Human Metabolome Database Version 3.5

Showing metabocard for Pyrimethamine (HMDB14350)

Record Information
Version 3.5
Creation Date 2012-09-06 09:16:49 -0600
Update Date 2013-02-08 17:31:19 -0700
Secondary Accession Numbers None
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 Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
  1. CD
  2. Chloridin
  3. Chloridine
  4. Chloridyn
  5. Diaminopyritamin
  6. Ethylpyrimidine
  7. Pirimetamin
  8. Pirimetamina
  9. Primethamine
  10. Pyremethamine
  11. Pyrimethamin
Chemical Formula C12H13ClN4
Average Molecular Weight 248.711
Monoisotopic Molecular Weight 248.082874143
IUPAC Name 5-(4-chlorophenyl)-6-ethylpyrimidine-2,4-diamine
Traditional IUPAC Name pyrimethamine
CAS Registry Number 58-14-0
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)
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Aromatic Heteropolycyclic Compounds
Class Diazines
Sub Class Pyrimidines and Pyrimidine Derivatives
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • Chlorobenzenes
  • Pyrimidines and Pyrimidine Derivatives
  • aminopyrimidine(ChEBI)
  • Aryl Chloride
  • Organochloride
  • Polyamine
Direct Parent Aminopyrimidines and Derivatives
Status Expected and Not Quantified
  • Drug
  • Antimalarials
  • Antiprotozoal Agents
  • Antiprotozoals
  • Folic Acid Antagonists
  • Pharmaceutical
Cellular locations
  • Membrane
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 233.5 °C Not Available
Boiling Point Not Available Not Available
Water Solubility 1.79e-01 g/L Not Available
LogP 2.7 Not Available
Predicted Properties
Property Value Source
Water Solubility 0.18 g/L ALOGPS
LogP 2.62 ALOGPS
LogP 2.75 ChemAxon
LogS -3.14 ALOGPS
pKa (strongest acidic) 17.22 ChemAxon
pKa (strongest basic) 7.77 ChemAxon
Hydrogen Acceptor Count 4 ChemAxon
Hydrogen Donor Count 2 ChemAxon
Polar Surface Area 77.82 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 71.54 ChemAxon
Polarizability 25.79 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 1 ChemAxon
Not Available
Biological Properties
Cellular Locations
  • Membrane
Biofluid Locations
  • Blood
  • Urine
Tissue Location Not Available
Pathways Not Available
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Expected but not Quantified
Not Applicable Not Available Not Available Taking drug identified by DrugBank entry DB00205
  • Not Applicable
Urine Expected but not Quantified
Not Applicable Not Available Not Available Taking drug identified by DrugBank entry DB00205
  • Not Applicable
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID DB00205 Link_out
DrugBank Metabolite ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID Not Available
KNApSAcK ID Not Available
Chemspider ID 4819 Link_out
KEGG Compound ID C07391 Link_out
BioCyc ID Not Available
BiGG ID Not Available
Wikipedia Link Pyrimethamine Link_out
NuGOwiki Link HMDB14350 Link_out
Metagene Link HMDB14350 Link_out
METLIN ID Not Available
PubChem Compound 4993 Link_out
PDB ID CP6 Link_out
ChEBI ID 8673 Link_out
Synthesis Reference Not Available
Material Safety Data Sheet (MSDS) Download (PDF)
General References
  1. 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 Link_out
  2. 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 Link_out

Name: Dihydrofolate reductase
Reactions: Not Available
Gene Name: DHFR
Uniprot ID: P00374 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytochrome P450 2C9
Reactions: Not Available
Gene Name: CYP2C9
Uniprot ID: P11712 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytochrome P450 2D6
Reactions: Not Available
Gene Name: CYP2D6
Uniprot ID: P10635 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Cytochrome P450 2C8
Reactions: Not Available
Gene Name: CYP2C8
Uniprot ID: P10632 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA