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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (4) Show 4 proteins XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:49 UTC

Update Date

2022-03-07 02:51:35 UTC

HMDB ID

HMDB0014350

Secondary Accession Numbers

HMDB14350

Metabolite Identification

Common Name

Pyrimethamine

Description

Pyrimethamine is only found in individuals that have used or taken this drug. It is one of the folic acid antagonists that is used as an antimalarial or with a sulfonamide to treat toxoplasmosis. [PubChem]Pyrimethamine inhibits the dihydrofolate reductase of plasmodia and thereby blocks the biosynthesis of purines and pyrimidines, which are essential for DNA synthesis and cell multiplication. This leads to failure of nuclear division at the time of schizont formation in erythrocytes and liver.

Structure

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

HMDB0014350
     RDKit          3D
Pyrimethamine
 30 31  0  0  0  0  0  0  0  0999 V2000
   -0.6254   -2.7624   -0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9510   -1.5574   -1.0915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3461   -0.3694   -0.3004 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6796   -0.1610   -0.0576 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1018    0.8678    0.6961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4989    1.0818    0.9521 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1872    1.6992    1.2110 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8590    1.5367    1.0002 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1257    2.3928    1.5318 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4168    0.4723    0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9928    0.2744   -0.0696 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8258   -0.6128    0.5740 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1477   -0.7387    0.2185 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7024    0.0221   -0.8003 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3997   -0.1688   -1.2248 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.8966    0.9176   -1.4594 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5779    1.0280   -1.0897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0211   -2.6440    0.7849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0490   -3.6812   -0.7533 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4628   -2.9293   -0.2487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0942   -1.2942   -1.7606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7952   -1.8202   -1.7621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0745    1.4105    0.1636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9308    0.9240    1.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2241    3.3435    1.0679 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7571    2.1991    2.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4203   -1.2203    1.3869 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8252   -1.4448    0.7170 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3314    1.5089   -2.2545 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9414    1.7258   -1.6010 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 14 16  1  0
 16 17  2  0
 10  3  1  0
 17 11  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  6 23  1  0
  6 24  1  0
  9 25  1  0
  9 26  1  0
 12 27  1  0
 13 28  1  0
 16 29  1  0
 17 30  1  0
M  END

205
  Mrv0541 02231214312D          

 17 18  0  0  0  0            999 V2000
    3.5220    3.0154    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -1.5222    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -1.5222    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -0.2846    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -2.7597    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -0.2846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -0.6971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -0.2846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    0.5404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -0.6971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    0.9529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365    0.9529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6655   -0.6971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -1.9347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    1.7779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365    1.7779    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 17  1  0  0  0  0
  2  7  1  0  0  0  0
  2 14  2  0  0  0  0
  3 10  2  0  0  0  0
  3 14  1  0  0  0  0
  4 10  1  0  0  0  0
  5 14  1  0  0  0  0
  6  7  2  0  0  0  0
  6  9  1  0  0  0  0
  6 10  1  0  0  0  0
  7  8  1  0  0  0  0
  8 13  1  0  0  0  0
  9 11  2  0  0  0  0
  9 12  1  0  0  0  0
 11 15  1  0  0  0  0
 12 16  2  0  0  0  0
 15 17  2  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014350

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC1=C(C(N)=NC(N)=N1)C1=CC=C(Cl)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C12H13ClN4/c1-2-9-10(11(14)17-12(15)16-9)7-3-5-8(13)6-4-7/h3-6H,2H2,1H3,(H4,14,15,16,17)

> <INCHI_KEY>
WKSAUQYGYAYLPV-UHFFFAOYSA-N

> <FORMULA>
C12H13ClN4

> <MOLECULAR_WEIGHT>
248.711

> <EXACT_MASS>
248.082874143

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
25.794130782433673

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-(4-chlorophenyl)-6-ethylpyrimidine-2,4-diamine

> <ALOGPS_LOGP>
2.62

> <JCHEM_LOGP>
2.748303154333333

> <ALOGPS_LOGS>
-3.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.222043955485603

