Structure of PDB 5ngs Chain A Binding Site BS01

Receptor Information
>5ngs 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 ID8WW
InChIInChI=1S/C13H13N5S/c14-13-17-11-10(15-8-16-11)12(18-13)19-7-6-9-4-2-1-3-5-9/h1-5,8H,6-7H2,(H3,14,15,16,17,18)
InChIKeyPAAAKNYXXIVNCJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)CCSc2c3c(nc[nH]3)nc(n2)N
CACTVS 3.385Nc1nc(SCCc2ccccc2)c3[nH]cnc3n1
FormulaC13 H13 N5 S
Name6-(2-phenylethylsulfanyl)-7~{H}-purin-2-amine
ChEMBLCHEMBL1437990
DrugBank
ZINCZINC000000540407
PDB chain5ngs 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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PDB5ngs Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		Y7 F27 N33 F72 W117 D119 D120
Binding residue
(residue number reindexed from 1)		Y5 F25 N31 F70 W115 D117 D118
Annotation score1
Binding affinityMOAD: ic50=170nM
PDBbind-CN: -logKd/Ki=6.77,IC50=0.17uM
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:5ngs, PDBe:5ngs, PDBj:5ngs
PDBsum5ngs
PubMed28929756
UniProtP36639|8ODP_HUMAN Oxidized purine nucleoside triphosphate hydrolase (Gene Name=NUDT1)

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