a literature review very few articles have been published on Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate. This compound has been identified in human blood as reported by (PMID: 31557052 ). Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate 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

  Mrv1652309112113092D          

 37 40  0  0  0  0            999 V2000
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   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 33 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
M  END

HMDB0252984
     RDKit          3D
Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl...
 62 65  0  0  0  0  0  0  0  0999 V2000
    7.1076   -3.9927    2.0836 C   0  0  0  0  0  0  0  0  0  0  0  0
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 37  6  1  0
 26 10  1  0
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M  END

  Mrv1652309112113092D          

 37 40  0  0  0  0            999 V2000
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 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0252984

> <DATABASE_NAME>
hmdb

> <SMILES>
CCOC(=O)C1=CC=C(C=C1)N1C=C(CC2=CN=C(OCC)N=C2)C(=O)N=C1SCC1=CC=C(F)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C27H25FN4O4S/c1-3-35-25(34)20-7-11-23(12-8-20)32-16-21(13-19-14-29-26(30-15-19)36-4-2)24(33)31-27(32)37-17-18-5-9-22(28)10-6-18/h5-12,14-16H,3-4,13,17H2,1-2H3

> <INCHI_KEY>
PTPNCCWOTBBVJR-UHFFFAOYSA-N

> <FORMULA>
C27H25FN4O4S

> <MOLECULAR_WEIGHT>
520.58

> <EXACT_MASS>
520.158054638

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
53.270443830088084

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
ethyl 4-{5-[(2-ethoxypyrimidin-5-yl)methyl]-2-{[(4-fluorophenyl)methyl]sulfanyl}-4-oxo-1,4-dihydropyrimidin-1-yl}benzoate

> <ALOGPS_LOGP>
4.48

> <JCHEM_LOGP>
5.503918701

> <ALOGPS_LOGS>
-5.51

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
0.6822052885889941

> <JCHEM_POLAR_SURFACE_AREA>
93.98

> <JCHEM_REFRACTIVITY>
141.38950000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.62e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ethyl 4-{5-[(2-ethoxypyrimidin-5-yl)methyl]-2-{[(4-fluorophenyl)methyl]sulfanyl}-4-oxopyrimidin-1-yl}benzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0252984
     RDKit          3D
Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl...
 62 65  0  0  0  0  0  0  0  0999 V2000
    7.1076   -3.9927    2.0836 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0433   -4.8349    1.4015 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0666   -3.9431    0.8980 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2941   -2.9530   -0.0202 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4553   -2.8015   -0.4712 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1814   -2.0916   -0.4581 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9167   -2.2760    0.0538 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8411   -1.5048   -0.3138 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -0.5060   -1.2326 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9210    0.3232   -1.6308 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1842   -0.1852   -2.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2360    0.6243   -2.5653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4604    0.0863   -3.1852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6159   -0.0219   -2.2884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5506    0.9758   -2.1922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5856    0.8258   -1.3529 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7226   -0.2738   -0.6120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8257   -0.3431    0.2301 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0117   -1.4920    1.0340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2744   -1.2773    1.8393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8116   -1.2618   -0.6974 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7502   -1.1821   -1.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0856    1.9683   -2.3212 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9486    2.8201   -2.5996 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0468    2.4530   -1.7464 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0402    1.6201   -1.4071 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5204    2.3154   -0.6521 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.3369    2.3386    1.1502 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2681    3.2926    1.4970 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6260    4.6058    1.7332 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7075    5.5790    2.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6242    5.2174    2.1613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5799    6.1460    2.4875 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9909    3.9129    1.9280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0612    2.9391    1.5955 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2927   -0.3000   -1.7611 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3612   -1.0855   -1.3790 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7546   -3.4864    1.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6850   -4.5815    2.8254 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5461   -3.1929    2.6308 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5385   -5.4050    2.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4570   -5.4814    0.6268 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7987   -3.0778    0.7811 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8634   -1.6849    0.1152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2441   -1.2713   -2.3662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2350   -0.9273   -3.6148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7375    0.7118   -4.0636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4974    1.9042   -2.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1322   -2.4017    0.3914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1159   -1.6468    1.6308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0599   -0.8698    1.1524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5826   -2.2612    2.2601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1053   -0.6176    2.7092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0402   -1.9952   -1.5563 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3058    2.5840    1.6255 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0795    1.2982    1.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6648    4.9396    1.6691 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9881    6.6149    2.2509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0331    3.5897    1.9951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3525    1.9277    1.4157 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3793    0.5063   -2.4827 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3305   -0.8932   -1.8160 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 17 21  1  0
 21 22  2  0
 12 23  1  0
 23 24  2  0
 23 25  1  0
 25 26  2  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  2  0
 30 31  1  0
 31 32  2  0
 32 33  1  0
 32 34  1  0
 34 35  2  0
  9 36  1  0
 36 37  2  0
 37  6  1  0
 26 10  1  0
 35 29  1  0
 22 14  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  2 41  1  0
  2 42  1  0
  7 43  1  0
  8 44  1  0
 11 45  1  0
 13 46  1  0
 13 47  1  0
 15 48  1  0
 19 49  1  0
 19 50  1  0
 20 51  1  0
 20 52  1  0
 20 53  1  0
 22 54  1  0
 28 55  1  0
 28 56  1  0
 30 57  1  0
 31 58  1  0
 34 59  1  0
 35 60  1  0
 36 61  1  0
 37 62  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      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -2.667  -3.080   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -5.335  -3.080   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       0.000  -7.700   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -1.334 -10.010   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -4.001 -10.010   0.000  0.00  0.00           O+0
HETATM   18  S   UNK     0       1.334 -10.010   0.000  0.00  0.00           S+0
HETATM   19  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   26  F   UNK     0       8.002 -12.320   0.000  0.00  0.00           F+0
HETATM   27  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
CONECT   10    7   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   27                                                  
CONECT   14   13   15   18                                                  
CONECT   15   14   16                                                       
CONECT   16   15   11   17                                                  
CONECT   17   16                                                            
CONECT   18   14   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24   20                                                       
CONECT   26   23                                                            
CONECT   27   13   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   33                                                  
CONECT   31   30   32                                                       
CONECT   32   31   27                                                       
CONECT   33   30   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