> <JCHEM_PKA_STRONGEST_BASIC>
7.773183579634736

> <JCHEM_POLAR_SURFACE_AREA>
77.82

> <JCHEM_REFRACTIVITY>
71.54200000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.79e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrimethamine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0014350
     RDKit          3D
Pyrimethamine
 30 31  0  0  0  0  0  0  0  0999 V2000
   -0.6254   -2.7624   -0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9510   -1.5574   -1.0915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3461   -0.3694   -0.3004 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6796   -0.1610   -0.0576 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1018    0.8678    0.6961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4989    1.0818    0.9521 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1872    1.6992    1.2110 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8590    1.5367    1.0002 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1257    2.3928    1.5318 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4168    0.4723    0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9928    0.2744   -0.0696 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8258   -0.6128    0.5740 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1477   -0.7387    0.2185 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7024    0.0221   -0.8003 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3997   -0.1688   -1.2248 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.8966    0.9176   -1.4594 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5779    1.0280   -1.0897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0211   -2.6440    0.7849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0490   -3.6812   -0.7533 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4628   -2.9293   -0.2487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0942   -1.2942   -1.7606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7952   -1.8202   -1.7621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0745    1.4105    0.1636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9308    0.9240    1.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2241    3.3435    1.0679 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7571    2.1991    2.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4203   -1.2203    1.3869 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8252   -1.4448    0.7170 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3314    1.5089   -2.2545 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9414    1.7258   -1.6010 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 14 16  1  0
 16 17  2  0
 10  3  1  0
 17 11  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  6 23  1  0
  6 24  1  0
  9 25  1  0
  9 26  1  0
 12 27  1  0
 13 28  1  0
 16 29  1  0
 17 30  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 205                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1 Cl   UNK     0       6.574   5.629   0.000  0.00  0.00          Cl+0
HETATM    2  N   UNK     0       7.908  -2.841   0.000  0.00  0.00           N+0
HETATM    3  N   UNK     0       5.241  -2.841   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0       3.907  -0.531   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       6.574  -5.151   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       6.574  -0.531   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.908  -1.301   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.242  -0.531   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.574   1.009   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.241  -1.301   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.241   1.779   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.908   1.779   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.576  -1.301   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.574  -3.611   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.241   3.319   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.908   3.319   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.574   4.089   0.000  0.00  0.00           C+0
CONECT    1   17                                                            
CONECT    2    7   14                                                       
CONECT    3   10   14                                                       
CONECT    4   10                                                            
CONECT    5   14                                                            
CONECT    6    7    9   10                                                  
CONECT    7    2    6    8                                                  
CONECT    8    7   13                                                       
CONECT    9    6   11   12                                                  
CONECT   10    3    4    6                                                  
CONECT   11    9   15                                                       
CONECT   12    9   16                                                       
CONECT   13    8                                                            
CONECT   14    2    3    5                                                  
CONECT   15   11   17                                                       
CONECT   16   12   17                                                       
CONECT   17    1   15   16                                                  
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0014350
HETATM    1  C1  UNL     1      -0.625  -2.762  -0.243  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.951  -1.557  -1.091  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.346  -0.369  -0.300  1.00  0.00           C  
HETATM    4  N1  UNL     1      -2.680  -0.161  -0.058  1.00  0.00           N  
HETATM    5  C4  UNL     1      -3.102   0.868   0.696  1.00  0.00           C  
HETATM    6  N2  UNL     1      -4.499   1.082   0.952  1.00  0.00           N  
HETATM    7  N3  UNL     1      -2.187   1.699   1.211  1.00  0.00           N  
HETATM    8  C5  UNL     1      -0.859   1.537   1.000  1.00  0.00           C  
HETATM    9  N4  UNL     1       0.126   2.393   1.532  1.00  0.00           N  
HETATM   10  C6  UNL     1      -0.417   0.472   0.220  1.00  0.00           C  
HETATM   11  C7  UNL     1       0.993   0.274  -0.070  1.00  0.00           C  
HETATM   12  C8  UNL     1       1.826  -0.613   0.574  1.00  0.00           C  
HETATM   13  C9  UNL     1       3.148  -0.739   0.218  1.00  0.00           C  
HETATM   14  C10 UNL     1       3.702   0.022  -0.800  1.00  0.00           C  
HETATM   15 CL1  UNL     1       5.400  -0.169  -1.225  1.00  0.00          CL  
HETATM   16  C11 UNL     1       2.897   0.918  -1.459  1.00  0.00           C  
HETATM   17  C12 UNL     1       1.578   1.028  -1.090  1.00  0.00           C  
HETATM   18  H1  UNL     1      -1.021  -2.644   0.785  1.00  0.00           H  
HETATM   19  H2  UNL     1      -1.049  -3.681  -0.753  1.00  0.00           H  
HETATM   20  H3  UNL     1       0.463  -2.929  -0.249  1.00  0.00           H  
HETATM   21  H4  UNL     1      -0.094  -1.294  -1.761  1.00  0.00           H  
HETATM   22  H5  UNL     1      -1.795  -1.820  -1.762  1.00  0.00           H  
HETATM   23  H6  UNL     1      -5.074   1.410   0.164  1.00  0.00           H  
HETATM   24  H7  UNL     1      -4.931   0.924   1.873  1.00  0.00           H  
HETATM   25  H8  UNL     1       0.224   3.343   1.068  1.00  0.00           H  
HETATM   26  H9  UNL     1       0.757   2.199   2.319  1.00  0.00           H  
HETATM   27  H10 UNL     1       1.420  -1.220   1.387  1.00  0.00           H  
HETATM   28  H11 UNL     1       3.825  -1.445   0.717  1.00  0.00           H  
HETATM   29  H12 UNL     1       3.331   1.509  -2.254  1.00  0.00           H  
HETATM   30  H13 UNL     1       0.941   1.726  -1.601  1.00  0.00           H  
CONECT    1    2   18   19   20
CONECT    2    3   21   22
CONECT    3    4    4   10
CONECT    4    5
CONECT    5    6    7    7
CONECT    6   23   24
CONECT    7    8
CONECT    8    9   10   10
CONECT    9   25   26
CONECT   10   11
CONECT   11   12   12   17
CONECT   12   13   27
CONECT   13   14   14   28
CONECT   14   15   16
CONECT   16   17   17   29
CONECT   17   30
END

