Structure of PDB 6eq2 Chain A Binding Site BS01

Receptor Information
>6eq2 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 IDBU8
InChIInChI=1S/C6H6N4/c7-6-9-4-2-1-3-8-5(4)10-6/h1-3H,(H3,7,8,9,10)
InChIKeyKXQPVJRJUJJWQJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1[nH]c2cccnc2n1
OpenEye OEToolkits 2.0.6c1cc2c(nc1)nc([nH]2)N
FormulaC6 H6 N4
Name1~{H}-imidazo[4,5-b]pyridin-2-amine
ChEMBLCHEMBL4589188
DrugBank
ZINCZINC000017060146
PDB chain6eq2 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6eq2 Ligand retargeting by binding site analogy.
Resolution1.802 Å
Binding residue
(original residue number in PDB)		N33 F72 W117 D119 D120
Binding residue
(residue number reindexed from 1)		N31 F70 W115 D117 D118
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.89,Kd=1.3uM
BindingDB: IC50=1100nM,Kd=1300nM
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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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6eq2, PDBe:6eq2, PDBj:6eq2
PDBsum6eq2
PubMed31077996
UniProtP36639|8ODP_HUMAN Oxidized purine nucleoside triphosphate hydrolase (Gene Name=NUDT1)

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