COMPND    HMDB0252984
HETATM    1  C1  UNL     1       7.108  -3.993   2.084  1.00  0.00           C  
HETATM    2  C2  UNL     1       6.043  -4.835   1.401  1.00  0.00           C  
HETATM    3  O1  UNL     1       5.067  -3.943   0.898  1.00  0.00           O  
HETATM    4  C3  UNL     1       5.294  -2.953  -0.020  1.00  0.00           C  
HETATM    5  O2  UNL     1       6.455  -2.801  -0.471  1.00  0.00           O  
HETATM    6  C4  UNL     1       4.181  -2.092  -0.458  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.917  -2.276   0.054  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.841  -1.505  -0.314  1.00  0.00           C  
HETATM    9  C7  UNL     1       2.037  -0.506  -1.233  1.00  0.00           C  
HETATM   10  N1  UNL     1       0.921   0.323  -1.631  1.00  0.00           N  
HETATM   11  C8  UNL     1      -0.184  -0.185  -2.197  1.00  0.00           C  
HETATM   12  C9  UNL     1      -1.236   0.624  -2.565  1.00  0.00           C  
HETATM   13  C10 UNL     1      -2.460   0.086  -3.185  1.00  0.00           C  
HETATM   14  C11 UNL     1      -3.616  -0.022  -2.288  1.00  0.00           C  
HETATM   15  C12 UNL     1      -4.551   0.976  -2.192  1.00  0.00           C  
HETATM   16  N2  UNL     1      -5.586   0.826  -1.353  1.00  0.00           N  
HETATM   17  C13 UNL     1      -5.723  -0.274  -0.612  1.00  0.00           C  
HETATM   18  O3  UNL     1      -6.826  -0.343   0.230  1.00  0.00           O  
HETATM   19  C14 UNL     1      -7.012  -1.492   1.034  1.00  0.00           C  
HETATM   20  C15 UNL     1      -8.274  -1.277   1.839  1.00  0.00           C  
HETATM   21  N3  UNL     1      -4.812  -1.262  -0.697  1.00  0.00           N  
HETATM   22  C16 UNL     1      -3.750  -1.182  -1.514  1.00  0.00           C  
HETATM   23  C17 UNL     1      -1.086   1.968  -2.321  1.00  0.00           C  
HETATM   24  O4  UNL     1      -1.949   2.820  -2.600  1.00  0.00           O  
HETATM   25  N4  UNL     1       0.047   2.453  -1.746  1.00  0.00           N  
HETATM   26  C18 UNL     1       1.040   1.620  -1.407  1.00  0.00           C  
HETATM   27  S1  UNL     1       2.520   2.315  -0.652  1.00  0.00           S  
HETATM   28  C19 UNL     1       2.337   2.339   1.150  1.00  0.00           C  
HETATM   29  C20 UNL     1       1.268   3.293   1.497  1.00  0.00           C  
HETATM   30  C21 UNL     1       1.626   4.606   1.733  1.00  0.00           C  
HETATM   31  C22 UNL     1       0.708   5.579   2.064  1.00  0.00           C  
HETATM   32  C23 UNL     1      -0.624   5.217   2.161  1.00  0.00           C  
HETATM   33  F1  UNL     1      -1.580   6.146   2.487  1.00  0.00           F  
HETATM   34  C24 UNL     1      -0.991   3.913   1.928  1.00  0.00           C  
HETATM   35  C25 UNL     1      -0.061   2.939   1.596  1.00  0.00           C  
HETATM   36  C26 UNL     1       3.293  -0.300  -1.761  1.00  0.00           C  