HMDB0014350
     RDKit          3D
Pyrimethamine
 30 31  0  0  0  0  0  0  0  0999 V2000
   -0.6254   -2.7624   -0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9510   -1.5574   -1.0915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3461   -0.3694   -0.3004 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6796   -0.1610   -0.0576 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1018    0.8678    0.6961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4989    1.0818    0.9521 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1872    1.6992    1.2110 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8590    1.5367    1.0002 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1257    2.3928    1.5318 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4168    0.4723    0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9928    0.2744   -0.0696 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8258   -0.6128    0.5740 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1477   -0.7387    0.2185 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7024    0.0221   -0.8003 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3997   -0.1688   -1.2248 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.8966    0.9176   -1.4594 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5779    1.0280   -1.0897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0211   -2.6440    0.7849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0490   -3.6812   -0.7533 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4628   -2.9293   -0.2487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0942   -1.2942   -1.7606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7952   -1.8202   -1.7621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0745    1.4105    0.1636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9308    0.9240    1.8735 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2241    3.3435    1.0679 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7571    2.1991    2.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4203   -1.2203    1.3869 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8252   -1.4448    0.7170 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3314    1.5089   -2.2545 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9414    1.7258   -1.6010 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 14 16  1  0
 16 17  2  0
 10  3  1  0
 17 11  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  6 23  1  0
  6 24  1  0
  9 25  1  0
  9 26  1  0
 12 27  1  0
 13 28  1  0
 16 29  1  0
 17 30  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2,4-Diamino-5-(4-chlorophenyl)-6-ethylpyrimidine	ChEBI
2,4-Diamino-5-(p-chlorophenyl)-6-ethylpyrimidine	ChEBI
2,4-Diamino-5-chlorophenyl-6-ethylpyrimidine	ChEBI
5-(4'-Chlorophenyl)-2,4-diamino-6-ethylpyrimidine	ChEBI
5-(4-Chlorophenyl)-6-ethyl-2,4-diaminopyrimidine	ChEBI
5-(4-Chlorophenyl)-6-ethyl-2,4-pyrimidinediamine	ChEBI
CD	ChEBI
Chloridine	ChEBI
Chloridyn	ChEBI
Diaminopyritamin	ChEBI
Ethylpyrimidine	ChEBI
Pirimetamina	ChEBI
Primethamine	ChEBI
Pyrimethaminum	ChEBI
Daraprim	Kegg
Chloridin	HMDB
Pirimetamin	HMDB
Pyremethamine	HMDB
Pyrimethamin	HMDB
Glaxo wellcome brand OF pyrimethamine	HMDB
GlaxoSmithKline brand OF pyrimethamine	HMDB
Tindurine	HMDB
Aventis brand OF pyrimethamine	HMDB
Wellcome brand OF pyrimethamine	HMDB
Malocide	HMDB

