Structure of PDB 6aa5 Chain A Binding Site BS01

Receptor Information
>6aa5 Chain A (length=162) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRE
LQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMR
PCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLRE
VDTVLEHHHHHH
Ligand information
Ligand IDMKU
InChIInChI=1S/C24H26O6/c1-12(2)6-7-14-19-17(10-15(25)23(14)28-5)29-18-11-16-13(8-9-24(3,4)30-16)21(26)20(18)22(19)27/h6,10-11,25-26H,7-9H2,1-5H3
InChIKeyKJCDBAVVDILRMP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC(=CCc1c2c(cc(c1OC)O)Oc3cc4c(c(c3C2=O)O)CCC(O4)(C)C)C
CACTVS 3.385COc1c(O)cc2Oc3cc4OC(C)(C)CCc4c(O)c3C(=O)c2c1CC=C(C)C
ACDLabs 12.01C\C(=C/Cc4c3C(c2c(c1CCC(C)(C)Oc1cc2Oc3cc(O)c4OC)O)=O)C
FormulaC24 H26 O6
Name5,9-dihydroxy-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H,6H-pyrano[3,2-b]xanthen-6-one;
3-isomangostin
ChEMBLCHEMBL464119
DrugBank
ZINCZINC000013382496
PDB chain6aa5 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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PDB6aa5 Discovery of a new class of MTH1 inhibitor by X-ray crystallographic screening.
Resolution1.901 Å
Binding residue
(original residue number in PDB)		Y7 F27 N33 F72 F74 M81 W117 D119 G141
Binding residue
(residue number reindexed from 1)		Y5 F25 N31 F70 F72 M79 W115 D117 G139
Annotation score1
Binding affinityMOAD: ic50=0.052uM
PDBbind-CN: -logKd/Ki=7.28,IC50=52nM
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:6aa5, PDBe:6aa5, PDBj:6aa5
PDBsum6aa5
PubMed30771603
UniProtP36639|8ODP_HUMAN Oxidized purine nucleoside triphosphate hydrolase (Gene Name=NUDT1)

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