HETATM   37  C27 UNL     1       4.361  -1.086  -1.379  1.00  0.00           C  
HETATM   38  H1  UNL     1       7.755  -3.486   1.340  1.00  0.00           H  
HETATM   39  H2  UNL     1       7.685  -4.581   2.825  1.00  0.00           H  
HETATM   40  H3  UNL     1       6.546  -3.193   2.631  1.00  0.00           H  
HETATM   41  H4  UNL     1       5.539  -5.405   2.222  1.00  0.00           H  
HETATM   42  H5  UNL     1       6.457  -5.481   0.627  1.00  0.00           H  
HETATM   43  H6  UNL     1       2.799  -3.078   0.781  1.00  0.00           H  
HETATM   44  H7  UNL     1       0.863  -1.685   0.115  1.00  0.00           H  
HETATM   45  H8  UNL     1      -0.244  -1.271  -2.366  1.00  0.00           H  
HETATM   46  H9  UNL     1      -2.235  -0.927  -3.615  1.00  0.00           H  
HETATM   47  H10 UNL     1      -2.738   0.712  -4.064  1.00  0.00           H  
HETATM   48  H11 UNL     1      -4.497   1.904  -2.780  1.00  0.00           H  
HETATM   49  H12 UNL     1      -7.132  -2.402   0.391  1.00  0.00           H  
HETATM   50  H13 UNL     1      -6.116  -1.647   1.631  1.00  0.00           H  
HETATM   51  H14 UNL     1      -9.060  -0.870   1.152  1.00  0.00           H  
HETATM   52  H15 UNL     1      -8.583  -2.261   2.260  1.00  0.00           H  
HETATM   53  H16 UNL     1      -8.105  -0.618   2.709  1.00  0.00           H  
HETATM   54  H17 UNL     1      -3.040  -1.995  -1.556  1.00  0.00           H  
HETATM   55  H18 UNL     1       3.306   2.584   1.625  1.00  0.00           H  
HETATM   56  H19 UNL     1       2.080   1.298   1.478  1.00  0.00           H  
HETATM   57  H20 UNL     1       2.665   4.940   1.669  1.00  0.00           H  
HETATM   58  H21 UNL     1       0.988   6.615   2.251  1.00  0.00           H  
HETATM   59  H22 UNL     1      -2.033   3.590   1.995  1.00  0.00           H  
HETATM   60  H23 UNL     1      -0.352   1.928   1.416  1.00  0.00           H  
HETATM   61  H24 UNL     1       3.379   0.506  -2.483  1.00  0.00           H  
HETATM   62  H25 UNL     1       5.330  -0.893  -1.816  1.00  0.00           H  
CONECT    1    2   38   39   40
CONECT    2    3   41   42
CONECT    3    4
CONECT    4    5    5    6
CONECT    6    7    7   37
CONECT    7    8   43
CONECT    8    9    9   44
CONECT    9   10   36
CONECT   10   11   26
CONECT   11   12   12   45
CONECT   12   13   23
CONECT   13   14   46   47
CONECT   14   15   15   22
CONECT   15   16   48
CONECT   16   17   17
CONECT   17   18   21
CONECT   18   19
CONECT   19   20   49   50
CONECT   20   51   52   53
CONECT   21   22   22
CONECT   22   54
CONECT   23   24   24   25
CONECT   25   26   26
CONECT   26   27
CONECT   27   28
CONECT   28   29   55   56
CONECT   29   30   30   35
CONECT   30   31   57
CONECT   31   32   32   58
CONECT   32   33   34
CONECT   34   35   35   59
CONECT   35   60
CONECT   36   37   37   61
CONECT   37   62
END