Chemical Formula

C₁₂H₁₃ClN₄

Average Molecular Weight

248.711

Monoisotopic Molecular Weight

248.082874143

IUPAC Name

5-(4-chlorophenyl)-6-ethylpyrimidine-2,4-diamine

Traditional Name

pyrimethamine

CAS Registry Number

58-14-0

SMILES

CCC1=C(C(N)=NC(N)=N1)C1=CC=C(Cl)C=C1

InChI Identifier

InChI=1S/C12H13ClN4/c1-2-9-10(11(14)17-12(15)16-9)7-3-5-8(13)6-4-7/h3-6H,2H2,1H3,(H4,14,15,16,17)

InChI Key

WKSAUQYGYAYLPV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Aminopyrimidines and derivatives

Alternative Parents

Substituents

Aminopyrimidine
Chlorobenzene
Halobenzene
Aryl chloride
Aryl halide
Monocyclic benzene moiety
Hydropyrimidine
Benzenoid
Heteroaromatic compound
Azacycle
Organochloride
Organohalogen compound
Amine
Hydrocarbon derivative
Organopnictogen compound
Organonitrogen compound
Primary amine
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:8673 )
monochlorobenzenes (CHEBI:8673 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Source

Exogenous

Exogenous (HMDB: HMDB0014350)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	233.5 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.18 g/L	Not Available
LogP	2.7	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	Not Available	155.779	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000988

