Structure of PDB 8rdz Chain B Binding Site BS03

Receptor Information
>8rdz Chain B (length=190) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTADGVAVIPVL
QRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETG
YKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFV
EVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain8rdz Chain B Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8rdz Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist.
Resolution2.02 Å
Binding residue
(original residue number in PDB)		A96 E116
Binding residue
(residue number reindexed from 1)		A78 E98
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.96: ADP-D-ribose pyrophosphorylase.
3.6.1.13: ADP-ribose diphosphatase.
3.6.1.58: 8-oxo-dGDP phosphatase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0016462 pyrophosphatase activity
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0016787 hydrolase activity
GO:0017110 nucleoside diphosphate phosphatase activity
GO:0019144 ADP-sugar diphosphatase activity
GO:0030515 snoRNA binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0044715 8-oxo-dGDP phosphatase activity
GO:0044716 8-oxo-GDP phosphatase activity
GO:0046872 metal ion binding
GO:0047631 ADP-ribose diphosphatase activity
GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006338 chromatin remodeling
GO:0006753 nucleoside phosphate metabolic process
GO:0009117 nucleotide metabolic process
GO:0009191 ribonucleoside diphosphate catabolic process
GO:0019303 D-ribose catabolic process
GO:0019693 ribose phosphate metabolic process
GO:0055086 nucleobase-containing small molecule metabolic process
GO:1990966 ATP generation from poly-ADP-D-ribose
Cellular Component
GO:0005634 nucleus
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8rdz, PDBe:8rdz, PDBj:8rdz
PDBsum8rdz
PubMed38635563
UniProtQ9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

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