Structure of PDB 6kpr Chain A Binding Site BS03

Receptor Information
>6kpr Chain A (length=534) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQVCDVFDIYAICACCKVESKKNEVFNNYTFRGLGNKGVLPWKCISLDMK
YFRAVTTYVNESKYEKLKYKRCKYLNKEKKLQNVVVMGRTNWESIPKKFK
PLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFILGGS
VVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSN
NTTLDFIIYKKTNNDDEEEDDFVYFNFNKENKNSIHPNDFQIYNSLKYKY
HPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTK
KLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHRE
VNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRI
LLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNI
ASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFP
TLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDM
Ligand information
Ligand IDDQF
InChIInChI=1S/C23H25ClN4O4/c24-16-6-1-5-15(13-16)21-19(27-23(26)28-22(21)25)9-3-11-31-17-7-2-8-18(14-17)32-12-4-10-20(29)30/h1-2,5-8,13-14H,3-4,9-12H2,(H,29,30)(H4,25,26,27,28)
InChIKeyOXGBDAHIBSSGDL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(cc(c1)Cl)c2c(nc(nc2N)N)CCCOc3cccc(c3)OCCCC(=O)O
CACTVS 3.385Nc1nc(N)c(c(CCCOc2cccc(OCCCC(O)=O)c2)n1)c3cccc(Cl)c3
FormulaC23 H25 Cl N4 O4
Name4-[3-[3-[2,6-bis(azanyl)-5-(3-chlorophenyl)pyrimidin-4-yl]propoxy]phenoxy]butanoic acid
ChEMBLCHEMBL4596447
DrugBank
ZINC
PDB chain6kpr Chain A Residue 703 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6kpr 6-Hydrophobic aromatic substituent pyrimethamine analogues as potential antimalarials for pyrimethamine-resistant Plasmodium falciparum.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		I14 C15 A16 L46 D54 F58 N108 S111 L164
Binding residue
(residue number reindexed from 1)		I12 C13 A14 L40 D48 F52 N91 S94 L147
Annotation score1
Binding affinityMOAD: Ki=0.98nM
Enzymatic activity
Catalytic site (original residue number in PDB) L46 D54 E382 W404 Y430 C490 R510 D513
Catalytic site (residue number reindexed from 1) L40 D48 E310 W332 Y358 C418 R438 D441
Enzyme Commision number 1.5.1.3: dihydrofolate reductase.
2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004146 dihydrofolate reductase activity
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0016491 oxidoreductase activity
GO:0016741 transferase activity, transferring one-carbon groups
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006730 one-carbon metabolic process
GO:0009165 nucleotide biosynthetic process
GO:0032259 methylation
GO:0046654 tetrahydrofolate biosynthetic process
Cellular Component
GO:0005739 mitochondrion
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6kpr, PDBe:6kpr, PDBj:6kpr
PDBsum6kpr
PubMed31685330
UniProtD9N170

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