Structure of PDB 3t60 Chain A Binding Site BS02

Receptor Information
>3t60 Chain A (length=143) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHLKIVCLSDEVREMYKNDSGLDLFIVKDEVLKPKSTTFVKLGIKAIALQ
YKSNYYNIVNTSFLLFPRSSISKTPLRLANSIGLIDAGYRGEIIAALDNT
SDQEYHIKKNDKLVQLVSFTGEPLSFELVEELDETSRGEGGFG
Ligand information
Ligand IDDUA
InChIInChI=1S/C28H27N3O4/c32-23-18-26(31-17-16-25(33)30-27(31)34)35-24(23)19-29-28(20-10-4-1-5-11-20,21-12-6-2-7-13-21)22-14-8-3-9-15-22/h1-17,23-24,26,29,32H,18-19H2,(H,30,33,34)/t23-,24+,26+/m0/s1
InChIKeyTUZNCXRMWDUVNX-BFLUCZKCSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CNC(c2ccccc2)(c3ccccc3)c4ccccc4)N5C=CC(=O)NC5=O
OpenEye OEToolkits 1.7.2c1ccc(cc1)C(c2ccccc2)(c3ccccc3)NCC4C(CC(O4)N5C=CC(=O)NC5=O)O
CACTVS 3.370O[CH]1C[CH](O[CH]1CNC(c2ccccc2)(c3ccccc3)c4ccccc4)N5C=CC(=O)NC5=O
OpenEye OEToolkits 1.7.2c1ccc(cc1)C(c2ccccc2)(c3ccccc3)NC[C@@H]4[C@H](C[C@@H](O4)N5C=CC(=O)NC5=O)O
ACDLabs 12.01O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CNC(c3ccccc3)(c4ccccc4)c5ccccc5
FormulaC28 H27 N3 O4
Name2',5'-dideoxy-5'-(tritylamino)uridine
ChEMBLCHEMBL377582
DrugBank
ZINCZINC000013673354
PDB chain3t60 Chain C Residue 182 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3t60 Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase.
Resolution2.396 Å
Binding residue
(original residue number in PDB)		S92 S93
Binding residue
(residue number reindexed from 1)		S69 S70
Annotation score2
Binding affinityMOAD: Ki=0.2uM
PDBbind-CN: -logKd/Ki=6.70,Ki=0.2uM
BindingDB: Ki=200nM
Enzymatic activity
Catalytic site (original residue number in PDB) S27 R91 S93 L99 D109
Catalytic site (residue number reindexed from 1) S20 R68 S70 L76 D86
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:3t60, PDBe:3t60, PDBj:3t60
PDBsum3t60
PubMed22049550
UniProtQ8II92

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