Structure of PDB 3t70 Chain B Binding Site BS03

Receptor Information
>3t70 Chain B (length=137) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHLKIVCLSDEVREMYKNHDSGLDLFIVKDEVLKPKSTTFVKLGIKAIAL
QYKSNYYYKCNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAA
LDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELD
Ligand information
Ligand IDDU4
InChIInChI=1S/C23H25N3O4/c1-25(22(16-8-4-2-5-9-16)17-10-6-3-7-11-17)15-19-18(27)14-21(30-19)26-13-12-20(28)24-23(26)29/h2-13,18-19,21-22,27H,14-15H2,1H3,(H,24,28,29)/t18-,19+,21+/m0/s1
InChIKeyGMULPQZINUAVEX-QKNQBKEWSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN(C[CH]1O[CH](C[CH]1O)N2C=CC(=O)NC2=O)C(c3ccccc3)c4ccccc4
ACDLabs 12.01O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CN(C(c3ccccc3)c4ccccc4)C
OpenEye OEToolkits 1.7.2C[N@](C[C@@H]1[C@H](C[C@@H](O1)N2C=CC(=O)NC2=O)O)C(c3ccccc3)c4ccccc4
CACTVS 3.370CN(C[C@H]1O[C@H](C[C@@H]1O)N2C=CC(=O)NC2=O)C(c3ccccc3)c4ccccc4
OpenEye OEToolkits 1.7.2CN(CC1C(CC(O1)N2C=CC(=O)NC2=O)O)C(c3ccccc3)c4ccccc4
FormulaC23 H25 N3 O4
Name2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine
ChEMBL
DrugBank
ZINCZINC000095920595
PDB chain3t70 Chain B Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3t70 Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		F46 N103 G106 I108 Y112 I117
Binding residue
(residue number reindexed from 1)		F40 N84 G87 I89 Y93 I98
Annotation score2
Binding affinityMOAD: Ki=0.5uM
PDBbind-CN: -logKd/Ki=6.30,Ki=0.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) S27 R91 S93 L99 D109
Catalytic site (residue number reindexed from 1) S21 R72 S74 L80 D90
Enzyme Commision number 3.6.1.23: dUTP diphosphatase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004170 dUTP diphosphatase activity
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006226 dUMP biosynthetic process
GO:0006260 DNA replication
GO:0006399 tRNA metabolic process
GO:0009117 nucleotide metabolic process
GO:0046081 dUTP catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3t70, PDBe:3t70, PDBj:3t70
PDBsum3t70
PubMed22049550
UniProtQ8II92

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