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.18 g/L	ALOGPS
logP	2.62	ALOGPS
logP	2.75	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	17.22	ChemAxon
pKa (Strongest Basic)	7.77	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	77.82 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	71.54 m³·mol⁻¹	ChemAxon
Polarizability	25.79 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	160.986	30932474
DeepCCS	[M-H]-	158.61	30932474
DeepCCS	[M-2H]-	191.496	30932474
DeepCCS	[M+Na]+	167.062	30932474
AllCCS	[M+H]+	155.0	32859911
AllCCS	[M+H-H2O]+	151.0	32859911
AllCCS	[M+NH4]+	158.6	32859911
AllCCS	[M+Na]+	159.7	32859911
AllCCS	[M-H]-	156.5	32859911
AllCCS	[M+Na-2H]-	156.6	32859911
AllCCS	[M+HCOO]-	156.7	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	3.44 minutes	32390414
Predicted by Siyang on May 30, 2022	12.0785 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.47 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	33.0 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1424.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	325.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	134.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	205.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	148.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	376.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	451.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	74.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	962.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	381.6 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1039.4 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	282.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	324.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	313.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	145.2 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	9.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pyrimethamine	CCC1=C(C(N)=NC(N)=N1)C1=CC=C(Cl)C=C1	3595.7	Standard polar	33892256
Pyrimethamine	CCC1=C(C(N)=NC(N)=N1)C1=CC=C(Cl)C=C1	2199.3	Standard non polar	33892256
Pyrimethamine	CCC1=C(C(N)=NC(N)=N1)C1=CC=C(Cl)C=C1	2284.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Pyrimethamine,1TMS,isomer #1	CCC1=NC(N)=NC(N[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2395.8	Semi standard non polar	33892256
Pyrimethamine,1TMS,isomer #1	CCC1=NC(N)=NC(N[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2114.0	Standard non polar	33892256
Pyrimethamine,1TMS,isomer #1	CCC1=NC(N)=NC(N[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	3446.8	Standard polar	33892256
Pyrimethamine,1TMS,isomer #2	CCC1=NC(N[Si](C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	2423.7	Semi standard non polar	33892256
Pyrimethamine,1TMS,isomer #2	CCC1=NC(N[Si](C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	2099.4	Standard non polar	33892256
Pyrimethamine,1TMS,isomer #2	CCC1=NC(N[Si](C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	3481.7	Standard polar	33892256
Pyrimethamine,2TMS,isomer #1	CCC1=NC(N[Si](C)(C)C)=NC(N[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2394.1	Semi standard non polar	33892256
Pyrimethamine,2TMS,isomer #1	CCC1=NC(N[Si](C)(C)C)=NC(N[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2194.4	Standard non polar	33892256
Pyrimethamine,2TMS,isomer #1	CCC1=NC(N[Si](C)(C)C)=NC(N[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	3276.2	Standard polar	33892256
Pyrimethamine,2TMS,isomer #2	CCC1=NC(N)=NC(N([Si](C)(C)C)[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2326.7	Semi standard non polar	33892256
Pyrimethamine,2TMS,isomer #2	CCC1=NC(N)=NC(N([Si](C)(C)C)[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2315.1	Standard non polar	33892256
Pyrimethamine,2TMS,isomer #2	CCC1=NC(N)=NC(N([Si](C)(C)C)[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	3280.3	Standard polar	33892256
Pyrimethamine,2TMS,isomer #3	CCC1=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	2362.6	Semi standard non polar	33892256
Pyrimethamine,2TMS,isomer #3	CCC1=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	2294.0	Standard non polar	33892256
Pyrimethamine,2TMS,isomer #3	CCC1=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	3236.0	Standard polar	33892256
Pyrimethamine,3TMS,isomer #1	CCC1=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC(N[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2388.5	Semi standard non polar	33892256
Pyrimethamine,3TMS,isomer #1	CCC1=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC(N[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2363.8	Standard non polar	33892256
Pyrimethamine,3TMS,isomer #1	CCC1=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC(N[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2970.5	Standard polar	33892256
Pyrimethamine,3TMS,isomer #2	CCC1=NC(N[Si](C)(C)C)=NC(N([Si](C)(C)C)[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2385.5	Semi standard non polar	33892256
Pyrimethamine,3TMS,isomer #2	CCC1=NC(N[Si](C)(C)C)=NC(N([Si](C)(C)C)[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2346.8	Standard non polar	33892256
Pyrimethamine,3TMS,isomer #2	CCC1=NC(N[Si](C)(C)C)=NC(N([Si](C)(C)C)[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	3044.1	Standard polar	33892256
Pyrimethamine,4TMS,isomer #1	CCC1=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC(N([Si](C)(C)C)[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2451.5	Semi standard non polar	33892256
Pyrimethamine,4TMS,isomer #1	CCC1=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC(N([Si](C)(C)C)[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2518.6	Standard non polar	33892256
Pyrimethamine,4TMS,isomer #1	CCC1=NC(N([Si](C)(C)C)[Si](C)(C)C)=NC(N([Si](C)(C)C)[Si](C)(C)C)=C1C1=CC=C(Cl)C=C1	2799.1	Standard polar	33892256
Pyrimethamine,1TBDMS,isomer #1	CCC1=NC(N)=NC(N[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2560.2	Semi standard non polar	33892256
Pyrimethamine,1TBDMS,isomer #1	CCC1=NC(N)=NC(N[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2336.5	Standard non polar	33892256
Pyrimethamine,1TBDMS,isomer #1	CCC1=NC(N)=NC(N[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	3466.6	Standard polar	33892256
Pyrimethamine,1TBDMS,isomer #2	CCC1=NC(N[Si](C)(C)C(C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	2580.3	Semi standard non polar	33892256
Pyrimethamine,1TBDMS,isomer #2	CCC1=NC(N[Si](C)(C)C(C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	2315.3	Standard non polar	33892256
