Structure of PDB 5nqr Chain A Binding Site BS01

Receptor Information
>5nqr Chain A (length=195) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGVA
VIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALREL
EEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKPG
DGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHAN
Ligand information
Ligand ID958
InChIInChI=1S/C19H21N7O3/c1-11-7-6-8-12(9-11)16-22-21-13(29-16)10-26-14-15(20-18(26)23(2)3)24(4)19(28)25(5)17(14)27/h6-9H,10H2,1-5H3
InChIKeyNHRNLJPTVPQENT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(C)c1nc2N(C)C(=O)N(C)C(=O)c2n1Cc3oc(nn3)c4cccc(C)c4
OpenEye OEToolkits 2.0.6Cc1cccc(c1)c2nnc(o2)Cn3c4c(nc3N(C)C)N(C(=O)N(C4=O)C)C
FormulaC19 H21 N7 O3
Name8-(dimethylamino)-1,3-dimethyl-7-[[5-(3-methylphenyl)-1,3,4-oxadiazol-2-yl]methyl]purine-2,6-dione;
TH5427
ChEMBL
DrugBank
ZINC
PDB chain5nqr Chain A Residue 301 [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]
PDB5nqr Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		W28 R51 D60 G61
Binding residue
(residue number reindexed from 1)		W15 R38 D47 G48
Annotation score1
Binding affinityMOAD: ic50=70nM
PDBbind-CN: -logKd/Ki=7.15,IC50=70nM
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:5nqr, PDBe:5nqr, PDBj:5nqr
PDBsum5nqr
PubMed29343827
UniProtQ9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

[Back to BioLiP]