Structure of PDB 6leu Chain B Binding Site BS03

Receptor Information
>6leu Chain B (length=529) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVCDVFDIYAICACCKVEEVFNNYTFRGLGNKGVLPWKCISLDMKYFRAV
TTYVNESKYEKLKYKRCKYLKLQNVVVMGRTNWESIPKKFKPLSNRINVI
LSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFILGGSVVYQEFLEK
KLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFIIY
KKTNNDDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPEYQ
YLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLR
GIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLG
PIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAW
NVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSI
FTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLN
PDIKNIEDFTISDFTIQNYVHHEKISMDM
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 chain6leu 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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PDB6leu Flexible diaminodihydrotriazine inhibitors of Plasmodium falciparum dihydrofolate reductase: Binding strengths, modes of binding and their antimalarial activities.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		A16 L40 G44 V45 L46 G105 R106 T107 N108 L127 S128 R129 N144 L164 G165 G166 S167 V168 E172
Binding residue
(residue number reindexed from 1)		A13 L29 G33 V34 L35 G79 R80 T81 N82 L101 S102 R103 N118 L138 G139 G140 S141 V142 E146
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) L35 D43 E305 W327 Y353 C413 R433 D436
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:6leu, PDBe:6leu, PDBj:6leu
PDBsum6leu
PubMed32294614
UniProtD9N170

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