Pyrimethamine,1TBDMS,isomer #2	CCC1=NC(N[Si](C)(C)C(C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	3474.8	Standard polar	33892256
Pyrimethamine,2TBDMS,isomer #1	CCC1=NC(N[Si](C)(C)C(C)(C)C)=NC(N[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2748.4	Semi standard non polar	33892256
Pyrimethamine,2TBDMS,isomer #1	CCC1=NC(N[Si](C)(C)C(C)(C)C)=NC(N[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2649.1	Standard non polar	33892256
Pyrimethamine,2TBDMS,isomer #1	CCC1=NC(N[Si](C)(C)C(C)(C)C)=NC(N[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	3329.3	Standard polar	33892256
Pyrimethamine,2TBDMS,isomer #2	CCC1=NC(N)=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2712.8	Semi standard non polar	33892256
Pyrimethamine,2TBDMS,isomer #2	CCC1=NC(N)=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2700.0	Standard non polar	33892256
Pyrimethamine,2TBDMS,isomer #2	CCC1=NC(N)=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	3312.0	Standard polar	33892256
Pyrimethamine,2TBDMS,isomer #3	CCC1=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	2727.7	Semi standard non polar	33892256
Pyrimethamine,2TBDMS,isomer #3	CCC1=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	2661.6	Standard non polar	33892256
Pyrimethamine,2TBDMS,isomer #3	CCC1=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC(N)=C1C1=CC=C(Cl)C=C1	3253.3	Standard polar	33892256
Pyrimethamine,3TBDMS,isomer #1	CCC1=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC(N[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2947.3	Semi standard non polar	33892256
Pyrimethamine,3TBDMS,isomer #1	CCC1=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC(N[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2959.1	Standard non polar	33892256
Pyrimethamine,3TBDMS,isomer #1	CCC1=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC(N[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	3173.9	Standard polar	33892256
Pyrimethamine,3TBDMS,isomer #2	CCC1=NC(N[Si](C)(C)C(C)(C)C)=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2958.9	Semi standard non polar	33892256
Pyrimethamine,3TBDMS,isomer #2	CCC1=NC(N[Si](C)(C)C(C)(C)C)=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	2947.6	Standard non polar	33892256
Pyrimethamine,3TBDMS,isomer #2	CCC1=NC(N[Si](C)(C)C(C)(C)C)=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	3226.9	Standard polar	33892256
Pyrimethamine,4TBDMS,isomer #1	CCC1=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	3178.8	Semi standard non polar	33892256
Pyrimethamine,4TBDMS,isomer #1	CCC1=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	3222.2	Standard non polar	33892256
Pyrimethamine,4TBDMS,isomer #1	CCC1=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1C1=CC=C(Cl)C=C1	3090.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Pyrimethamine CI-B (Non-derivatized)	splash10-0002-0090000000-4e966bed391e234a23e3	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Pyrimethamine CI-B (Non-derivatized)	splash10-0002-0090000000-4e966bed391e234a23e3	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pyrimethamine GC-MS (Non-derivatized) - 70eV, Positive	splash10-01pk-0290000000-f67f41257c448ad0d840	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pyrimethamine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-0002-2590000000-6434b6f0181741b3ca41	2014-09-20	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine LC-ESI-QTOF , positive-QTOF	splash10-0002-0090000000-a146b85d59fc9835ed4c	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine LC-ESI-QTOF , positive-QTOF	splash10-0002-0090000000-84e4cea277c64351f21b	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine LC-ESI-QTOF , positive-QTOF	splash10-0002-0190000000-d931593de00f33f04587	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine LC-ESI-QTOF , positive-QTOF	splash10-0059-0980000000-a232e355dd50976aea07	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine LC-ESI-QTOF , positive-QTOF	splash10-005a-0920000000-7d48f7cfecbd7823803a	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine , positive-QTOF	splash10-0002-0290000000-b6d3f56ade24c0e6984c	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine , positive-QTOF	splash10-0002-0290000000-415b60a9caab352df184	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine , positive-QTOF	splash10-0032-2960000000-583d00b81182f34e5a94	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 20V, Positive-QTOF	splash10-0002-0090000000-84e4cea277c64351f21b	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 10V, Positive-QTOF	splash10-0002-0090000000-a146b85d59fc9835ed4c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 40V, Positive-QTOF	splash10-0059-0980000000-a232e355dd50976aea07	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 30V, Positive-QTOF	splash10-0002-0190000000-d931593de00f33f04587	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 30V, Positive-QTOF	splash10-0002-0090000000-a5bd8cb5be16b08fe352	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 45V, Positive-QTOF	splash10-0002-0090000000-ec976a2cca417c4abd83	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 15V, Positive-QTOF	splash10-0002-0090000000-142231cbd9fb9d4cd7ca	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 50V, Positive-QTOF	splash10-005a-0920000000-7d48f7cfecbd7823803a	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 90V, Positive-QTOF	splash10-005a-0910000000-74228f82abe0906b09dd	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 30V, Positive-QTOF	splash10-0002-0190000000-2277a786baa63a6f391c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyrimethamine 50V, Positive-QTOF	splash10-005a-0920000000-aacf5c362f2e7330e364	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyrimethamine 10V, Positive-QTOF	splash10-0002-0090000000-cc03baac614916e188ae	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyrimethamine 20V, Positive-QTOF	splash10-0002-0190000000-8c90fdad9d6f513cfdcf	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyrimethamine 40V, Positive-QTOF	splash10-03ec-2940000000-ad7ab31613780bee7745	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyrimethamine 10V, Negative-QTOF	splash10-0002-0090000000-7cec7981debaccce56c0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyrimethamine 20V, Negative-QTOF	splash10-0002-1190000000-3e6ac4ed3d9334756216	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pyrimethamine 40V, Negative-QTOF	splash10-0006-9740000000-b92682f3660029c1045d	2016-08-03	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00205	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00205	21059682	details

