Structure of PDB 1vyq Chain B Binding Site BS01

Receptor Information
>1vyq Chain B (length=140) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHLKIVCLSDEVREMYKNHKTHHEGDSGLDLFIVKDEVLKPKSTTFVKLG
IKAIALQYKSNYYYKNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRG
EIIAALDNTSDQEYHIKKNDKLVQLVSFTGEPLSFELVEE
Ligand information
Ligand IDDUX
InChIInChI=1S/C28H25FN2O4/c29-23-18-26(31-17-16-25(32)30-27(31)33)35-24(23)19-34-28(20-10-4-1-5-11-20,21-12-6-2-7-13-21)22-14-8-3-9-15-22/h1-17,23-24,26H,18-19H2,(H,30,32,33)/t23-,24+,26+/m0/s1
InChIKeyGJNIPWYJQUGERM-BFLUCZKCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(c2ccccc2)(c3ccccc3)OCC4C(CC(O4)N5C=CC(=O)NC5=O)F
CACTVS 3.341F[CH]1C[CH](O[CH]1COC(c2ccccc2)(c3ccccc3)c4ccccc4)N5C=CC(=O)NC5=O
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(F)C2)COC(c3ccccc3)(c4ccccc4)c5ccccc5
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(c2ccccc2)(c3ccccc3)OC[C@@H]4[C@H](C[C@@H](O4)N5C=CC(=O)NC5=O)F
CACTVS 3.341F[C@H]1C[C@@H](O[C@@H]1COC(c2ccccc2)(c3ccccc3)c4ccccc4)N5C=CC(=O)NC5=O
FormulaC28 H25 F N2 O4
Name2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE;
1-{(2S,5S)-4-FLUORO-5-[(TRITYLOXY)METHYL]TETRAHYDROFURAN-2-YL}PYRIMIDINE-2,4(1H,3H)-DIONE
ChEMBLCHEMBL209720
DrugBankDB04685
ZINCZINC000012504465
PDB chain1vyq Chain A Residue 1160 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1vyq Dutpase as a Platform for Antimalarial Drug Design: Structural Basis for the Selectivity of a Class of Nucleoside Inhibitors.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		S92 S93
Binding residue
(residue number reindexed from 1)		S78 S79
Annotation score1
Binding affinityMOAD: Ki=4.98uM
PDBbind-CN: -logKd/Ki=5.30,Ki=4.98uM
BindingDB: Ki=5000nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:1vyq, PDBe:1vyq, PDBj:1vyq
PDBsum1vyq
PubMed15698576
UniProtQ8II92

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