Structure of PDB 8jfb Chain B Binding Site BS02

Receptor Information
>8jfb Chain B (length=525) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQVCDVFDIYAICACCKVESKNEVFNNYTFRGLGNKGVLPWKCISLDMKY
FRAVTTYVNESKYEKLKYKRCKYLNKETVKLQNVVVMGRTNWESIPKKFK
PLSNRINVILSRTLKKEDVYIINKVEDLIVLLGKLNYYKCFILGGSVVYQ
EFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTL
DFIIYKKTNEEEDDFVYFNFNKNKNSIHPNDFQIYNSLKYKYHPEYQYLN
IIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGII
EELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIY
GFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVK
DLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTH
MIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDI
KNIEDFTISDFTIQNYVHHEKISMD
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 chain8jfb Chain B Residue 701 [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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PDB8jfb Discovery of rigid biphenyl Plasmodium falciparum DHFR inhibitors using a fragment linking strategy.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		C15 A16 L40 G41 G44 V45 L46 G105 R106 T107 N108 L127 S128 R129 T130 N144 L164 G166 S167 Y170 E172
Binding residue
(residue number reindexed from 1)		C13 A14 L33 G34 G37 V38 L39 G88 R89 T90 N91 L110 S111 R112 T113 N123 L143 G145 S146 Y149 E151
Annotation score4
Enzymatic activity
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
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Biological Process
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Cellular Component
External links
PDB RCSB:8jfb, PDBe:8jfb, PDBj:8jfb
PDBsum8jfb
PubMed37731689
UniProtD9N170

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