Structure of PDB 5qjk Chain B Binding Site BS04

Receptor Information
>5qjk Chain B (length=194) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKQTADGVAV
IPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRELE
EETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPGD
GEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN
Ligand information
Ligand IDK1D
InChIInChI=1S/C8H9N5/c1-2-13(3-1)8-6-7(10-4-9-6)11-5-12-8/h4-5H,1-3H2,(H,9,10,11,12)
InChIKeyACPXQMYLXLKGKU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1[nH]c2c(n1)c(ncn2)N3CCC3
ACDLabs 12.01n2cnc1ncnc1c2N3CCC3
CACTVS 3.385C1CN(C1)c2ncnc3[nH]cnc23
FormulaC8 H9 N5
Name6-(azetidin-1-yl)-9H-purine
ChEMBL
DrugBank
ZINCZINC000197371642
PDB chain5qjk Chain B Residue 304 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5qjk PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)
Resolution1.65 Å
Binding residue
(original residue number in PDB)		W46 E47
Binding residue
(residue number reindexed from 1)		W33 E34
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5qjk, PDBe:5qjk, PDBj:5qjk
PDBsum5qjk
PubMed
UniProtQ9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

[Back to BioLiP]