Structure of PDB 6eq5 Chain A Binding Site BS01

Receptor Information
>6eq5 Chain A (length=155) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARR
ELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEM
RPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLR
EVDTV
Ligand information
Ligand IDAX7
InChIInChI=1S/C7H7N3/c8-7-9-5-3-1-2-4-6(5)10-7/h1-4H,(H3,8,9,10)
InChIKeyJWYUFVNJZUSCSM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1[nH]c2ccccc2n1
ACDLabs 10.04n2c1ccccc1nc2N
OpenEye OEToolkits 1.5.0c1ccc2c(c1)[nH]c(n2)N
FormulaC7 H7 N3
Name1H-benzimidazol-2-amine
ChEMBLCHEMBL305513
DrugBank
ZINCZINC000016889973
PDB chain6eq5 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6eq5 Ligand retargeting by binding site analogy.
Resolution1.801 Å
Binding residue
(original residue number in PDB)		F72 F74 M81 W117 D119
Binding residue
(residue number reindexed from 1)		F71 F73 M80 W116 D118
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.74,Kd=18uM
BindingDB: IC50=44000nM,Kd=18000nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6eq5, PDBe:6eq5, PDBj:6eq5
PDBsum6eq5
PubMed31077996
UniProtP36639|8ODP_HUMAN Oxidized purine nucleoside triphosphate hydrolase (Gene Name=NUDT1)

[Back to BioLiP]