HMDB0252984
     RDKit          3D
Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl...
 62 65  0  0  0  0  0  0  0  0999 V2000
    7.1076   -3.9927    2.0836 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0433   -4.8349    1.4015 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0666   -3.9431    0.8980 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2941   -2.9530   -0.0202 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4553   -2.8015   -0.4712 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1814   -2.0916   -0.4581 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9167   -2.2760    0.0538 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8411   -1.5048   -0.3138 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -0.5060   -1.2326 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9210    0.3232   -1.6308 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1842   -0.1852   -2.1966 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2360    0.6243   -2.5653 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4604    0.0863   -3.1852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6159   -0.0219   -2.2884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5506    0.9758   -2.1922 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5856    0.8258   -1.3529 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7226   -0.2738   -0.6120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8257   -0.3431    0.2301 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0117   -1.4920    1.0340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2744   -1.2773    1.8393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8116   -1.2618   -0.6974 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7502   -1.1821   -1.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0856    1.9683   -2.3212 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9486    2.8201   -2.5996 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0468    2.4530   -1.7464 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0402    1.6201   -1.4071 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5204    2.3154   -0.6521 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.3369    2.3386    1.1502 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2681    3.2926    1.4970 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6260    4.6058    1.7332 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7075    5.5790    2.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6242    5.2174    2.1613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5799    6.1460    2.4875 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9909    3.9129    1.9280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0612    2.9391    1.5955 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2927   -0.3000   -1.7611 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3612   -1.0855   -1.3790 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7546   -3.4864    1.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6850   -4.5815    2.8254 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5461   -3.1929    2.6308 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5385   -5.4050    2.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4570   -5.4814    0.6268 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7987   -3.0778    0.7811 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8634   -1.6849    0.1152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2441   -1.2713   -2.3662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2350   -0.9273   -3.6148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7375    0.7118   -4.0636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4974    1.9042   -2.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1322   -2.4017    0.3914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1159   -1.6468    1.6308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0599   -0.8698    1.1524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5826   -2.2612    2.2601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1053   -0.6176    2.7092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0402   -1.9952   -1.5563 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3058    2.5840    1.6255 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0795    1.2982    1.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6648    4.9396    1.6691 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9881    6.6149    2.2509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0331    3.5897    1.9951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3525    1.9277    1.4157 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3793    0.5063   -2.4827 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3305   -0.8932   -1.8160 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 17 21  1  0
 21 22  2  0
 12 23  1  0
 23 24  2  0
 23 25  1  0
 25 26  2  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  2  0
 30 31  1  0
 31 32  2  0
 32 33  1  0
 32 34  1  0
 34 35  2  0
  9 36  1  0
 36 37  2  0
 37  6  1  0
 26 10  1  0
 35 29  1  0
 22 14  1  0
  1 38  1  0
  1 39  1  0
  1 40  1  0
  2 41  1  0
  2 42  1  0
  7 43  1  0
  8 44  1  0
 11 45  1  0
 13 46  1  0
 13 47  1  0
 15 48  1  0
 19 49  1  0
 19 50  1  0
 20 51  1  0
 20 52  1  0
 20 53  1  0
 22 54  1  0
 28 55  1  0
 28 56  1  0
 30 57  1  0
 31 58  1  0
 34 59  1  0
 35 60  1  0
 36 61  1  0
 37 62  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoic acid	Generator
Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulphanyl]-4-oxopyrimidin-1-yl]benzoate	Generator
Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulphanyl]-4-oxopyrimidin-1-yl]benzoic acid	Generator

