Structure of PDB 3t6y Chain A Binding Site BS02

Receptor Information
>3t6y Chain A (length=150) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHLKIVCLSDEVREMYKNHKGDSGLDLFIVKDEVLKPKSTTFVKLGIKAI
ALQYKSNYYYKSNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEII
AALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETSRGEGGFGS
Ligand information
Ligand IDDU2
InChIInChI=1S/C20H23N5O4/c1-24-10-8-21-19(24)18(13-5-3-2-4-6-13)22-12-15-14(26)11-17(29-15)25-9-7-16(27)23-20(25)28/h2-10,14-15,17-18,22,26H,11-12H2,1H3,(H,23,27,28)/t14-,15+,17+,18?/m0/s1
InChIKeyKPWKGDCQLFIJMC-URHIDPGUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2Cn1ccnc1C(c2ccccc2)NCC3C(CC(O3)N4C=CC(=O)NC4=O)O
CACTVS 3.370Cn1ccnc1[C@H](NC[C@H]2O[C@H](C[C@@H]2O)N3C=CC(=O)NC3=O)c4ccccc4
ACDLabs 12.01O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CNC(c3ccccc3)c4nccn4C
OpenEye OEToolkits 1.7.2Cn1ccnc1C(c2ccccc2)NC[C@@H]3[C@H](C[C@@H](O3)N4C=CC(=O)NC4=O)O
CACTVS 3.370Cn1ccnc1[CH](NC[CH]2O[CH](C[CH]2O)N3C=CC(=O)NC3=O)c4ccccc4
FormulaC20 H23 N5 O4
Name2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine
ChEMBL
DrugBank
ZINC
PDB chain3t6y Chain A Residue 400 [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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PDB3t6y Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		F46 N103 G106 I108 Y112 I116 I117
Binding residue
(residue number reindexed from 1)		F42 N86 G89 I91 Y95 I99 I100
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.52,Ki=3.0uM
Enzymatic activity
Catalytic site (original residue number in PDB) S27 R91 S93 L99 D109
Catalytic site (residue number reindexed from 1) S23 R74 S76 L82 D92
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:3t6y, PDBe:3t6y, PDBj:3t6y
PDBsum3t6y
PubMed22049550
UniProtQ8II92

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