Structure of PDB 4n1t Chain A Binding Site BS01

Receptor Information
>4n1t 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 ID2GD
InChIInChI=1S/C11H10Cl2N4/c1-15-9-5-8(16-11(14)17-9)6-3-2-4-7(12)10(6)13/h2-5H,1H3,(H3,14,15,16,17)
InChIKeyURWCXPXBBITYLR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CNc1cc(nc(n1)N)c2cccc(c2Cl)Cl
ACDLabs 12.01Clc2c(Cl)c(c1nc(nc(c1)NC)N)ccc2
CACTVS 3.385CNc1cc(nc(N)n1)c2cccc(Cl)c2Cl
FormulaC11 H10 Cl2 N4
Name6-(2,3-dichlorophenyl)-N~4~-methylpyrimidine-2,4-diamine
ChEMBLCHEMBL3781316
DrugBank
ZINCZINC000098208167
PDB chain4n1t 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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PDB4n1t MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		N33 G37 F72 M81 V83 W117 D119 D120 F139
Binding residue
(residue number reindexed from 1)		N31 G35 F70 M79 V81 W115 D117 D118 F137
Annotation score1
Binding affinityMOAD: ic50=0.8nM
PDBbind-CN: -logKd/Ki=9.10,IC50=0.8nM
BindingDB: IC50=0.800000nM
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:4n1t, PDBe:4n1t, PDBj:4n1t
PDBsum4n1t
PubMed24695224
UniProtP36639|8ODP_HUMAN Oxidized purine nucleoside triphosphate hydrolase (Gene Name=NUDT1)

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