Chemical Formula

C₂₇H₂₅FN₄O₄S

Average Molecular Weight

520.58

Monoisotopic Molecular Weight

520.158054638

IUPAC Name

ethyl 4-{5-[(2-ethoxypyrimidin-5-yl)methyl]-2-{[(4-fluorophenyl)methyl]sulfanyl}-4-oxo-1,4-dihydropyrimidin-1-yl}benzoate

Traditional Name

ethyl 4-{5-[(2-ethoxypyrimidin-5-yl)methyl]-2-{[(4-fluorophenyl)methyl]sulfanyl}-4-oxopyrimidin-1-yl}benzoate

CAS Registry Number

Not Available

SMILES

CCOC(=O)C1=CC=C(C=C1)N1C=C(CC2=CN=C(OCC)N=C2)C(=O)N=C1SCC1=CC=C(F)C=C1

InChI Identifier

InChI=1S/C27H25FN4O4S/c1-3-35-25(34)20-7-11-23(12-8-20)32-16-21(13-19-14-29-26(30-15-19)36-4-2)24(33)31-27(32)37-17-18-5-9-22(28)10-6-18/h5-12,14-16H,3-4,13,17H2,1-2H3

InChI Key

PTPNCCWOTBBVJR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzoic acid esters. These are ester derivatives of benzoic acid.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Benzoic acid esters

Alternative Parents

Substituents

Benzoate ester
Aryl thioether
Benzoyl
Alkyl aryl ether
Fluorobenzene
Alkylarylthioether
Halobenzene
Pyrimidone
Aryl fluoride
Aryl halide
Hydropyrimidine
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Carboxylic acid ester
Thioether
Sulfenyl compound
Organoheterocyclic compound
Ether
Carboxylic acid derivative
Azacycle
Organooxygen compound
Organonitrogen compound
Organofluoride
Organohalogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organosulfur 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)

Source

Exogenous

Exogenous (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	4.48	ALOGPS
logP	5.5	ChemAxon
logS	-5.5	ALOGPS
pKa (Strongest Basic)	0.68	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	93.98 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	141.39 m³·mol⁻¹	ChemAxon
Polarizability	53.27 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	215.074	30932474
DeepCCS	[M-H]-	212.678	30932474
DeepCCS	[M-2H]-	245.562	30932474
DeepCCS	[M+Na]+	220.986	30932474
AllCCS	[M+H]+	221.8	32859911
AllCCS	[M+H-H2O]+	220.1	32859911
AllCCS	[M+NH4]+	223.3	32859911
AllCCS	[M+Na]+	223.7	32859911
AllCCS	[M-H]-	203.1	32859911
AllCCS	[M+Na-2H]-	203.2	32859911
AllCCS	[M+HCOO]-	203.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate	CCOC(=O)C1=CC=C(C=C1)N1C=C(CC2=CN=C(OCC)N=C2)C(=O)N=C1SCC1=CC=C(F)C=C1	5361.7	Standard polar	33892256
Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate	CCOC(=O)C1=CC=C(C=C1)N1C=C(CC2=CN=C(OCC)N=C2)C(=O)N=C1SCC1=CC=C(F)C=C1	4123.8	Standard non polar	33892256
Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate	CCOC(=O)C1=CC=C(C=C1)N1C=C(CC2=CN=C(OCC)N=C2)C(=O)N=C1SCC1=CC=C(F)C=C1	4323.0	Semi standard non polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate 10V, Positive-QTOF	splash10-00di-0000090000-da548f50bcedb49b6c58	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate 20V, Positive-QTOF	splash10-00b9-0200890000-db43a25d470bfb34082a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate 40V, Positive-QTOF	splash10-0a4i-0901300000-4f099ffe802098264645	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate 10V, Negative-QTOF	splash10-014i-0000090000-f7a49d845050f67dbf2c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate 20V, Negative-QTOF	splash10-016u-0209430000-60998ed32c38a0b75254	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate 40V, Negative-QTOF	splash10-052b-1019100000-a58877a3e0437bb8b9b1	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

9866850

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11692123

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 Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate (HMDB0252984)

MOL for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

3D MOL for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

3D SDF for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

3D-SDF for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

PDB for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

3D PDB for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

SMILES for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

INCHI for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

Structure for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

3D Structure for HMDB0252984 (Ethyl 4-[5-[(2-ethoxypyrimidin-5-yl)methyl]-2-[(4-fluorophenyl)methylsulfanyl]-4-oxopyrimidin-1-yl]benzoate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

MS/MS Spectra