Structure of PDB 6eq3 Chain A Binding Site BS01

Receptor Information
>6eq3 Chain A (length=154) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRE
LQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMR
PCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLRE
VDTV
Ligand information
Ligand IDBU5
InChIInChI=1S/C11H9N3OS/c15-5-7-6-16-11(14-7)9-2-4-13-10-8(9)1-3-12-10/h1-4,6,15H,5H2,(H,12,13)
InChIKeyDEQVBJXGQZCGGU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OCc1csc(n1)c2ccnc3[nH]ccc23
OpenEye OEToolkits 2.0.6c1c[nH]c2c1c(ccn2)c3nc(cs3)CO
FormulaC11 H9 N3 O S
Name[2-(1~{H}-pyrrolo[2,3-b]pyridin-4-yl)-1,3-thiazol-4-yl]methanol
ChEMBLCHEMBL4446950
DrugBank
ZINC
PDB chain6eq3 Chain A Residue 201 [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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PDB6eq3 Ligand retargeting by binding site analogy.
Resolution1.798 Å
Binding residue
(original residue number in PDB)		Y7 T8 F27 N33 G37 F72 M81 V83 W117 D119 D120
Binding residue
(residue number reindexed from 1)		Y5 T6 F25 N31 G35 F70 M79 V81 W115 D117 D118
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.15,Kd=0.7uM
BindingDB: Kd=700nM,IC50=400nM
Enzymatic activity
Enzyme Commision number 3.6.1.-
3.6.1.56: 2-hydroxy-dATP diphosphatase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
GO:0008828 dATP diphosphatase activity
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0030515 snoRNA binding
GO:0035539 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity
GO:0046872 metal ion binding
GO:0047693 ATP diphosphatase activity
GO:0106377 2-hydroxy-ATP hydrolase activity
GO:0106378 2-hydroxy-dATP hydrolase activity
GO:0106431 N6-methyl-(d)ATP hydrolase activity
GO:0106433 O6-methyl-dGTP hydrolase activity
GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
Biological Process
GO:0006152 purine nucleoside catabolic process
GO:0006281 DNA repair
GO:0006979 response to oxidative stress
GO:0008584 male gonad development
GO:0042262 DNA protection
GO:0046686 response to cadmium ion
Cellular Component
GO:0001669 acrosomal vesicle
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0031965 nuclear membrane

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Biological Process
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Cellular Component
External links
PDB RCSB:6eq3, PDBe:6eq3, PDBj:6eq3
PDBsum6eq3
PubMed31077996
UniProtP36639|8ODP_HUMAN Oxidized purine nucleoside triphosphate hydrolase (Gene Name=NUDT1)

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