Structure of PDB 3t64 Chain A Binding Site BS02

Receptor Information
>3t64 Chain A (length=153) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLG
IKAIALQYKSNYYYKNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRG
EIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETSRGEGG
FGS
Ligand information
Ligand IDDU3
InChIInChI=1S/C22H23N3O4/c26-17-13-20(25-12-11-19(27)24-22(25)28)29-18(17)14-23-21(15-7-3-1-4-8-15)16-9-5-2-6-10-16/h1-12,17-18,20-21,23,26H,13-14H2,(H,24,27,28)/t17-,18+,20+/m0/s1
InChIKeyJJVBLAPDVHVENR-NLWGTHIKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1ccc(cc1)C(c2ccccc2)NC[C@@H]3[C@H](C[C@@H](O3)N4C=CC(=O)NC4=O)O
CACTVS 3.370O[CH]1C[CH](O[CH]1CNC(c2ccccc2)c3ccccc3)N4C=CC(=O)NC4=O
ACDLabs 12.01O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CNC(c3ccccc3)c4ccccc4
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CNC(c2ccccc2)c3ccccc3)N4C=CC(=O)NC4=O
OpenEye OEToolkits 1.7.2c1ccc(cc1)C(c2ccccc2)NCC3C(CC(O3)N4C=CC(=O)NC4=O)O
FormulaC22 H23 N3 O4
Name2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine
ChEMBLCHEMBL2420340
DrugBank
ZINCZINC000095920839
PDB chain3t64 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3t64 Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		F46 N103 G106 I108 Y112 I117
Binding residue
(residue number reindexed from 1)		F46 N89 G92 I94 Y98 I103
Annotation score2
Binding affinityMOAD: Ki=0.2uM
PDBbind-CN: -logKd/Ki=6.70,Ki=0.2uM
Enzymatic activity
Catalytic site (original residue number in PDB) S27 R91 S93 L99 D109
Catalytic site (residue number reindexed from 1) S27 R77 S79 L85 D95
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:3t64, PDBe:3t64, PDBj:3t64
PDBsum3t64
PubMed22049550
UniProtQ8II92

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