Structure of PDB 8rdz Chain A Binding Site BS02

Receptor Information
>8rdz Chain A (length=189) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTADGVAVIPVL
QRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELEEETG
YKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGDGEFV
EVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHA
Ligand information
Ligand IDA1H14
InChIInChI=1S/C25H24N6O2/c1-2-21(32)30-14-6-7-18(15-30)31-25-22(24(26)27-16-28-25)23(29-31)17-10-12-20(13-11-17)33-19-8-4-3-5-9-19/h2-5,8-13,16,18H,1,6-7,14-15H2,(H2,26,27,28)/t18-/m0/s1
InChIKeyXYFPWWZEPKGCCK-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2n(nc(c3ccc(Oc4ccccc4)cc3)c12)[CH]5CCCN(C5)C(=O)C=C
OpenEye OEToolkits 2.0.7C=CC(=O)N1CCCC(C1)n2c3c(c(n2)c4ccc(cc4)Oc5ccccc5)c(ncn3)N
OpenEye OEToolkits 2.0.7C=CC(=O)N1CCC[C@@H](C1)n2c3c(c(n2)c4ccc(cc4)Oc5ccccc5)c(ncn3)N
CACTVS 3.385Nc1ncnc2n(nc(c3ccc(Oc4ccccc4)cc3)c12)[C@H]5CCCN(C5)C(=O)C=C
FormulaC25 H24 N6 O2
NameIbrutinib (unbound form);
1-[(3S)-3-[4-azanyl-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]prop-2-en-1-one
ChEMBL
DrugBank
ZINC
PDB chain8rdz Chain A Residue 502 [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)		W28 R51 D60 N138 C139 D164
Binding residue
(residue number reindexed from 1)		W15 R38 D42 N120 C121 D146
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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