Structure of PDB 6kpr Chain B Binding Site BS03

Receptor Information
>6kpr Chain B (length=534) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQVCDVFDIYAICACCKVESEVFNNYTFRGLGNKGVLPWKCISLDMKYFR
AVTTYVNESKYEKLKYKRCKYLNKETVDSKKLQNVVVMGRTNWESIPKKF
KPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFILGG
SVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTS
NNTTLDFIIYKKTNNDDEEEDDFVYFNFNKENKNSIHPNDFQIYNSLKYK
YHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTT
KKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHR
EVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRR
ILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFN
IASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPF
PTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMD
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain6kpr Chain B Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)		C15 A16 L40 G44 V45 G105 R106 T107 N108 L127 S128 R129 T130 N144 K145 L164 G166 S167 V168 V169 E172 V195
Binding residue
(residue number reindexed from 1)		C13 A14 L31 G35 V36 G89 R90 T91 N92 L111 S112 R113 T114 N128 K129 L148 G150 S151 V152 V153 E156 V179
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) L46 D54 E382 W404 Y430 C490 R510 D513
Catalytic site (residue number reindexed from 1) L37 D45 E311 W333 Y359 C419 R439 D442
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

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

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