Structure of PDB 8jfd Chain B Binding Site BS03

Receptor Information
>8jfd Chain B (length=528) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVCDVFDIYAICACCKVENEVFNNYTFRGLGNKGVLPWKCISLDMKYFRA
VTTYVNESKYEKLKYKRCKYLNKETVDKLQNVVVMGRTNWESIPKKFKPL
SNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFILGGSVV
YQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNT
TLDFIIYKKTDDEEEDDFVYFNFNKENKNSIHPNDFQIYNSLKYKYHPEY
QYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFL
RGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDL
GPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCA
WNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYS
IFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKL
NPDIKNIEDFTISDFTIQNYVHHEKISM
Ligand information
Ligand IDUMP
InChIInChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBLCHEMBL211312
DrugBankDB03800
ZINCZINC000004228260
PDB chain8jfd Chain B Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8jfd Discovery of rigid biphenyl Plasmodium falciparum DHFR inhibitors using a fragment linking strategy.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R345 C490 H491 Q509 R510 S511 D513 N521 H551 Y553
Binding residue
(residue number reindexed from 1)		R269 C414 H415 Q433 R434 S435 D437 N445 H475 Y477
Annotation score3
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8jfd, PDBe:8jfd, PDBj:8jfd
PDBsum8jfd
PubMed37731689
UniProtD9N170

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