Abnormal Concentrations

Not Available

Predicted Concentrations

Biospecimen	Value	Original age	Original sex	Original condition	Comments
Blood	0.000 uM	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities
Blood	0.000 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00205

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4819

KEGG Compound ID

C07391

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pyrimethamine

METLIN ID

Not Available

PubChem Compound

4993

PDB ID

CP6

ChEBI ID

8673

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)

Download (PDF)

General References

Sirichaiwat C, Intaraudom C, Kamchonwongpaisan S, Vanichtanankul J, Thebtaranonth Y, Yuthavong Y: Target guided synthesis of 5-benzyl-2,4-diamonopyrimidines: their antimalarial activities and binding affinities to wild type and mutant dihydrofolate reductases from Plasmodium falciparum. J Med Chem. 2004 Jan 15;47(2):345-54. [PubMed:14711307 ]
Gatton ML, Martin LB, Cheng Q: Evolution of resistance to sulfadoxine-pyrimethamine in Plasmodium falciparum. Antimicrob Agents Chemother. 2004 Jun;48(6):2116-23. [PubMed:15155209 ]

Enzymes

Enzyme Details

1. Dihydrofolate reductase

General function:: Involved in dihydrofolate reductase activity
Specific function:: Key enzyme in folate metabolism. Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis. Binds its own mRNA and that of DHFRL1.
Gene Name:: DHFR
Uniprot ID:: P00374
Molecular weight:: 21452.61

References

Rastelli G, Pacchioni S, Parenti MD: Structure of Plasmodium vivax dihydrofolate reductase determined by homology modeling and molecular dynamics refinement. Bioorg Med Chem Lett. 2003 Oct 6;13(19):3257-60. [PubMed:12951104 ]
Fidock DA, Wellems TE: Transformation with human dihydrofolate reductase renders malaria parasites insensitive to WR99210 but does not affect the intrinsic activity of proguanil. Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10931-6. [PubMed:9380737 ]
Wooden JM, Hartwell LH, Vasquez B, Sibley CH: Analysis in yeast of antimalaria drugs that target the dihydrofolate reductase of Plasmodium falciparum. Mol Biochem Parasitol. 1997 Mar;85(1):25-40. [PubMed:9108546 ]
Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]

Enzyme Details

2. Cytochrome P450 2C9

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.
Gene Name:: CYP2C9
Uniprot ID:: P11712
Molecular weight:: 55627.365

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

3. Cytochrome P450 2D6

General function:: Involved in monooxygenase activity
Specific function:: Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.
Gene Name:: CYP2D6
Uniprot ID:: P10635
Molecular weight:: 55768.94

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

4. Cytochrome P450 2C8

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. In the epoxidation of arachidonic acid it generates only 14,15- and 11,12-cis-epoxyeicosatrienoic acids. It is the principal enzyme responsible for the metabolism the anti-cancer drug paclitaxel (taxol).
Gene Name:: CYP2C8
Uniprot ID:: P10632
Molecular weight:: 55824.275

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Showing metabocard for Pyrimethamine (HMDB0014350)

MOL for HMDB0014350 (Pyrimethamine)

3D MOL for HMDB0014350 (Pyrimethamine)

3D SDF for HMDB0014350 (Pyrimethamine)

3D-SDF for HMDB0014350 (Pyrimethamine)

PDB for HMDB0014350 (Pyrimethamine)

3D PDB for HMDB0014350 (Pyrimethamine)

SMILES for HMDB0014350 (Pyrimethamine)

INCHI for HMDB0014350 (Pyrimethamine)

Structure for HMDB0014350 (Pyrimethamine)

3D Structure for HMDB0014350 (Pyrimethamine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

Enzymes

References

References

References

References