Structure of PDB 2y8c Chain B Binding Site BS01

Receptor Information
>2y8c Chain B (length=123) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHLKIVCLSDEVREMYKNHDSGLDLFIVKDEVLKPKSTTFVKLGIKAIAL
QNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNTSDQEYHIK
KNDKLVQLVSFTGEPLSFELVEE
Ligand information
Ligand IDDUQ
InChIInChI=1S/C30H31N3O5/c34-20-18-31-28(36)23(22-33-19-16-27(35)32-29(33)37)17-21-38-30(24-10-4-1-5-11-24,25-12-6-2-7-13-25)26-14-8-3-9-15-26/h1-16,19,23,34H,17-18,20-22H2,(H,31,36)(H,32,35,37)/t23-/m0/s1
InChIKeyPOOIRAMVDDLAIT-QHCPKHFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.352OCCNC(=O)[CH](CCOC(c1ccccc1)(c2ccccc2)c3ccccc3)CN4C=CC(=O)NC4=O
OpenEye OEToolkits 1.6.1c1ccc(cc1)C(c2ccccc2)(c3ccccc3)OCC[C@@H](CN4C=CC(=O)NC4=O)C(=O)NCCO
OpenEye OEToolkits 1.6.1c1ccc(cc1)C(c2ccccc2)(c3ccccc3)OCCC(CN4C=CC(=O)NC4=O)C(=O)NCCO
CACTVS 3.352OCCNC(=O)[C@@H](CCOC(c1ccccc1)(c2ccccc2)c3ccccc3)CN4C=CC(=O)NC4=O
FormulaC30 H31 N3 O5
Name(2S)-2-[(2,4-dioxopyrimidin-1-yl)methyl]-N-(2-hydroxyethyl)-4-trityloxy-butanamide;
5'-TRITYLATED DEOXYURIDINE ANALOGUE
ChEMBL
DrugBank
ZINCZINC000071316960
PDB chain2y8c 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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PDB2y8c Beta-Branched Acyclic Nucleoside Analogues as Inhibitors of Plasmodium Falciparum Dutpase
Resolution2.1 Å
Binding residue
(original residue number in PDB)		F46 N103 G106 Y112 I117
Binding residue
(residue number reindexed from 1)		F40 N72 G75 Y81 I86
Annotation score1
Binding affinityMOAD: Ki=0.4uM
PDBbind-CN: -logKd/Ki=6.40,Ki=0.4uM
Enzymatic activity
Catalytic site (original residue number in PDB) S27 R91 S93 L99 D109
Catalytic site (residue number reindexed from 1) S21 R60 S62 L68 D78
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:2y8c, PDBe:2y8c, PDBj:2y8c
PDBsum2y8c
PubMed21411327
UniProtQ8II92

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