Structure of PDB 6f23 Chain B Binding Site BS01

Receptor Information
>6f23 Chain B (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 IDC8Z
InChIInChI=1S/C17H17N3/c1-2-5-13(6-3-1)15-7-4-12-20(15)16-9-11-19-17-14(16)8-10-18-17/h1-3,5-6,8-11,15H,4,7,12H2,(H,18,19)/t15-/m1/s1
InChIKeyGUMMAYIOLPYJKE-OAHLLOKOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)C2CCCN2c3ccnc4c3cc[nH]4
CACTVS 3.385C1C[CH](N(C1)c2ccnc3[nH]ccc23)c4ccccc4
OpenEye OEToolkits 2.0.6c1ccc(cc1)[C@H]2CCCN2c3ccnc4c3cc[nH]4
CACTVS 3.385C1C[C@@H](N(C1)c2ccnc3[nH]ccc23)c4ccccc4
FormulaC17 H17 N3
Name4-[(2~{R})-2-phenylpyrrolidin-1-yl]-1~{H}-pyrrolo[2,3-b]pyridine
ChEMBL
DrugBank
ZINC
PDB chain6f23 Chain B Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6f23 Creation of a Novel Class of Potent and Selective MutT Homologue 1 (MTH1) Inhibitors Using Fragment-Based Screening and Structure-Based Drug Design.
Resolution1.84 Å
Binding residue
(original residue number in PDB)
F27 F72 M81 W117 D119 D120
Binding residue
(residue number reindexed from 1)
F25 F70 M79 W115 D117 D118
Annotation score1
Binding affinityMOAD: ic50=0.005uM
BindingDB: EC50=63nM,IC50=5.0nM
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:6f23, PDBe:6f23, PDBj:6f23
PDBsum6f23
PubMed29485874
UniProtP36639|8ODP_HUMAN Oxidized purine nucleoside triphosphate hydrolase (Gene Name=NUDT1)

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